Hi all,
I am trying to refine a structure with a PEG400 molecule using
refmac 5.3. I have created the necessary library file and read it into
the refinement, but for some reason refmac still quites and complains
that it has come across a new ligand. I am obviously doing something
stupid, but could someone please tell me what it is. I have attached the
refmac log file and the library file.
Thanks
Craig
--
Craig McElroy, Ph.D.
Department of Molecular and Cellular Biochemistry
Ohio State University
483 Hamilton Hall
1645 Neil Ave.
Columbus, OH 43210
(614) 688-8630
global_
_lib_name mon_lib
_lib_version 4.30
_lib_update 02/03/07
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
1PE 1PE '. ' . 38 16 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_1PE
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
1PE OH7 O OH1 0.000 7.502 80.947 62.566
1PE HOH7 H H 0.000 6.928 80.255 62.922
1PE C16 C CH2 0.000 7.150 81.207 61.200
1PE H161 H H 0.000 6.086 81.445 61.142
1PE H162 H H 0.000 7.356 80.318 60.601
1PE C26 C CH2 0.000 7.971 82.389 60.665
1PE H261 H H 0.000 7.727 83.290 61.232
1PE H262 H H 0.000 7.738 82.549 59.611
1PE OH6 O O2 0.000 9.361 82.097 60.808
1PE C15 C CH2 0.000 10.112 83.217 60.305
1PE H151 H H 0.000 9.856 84.115 60.871
1PE H152 H H 0.000 9.876 83.373 59.251
1PE C25 C CH2 0.000 11.614 82.924 60.458
1PE H251 H H 0.000 12.133 83.816 60.815
1PE H252 H H 0.000 12.034 82.620 59.497
1PE OH5 O O2 0.000 11.776 81.863 61.409
1PE C14 C CH2 0.000 13.161 81.589 61.545
1PE H141 H H 0.000 13.685 82.479 61.900
1PE H142 H H 0.000 13.578 81.282 60.584
1PE C24 C CH2 0.000 13.330 80.458 62.559
1PE H241 H H 0.000 12.599 80.587 63.360
1PE H242 H H 0.000 14.338 80.504 62.978
1PE OH4 O O2 0.000 13.130 79.184 61.926
1PE C13 C CH2 0.000 13.313 78.221 62.961
1PE H131 H H 0.000 12.580 78.420 63.745
1PE H132 H H 0.000 14.320 78.344 63.367
1PE C23 C CH2 0.000 13.139 76.788 62.449
1PE H231 H H 0.000 13.418 76.714 61.396
1PE H232 H H 0.000 12.109 76.451 62.577
1PE OH3 O O2 0.000 14.011 75.969 63.233
1PE C22 C CH2 0.000 13.890 74.609 62.815
1PE H221 H H 0.000 14.162 74.514 61.762
1PE H222 H H 0.000 12.866 74.260 62.959
1PE C12 C CH2 0.000 14.847 73.762 63.671
1PE H121 H H 0.000 14.816 74.121 64.702
1PE H122 H H 0.000 15.861 73.866 63.282
1PE OH2 O OH1 0.000 14.460 72.395 63.632
1PE HOH2 H H 0.000 15.112 71.864 64.108
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
1PE OH7 n/a C16 START
1PE HOH7 OH7 . .
1PE C16 OH7 C26 .
1PE H161 C16 . .
1PE H162 C16 . .
1PE C26 C16 OH6 .
1PE H261 C26 . .
1PE H262 C26 . .
1PE OH6 C26 C15 .
1PE C15 OH6 C25 .
1PE H151 C15 . .
1PE H152 C15 . .
1PE C25 C15 OH5 .
1PE H251 C25 . .
1PE H252 C25 . .
1PE OH5 C25 C14 .
1PE C14 OH5 C24 .
1PE H141 C14 . .
1PE H142 C14 . .
1PE C24 C14 OH4 .
1PE H241 C24 . .
1PE H242 C24 . .
1PE OH4 C24 C13 .
1PE C13 OH4 C23 .
1PE H131 C13 . .
1PE H132 C13 . .
1PE C23 C13 OH3 .
1PE H231 C23 . .
1PE H232 C23 . .
1PE OH3 C23 C22 .
1PE C22 OH3 C12 .
1PE H221 C22 . .
1PE H222 C22 . .
1PE C12 C22 OH2 .
1PE H121 C12 . .
1PE H122 C12 . .
1PE OH2 C12 HOH2 .
1PE HOH2 OH2 . END
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
1PE OH2 C12 single 1.432 0.020
1PE C12 C22 single 1.524 0.020
1PE C22 OH3 single 1.426 0.020
1PE OH3 C23 single 1.426 0.020
1PE C23 C13 single 1.524 0.020
1PE C13 OH4 single 1.426 0.020
1PE OH4 C24 single 1.426 0.020
1PE C24 C14 single 1.524 0.020
1PE C14 OH5 single 1.426 0.020
1PE OH5 C25 single 1.426 0.020
1PE C25 C15 single 1.524 0.020
1PE C15 OH6 single 1.426 0.020
1PE OH6 C26 single 1.426 0.020
1PE C26 C16 single 1.524 0.020
1PE C16 OH7 single 1.432 0.020
1PE HOH2 OH2 single 0.967 0.020
1PE H121 C12 single 1.092 0.020
1PE H122 C12 single 1.092 0.020
1PE H221 C22 single 1.092 0.020
1PE H222 C22 single 1.092 0.020
1PE H131 C13 single 1.092 0.020
1PE H132 C13 single 1.092 0.020
1PE H231 C23 single 1.092 0.020
1PE H232 C23 single 1.092 0.020
1PE H141 C14 single 1.092 0.020
1PE H142 C14 single 1.092 0.020
1PE H241 C24 single 1.092 0.020
1PE H242 C24 single 1.092 0.020
1PE H151 C15 single 1.092 0.020
1PE H152 C15 single 1.092 0.020
1PE H251 C25 single 1.092 0.020
1PE H252 C25 single 1.092 0.020
1PE H161 C16 single 1.092 0.020
1PE H162 C16 single 1.092 0.020
1PE H261 C26 single 1.092 0.020
1PE H262 C26 single 1.092 0.020
1PE HOH7 OH7 single 0.967 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
1PE HOH7 OH7 C16 109.470 3.000
1PE OH7 C16 H161 109.470 3.000
1PE OH7 C16 H162 109.470 3.000
1PE OH7 C16 C26 109.470 3.000
1PE H161 C16 H162 107.900 3.000
1PE H161 C16 C26 109.470 3.000
1PE H162 C16 C26 109.470 3.000
1PE C16 C26 H261 109.470 3.000
1PE C16 C26 H262 109.470 3.000
1PE C16 C26 OH6 109.470 3.000
1PE H261 C26 H262 107.900 3.000
1PE H261 C26 OH6 109.470 3.000
1PE H262 C26 OH6 109.470 3.000
1PE C26 OH6 C15 111.800 3.000
1PE OH6 C15 H151 109.470 3.000
1PE OH6 C15 H152 109.470 3.000
1PE OH6 C15 C25 109.470 3.000
1PE H151 C15 H152 107.900 3.000
1PE H151 C15 C25 109.470 3.000
1PE H152 C15 C25 109.470 3.000
1PE C15 C25 H251 109.470 3.000
1PE C15 C25 H252 109.470 3.000
1PE C15 C25 OH5 109.470 3.000
1PE H251 C25 H252 107.900 3.000
1PE H251 C25 OH5 109.470 3.000
1PE H252 C25 OH5 109.470 3.000
1PE C25 OH5 C14 111.800 3.000
1PE OH5 C14 H141 109.470 3.000
1PE OH5 C14 H142 109.470 3.000
1PE OH5 C14 C24 109.470 3.000
1PE H141 C14 H142 107.900 3.000
1PE H141 C14 C24 109.470 3.000
1PE H142 C14 C24 109.470 3.000
1PE C14 C24 H241 109.470 3.000
1PE C14 C24 H242 109.470 3.000
1PE C14 C24 OH4 109.470 3.000
1PE H241 C24 H242 107.900 3.000
1PE H241 C24 OH4 109.470 3.000
1PE H242 C24 OH4 109.470 3.000
1PE C24 OH4 C13 111.800 3.000
1PE OH4 C13 H131 109.470 3.000
1PE OH4 C13 H132 109.470 3.000
1PE OH4 C13 C23 109.470 3.000
1PE H131 C13 H132 107.900 3.000
1PE H131 C13 C23 109.470 3.000
1PE H132 C13 C23 109.470 3.000
1PE C13 C23 H231 109.470 3.000
1PE C13 C23 H232 109.470 3.000
1PE C13 C23 OH3 109.470 3.000
1PE H231 C23 H232 107.900 3.000
1PE H231 C23 OH3 109.470 3.000
1PE H232 C23 OH3 109.470 3.000
1PE C23 OH3 C22 111.800 3.000
1PE OH3 C22 H221 109.470 3.000
1PE OH3 C22 H222 109.470 3.000
1PE OH3 C22 C12 109.470 3.000
1PE H221 C22 H222 107.900 3.000
1PE H221 C22 C12 109.470 3.000
1PE H222 C22 C12 109.470 3.000
1PE C22 C12 H121 109.470 3.000
1PE C22 C12 H122 109.470 3.000
1PE C22 C12 OH2 109.470 3.000
1PE H121 C12 H122 107.900 3.000
1PE H121 C12 OH2 109.470 3.000
1PE H122 C12 OH2 109.470 3.000
1PE C12 OH2 HOH2 109.470 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
1PE var_1 HOH7 OH7 C16 C26 175.000 20.000 1
1PE var_2 OH7 C16 C26 OH6 57.049 20.000 3
1PE var_3 C16 C26 OH6 C15 -179.843 20.000 1
1PE var_4 C26 OH6 C15 C25 179.688 20.000 1
1PE var_5 OH6 C15 C25 OH5 -18.053 20.000 3
1PE var_6 C15 C25 OH5 C14 179.730 20.000 1
1PE var_7 C25 OH5 C14 C24 -179.980 20.000 1
1PE var_8 OH5 C14 C24 OH4 82.473 20.000 3
1PE var_9 C14 C24 OH4 C13 179.944 20.000 1
1PE var_10 C24 OH4 C13 C23 -179.732 20.000 1
1PE var_11 OH4 C13 C23 OH3 148.383 20.000 3
1PE var_12 C13 C23 OH3 C22 179.498 20.000 1
1PE var_13 C23 OH3 C22 C12 179.597 20.000 1
1PE var_14 OH3 C22 C12 OH2 160.300 20.000 3
1PE var_15 C22 C12 OH2 HOH2 175.000 20.000 1
# ------------------------------------------------------
# ------------------------------------------------------
#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 08 Aug 2007 15:51:43
#CCP4I USER mcelroy
#CCP4I PROJECT final
#CCP4I JOB_ID 30
#CCP4I SCRATCH /tmp/mcelroy
#CCP4I HOSTNAME craig-mac.local
#CCP4I PID 5138
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.0: Refmac_5.3.0027 version 5.3.0027 : 02/01/06##
###############################################################
User: mcelroy Run date: 8/ 8/2007 Run time: 15:52:28
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
$TEXT:Reference1: $$ comment $$
"Refinement of Macromolecular Structures by the Maximum-Likelihood Method:"
G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
Acta Crystallogr. D53, 240-255
EU Validation contract: BIO2CT-92-0524
$$
$SUMMARY :Reference1: $$ Refmac: $$
:TEXT:Reference1: $$
Data line--- make check NONE
MAKE
Data line--- make hydrogen YES hout NO peptide NO cispeptide
YES ssbridge YES symmetry NO sugar YES connectivity YES
link NO
MAKE
Data line--- ncsr nchains 2 chains A C nspans 1 1 154 3
NCSR
Data line--- ncsr nchains 2 chains B D nspans 1 1 220 3
NCSR
Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF
meth CGMAT bref ISOT
REFI
Data line--- ncyc 10
NCYC
Data line--- scal type BULK reso 2.676 14.812 LSSC ANISO
EXPE
SCAL
Data line--- solvent YES VDWProb 1.2 IONProb 0.8 RSHRink 0.8
SOLV
Data line--- weight auto
WEIG
Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0
plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0
ncsr 10.0
MONI
Data line--- labin FP=FHsha SIGFP=SIGF_nat HLA=HLA HLB=HLB HLC=HLC HLD=HLD
FREE=FreeR_flag
LABI
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
LABO
Data line--- torsion 5.0 15.0 3.0 15.0 20.0
TORS
Data line--- NOHARVEST
NOHA
Data line--- END
END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename:
/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refine3/refine4/refmac/cns/refmac/refmac_ncs/cns_ncs/final_2.0/phenix/ccp4_refine42_combine.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /usr/local/lib/solve/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - XYZIN
Output coordinate file. Logical name - XYZOUT actual file name -
/tmp/mcelroy/final_30_2_pdb_1.tmp
==> WARNING: HKLIN has not been defined
Output reflection file. Logical name - HKLOUT actual file name -
/tmp/mcelroy/final_30_4_mtz_1.tmp
Cell from mtz : 47.202 113.021 87.534 90.000 105.095 90.000
Space group from mtz: number - 4; name - P 1 21 1
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints :
/sw/share/xtal/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW:
/sw/share/xtal/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
Program will rely on residue and atom names. No checking
If this option is used then monomers should be checked carefully before
using
Hydrogens in input coordinate file will be kept
Links between monomers will be checked. Only those links present in the
coordinate file will be used
All links to sugar will be analysed and used
For new ligands "ideal restraint" values will be taken from the energetic
libary ener_lib.cif
Symmetry related links will not be analysed
Cis peptides will be found and used automatically
Residual : Phase modified Maximum Likelihood
for Fs
Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00
**** Least-square scaling parameters ****
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Bulk solvent based on Babinet"s principle
Constant bulk solvent in non protein region
Probe radii for non-ions 1.200
Probe radii for ions 0.800
Shrinkage of the mask by 0.800
Method of minimisation : Sparse Matrix
Experimental sigmas used for weighting
Number of Bins and width: 20 0.0070
Refinement of individual isotropic Bfactors
Refinement resln : 14.8120 2.6761
Estimated number of reflections : 35758
Free R exclusion - flag equals: 0
Auto weighting. An attempt
Refinement cycles : 10
Scaling type :
Bulk solvent using using Babinet principle
using working set of reflns and experimental sigmas
Estimation of SigmaA Using 2 Gaussians:
using free set of reflns with experimental sigmas
Input phases not used in SigmaA estimation
Scaling and SigmaA resln: 14.8120 2.6760
Damping factors: 1.0000 1.0000
**** Geometry restraints and weights ****
Sigma:
Bonding distances
Weight = 1.00
Bond angles
Weight = 1.00
Planar groups
WEIGHT= 1.00
Chiral centers
Weight= 1.00
NON-BONDED CONTACTS
Overall weight = 1.00
Sigma for simple VDW = 0.20
Sigma for VDW trhough torsion angle = 0.20
Sigma for HBOND = 0.20
Sigma for metal-ion = 0.20
Sigma for DUMMY and other atom = 0.30
Distance for donor-accepetor = vdw1+vdw2+(-0.30)
Distance for acceptor - H = vdw1+ ( 0.10)
VDW distance through torsion = vdw1+vdw2+(-0.30)
Distance for DUMMY-others = vdw1+vdw2+(-0.70)
TORSION ANGLES
Weight= 5.00
THERMAL FACTORS
Weight= 1.00
Main chain bond (1-2 neighbour) 1.50A**2
Main chain angle (1-3 neighbour) 2.00A**2
Side chain bond 3.00A**2
Side chain angle 4.50A**2
**** NCS restraints parameters ****
Number of different NCS restraints 2
NCS restraint : 1
Number of chains : 2
Number of pieces : 1
Weights for this ncs: on positional - 0.050 and on thermal - 0.500
Residues from 1 to 154
Chain names : A C
NCS restraint : 2
Number of chains : 2
Number of pieces : 1
Weights for this ncs: on positional - 0.050 and on thermal - 0.500
Residues from 1 to 220
Chain names : B D
Old ncs restraints weighting scheme
Weight= 1.00
Positional, tight class 0.05A
Positional, medium class 0.50A
Positional, weak class 5.00A
Thermal, tight class 0.50A**2
Thermal, medium class 2.00A**2
Thermal, weak class 10.00A**2
RESTRAINTS AGAINST EXCESSIVE SHIFTS
Positional parameters 0.00A
Thermal parameters 0.00A
Occupancy parameters 0.00
RADIUS OF CONFIDENCE
Positional parameters 0.30A
Thermal parameters 0.03A**2
Occupancy parameters 0.50
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed
out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be
printed out
Distance outliers 10.000
Angle outliers 10.000
Torsion outliers 10.000
Chiral volume outliers 10.000
Plane outliers 10.000
Non-bonding outliers 10.000
B value outliers 10.000
NCS outliers 10.000
---------------------------------------------------------------
Input file :/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refin
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.30
_lib_update 02/03/07
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2433
with complete description : 450
NUMBER OF MODIFICATIONS : 47
NUMBER OF LINKS : 64
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
FORMATTED OLD file opened on unit 45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /sw/share/xtal/ccp4-6.0.2/lib/data/atomsf.lib
<!--SUMMARY_END--></FONT></B>
Number of atoms : 4830
Number of residues : 650
Number of chains : 6
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: 1PE 340 chain:EE - is not in the library
* Plotfile: /tmp/mcelroy/refmac5_temp1.05139_new_1PE.ps
WARNING : link:SS is found dist = 2.028 ideal_dist= 2.031
ch:AA res: 34 CYS at:SG .->AA res: 129 CYS at:SG
.
WARNING : link:SS is found dist = 2.032 ideal_dist= 2.031
ch:AA res: 47 CYS at:SG .->AA res: 141 CYS at:SG
.
WARNING : link:SS is found dist = 2.039 ideal_dist= 2.031
ch:BB res: 22 CYS at:SG .->BB res: 37 CYS at:SG
.
WARNING : link:SS is found dist = 2.038 ideal_dist= 2.031
ch:BB res: 54 CYS at:SG .->BB res: 62 CYS at:SG
.
WARNING : link:SS is found dist = 2.041 ideal_dist= 2.031
ch:BB res: 88 CYS at:SG .->BB res: 98 CYS at:SG
.
WARNING : link:SS is found dist = 2.031 ideal_dist= 2.031
ch:CC res: 34 CYS at:SG .->CC res: 129 CYS at:SG
.
WARNING : link:SS is found dist = 2.034 ideal_dist= 2.031
ch:CC res: 47 CYS at:SG .->CC res: 141 CYS at:SG
.
WARNING : link:SS is found dist = 2.038 ideal_dist= 2.031
ch:DD res: 22 CYS at:SG .->DD res: 37 CYS at:SG
.
WARNING : link:SS is found dist = 2.037 ideal_dist= 2.031
ch:DD res: 54 CYS at:SG .->DD res: 62 CYS at:SG
.
WARNING : link:SS is found dist = 2.034 ideal_dist= 2.031
ch:DD res: 88 CYS at:SG .->DD res: 98 CYS at:SG
.
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
Number of chains : 6
Total number of monomers : 650
Number of atoms : 4830
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 4904
Number of angles restraints : 6642
Number of torsions restraints : 3361
Number of chiralities : 761
Number of planar groups : 833
I am writing new library:
new.lib
Important, Important, Important!!!!!
Your coordinate file has a ligand which has either minimum or no description in
the library
A new ligand description has been added to
Picture of the new ligand can be viewed using postscript file. See above
Check description in this file and, if satisfied, use it as the input library
Otherwise either edit bond orders manually or use CCP4i Sketcher to view and
edit the ligand
and create a library entry by running libcheck
It is strongly recommended that dictionary entry should be checked carefully
before using it
If you are happy with the library description then use the keyword (MAKE CHECK
NONE)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Refmac_5.3.0027: New ligand has been encountered. Stopping now
Times: User: 9.0s System: 0.2s Elapsed: 0:09
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: refmac5 XYZIN
"/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refine3/refine4/refmac/cns/refmac/refmac_ncs/cns_ncs/final_2.0/phenix/final/final_sw/071707_unglycosylated_final/cns_sw/ccp4_refcam5.pdb"
XYZOUT "/tmp/mcelroy/final_30_2_pdb_1.tmp" HKLIN
"/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refine3/refine4/refmac/cns/refmac/refmac_ncs/cns_ncs/final_2.0/phenix/ccp4_refine42_combine.mtz"
HKLOUT "/tmp/mcelroy/final_30_4_mtz_1.tmp" LIBIN
"/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refine3/refine4/refmac/cns/refmac/refmac_ncs/cns_ncs/final_2.0/phenix/final/final_sw/071707_unglycosylated_final/cns_sw/1pe.cif"
LIBOUT
"/usr/people/mcelroy/combine_041007/resolve_build/cns/refine2/refine3/refine4/refmac/cns/refmac/refmac_ncs/cns_ncs/final_2.0/phenix/final/final_sw/071707_unglycosylated_final/cns_sw/final_30_lib.cif"
has failed with error message
Refmac_5.3.0027: New ligand has been encountered. Stopping now
***************************************************************************
#CCP4I TERMINATION STATUS 0 Refmac_5.3.0027: New ligand has been encountered.
Stopping now
#CCP4I TERMINATION TIME 08 Aug 2007 15:52:37
#CCP4I MESSAGE Task failed
