Starting phenix.real_space_refine (version: dev) on Tue Feb 21 17:05:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/02_2023/6i53_4411_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "E ARG 180": "NH1" <-> "NH2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15362 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2754 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2823 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 334} Chain breaks: 1 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2770 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2805 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 8.99, per 1000 atoms: 0.59 Number of scatterers: 15362 At special positions: 0 Unit cell: (97.37, 123.05, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 9 15.00 O 2854 8.00 N 2474 7.00 C 9943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN E 149 " " NAG H 1 " - " ASN E 80 " " NAG I 1 " - " ASN A 111 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " " NAG L 1 " - " ASN C 208 " " NAG M 1 " - " ASN D 111 " Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 24 sheets defined 31.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'E' and resid 11 through 19 removed outlier: 3.547A pdb=" N ASP E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.530A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.998A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.717A pdb=" N LEU E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.681A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.648A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 445 removed outlier: 3.680A pdb=" N ASP E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.636A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.730A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 252 through 271 removed outlier: 4.754A pdb=" N VAL A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 4.031A pdb=" N VAL A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.732A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 4.175A pdb=" N TRP A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.625A pdb=" N LYS B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.523A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.223A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.560A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.832A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.612A pdb=" N MET B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 removed outlier: 3.730A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.889A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.705A pdb=" N SER C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 255 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 3.738A pdb=" N GLY C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 322 removed outlier: 3.586A pdb=" N ILE C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 307 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 432 removed outlier: 4.425A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.514A pdb=" N PHE C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.633A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.772A pdb=" N VAL D 227 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 228 " --> pdb=" O TYR D 225 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN D 229 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.603A pdb=" N LEU D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 252 through 272 removed outlier: 4.641A pdb=" N VAL D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.628A pdb=" N VAL D 292 " --> pdb=" O TRP D 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 414 removed outlier: 3.659A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.540A pdb=" N GLY D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.305A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 66 through 68 removed outlier: 4.477A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.748A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.953A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= G, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.226A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 210 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.489A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 66 through 68 Processing sheet with id= J, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.521A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 191 through 200 removed outlier: 3.650A pdb=" N GLY B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.870A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= O, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.702A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.762A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 167 through 171 removed outlier: 5.970A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP D 70 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 83 through 85 Processing sheet with id= S, first strand: chain 'D' and resid 150 through 158 Processing sheet with id= T, first strand: chain 'D' and resid 196 through 199 Processing sheet with id= U, first strand: chain 'D' and resid 202 through 204 Processing sheet with id= V, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.495A pdb=" N THR G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'G' and resid 117 through 119 removed outlier: 3.565A pdb=" N MET G 34 " --> pdb=" O MET G 51 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2299 1.30 - 1.43: 4524 1.43 - 1.56: 8729 1.56 - 1.68: 45 1.68 - 1.81: 147 Bond restraints: 15744 Sorted by residual: bond pdb=" C21 POV A 609 " pdb=" O21 POV A 609 " ideal model delta sigma weight residual 1.330 1.474 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C21 POV E 508 " pdb=" O21 POV E 508 " ideal model delta sigma weight residual 1.330 1.473 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 POV D 507 " pdb=" O21 POV D 507 " ideal model delta sigma weight residual 1.330 1.472 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C36 POV A 609 " pdb=" C37 POV A 609 " ideal model delta sigma weight residual 1.523 1.611 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C36 POV E 508 " pdb=" C37 POV E 508 " ideal model delta sigma weight residual 1.523 1.611 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 15739 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.39: 295 105.39 - 112.55: 8180 112.55 - 119.71: 5143 119.71 - 126.86: 7554 126.86 - 134.02: 213 Bond angle restraints: 21385 Sorted by residual: angle pdb=" C GLY G 103 " pdb=" N LEU G 104 " pdb=" CA LEU G 104 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C4 PIO A 601 " pdb=" O4 PIO A 601 " pdb=" P4 PIO A 601 " ideal model delta sigma weight residual 118.46 132.99 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C4 PIO D 501 " pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 118.46 132.03 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C ASP C 192 " pdb=" N THR C 193 " pdb=" CA THR C 193 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N PRO D 175 " pdb=" CA PRO D 175 " pdb=" C PRO D 175 " ideal model delta sigma weight residual 112.47 120.66 -8.19 2.06e+00 2.36e-01 1.58e+01 ... (remaining 21380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8964 17.24 - 34.48: 205 34.48 - 51.71: 51 51.71 - 68.95: 7 68.95 - 86.19: 7 Dihedral angle restraints: 9234 sinusoidal: 3874 harmonic: 5360 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 161.27 -68.27 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA GLU D 174 " pdb=" C GLU D 174 " pdb=" N PRO D 175 " pdb=" CA PRO D 175 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PRO D 154 " pdb=" C PRO D 154 " pdb=" N LEU D 155 " pdb=" CA LEU D 155 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 9231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2236 0.081 - 0.162: 238 0.162 - 0.243: 7 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 149 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2481 not shown) Planarity restraints: 2603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.051 2.00e-02 2.50e+03 4.21e-02 2.22e+01 pdb=" C7 NAG M 1 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.065 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.030 2.00e-02 2.50e+03 2.49e-02 7.76e+00 pdb=" C7 NAG I 1 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.039 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 432 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 ... (remaining 2600 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3762 2.79 - 3.32: 12762 3.32 - 3.85: 25095 3.85 - 4.37: 30613 4.37 - 4.90: 52209 Nonbonded interactions: 124441 Sorted by model distance: nonbonded pdb=" O THR D 172 " pdb=" OG SER D 178 " model vdw 2.264 2.440 nonbonded pdb=" O ALA E 280 " pdb=" OH TYR E 442 " model vdw 2.326 2.440 nonbonded pdb=" NE2 HIS A 110 " pdb=" OG1 THR A 134 " model vdw 2.327 2.520 nonbonded pdb=" OH TYR A 60 " pdb=" O PRO A 154 " model vdw 2.332 2.440 nonbonded pdb=" NE2 HIS D 110 " pdb=" OG1 THR D 134 " model vdw 2.335 2.520 ... (remaining 124436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 322 or resid 384 through 417 or resid 601 throu \ gh 609)) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 10 through 447) selection = (chain 'E' and resid 10 through 447) } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 2 or resid 5 through 7)) selection = (chain 'J' and (resid 1 or resid 4 through 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 82 5.16 5 C 9943 2.51 5 N 2474 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.960 Check model and map are aligned: 0.210 Process input model: 40.880 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.144 15744 Z= 0.428 Angle : 0.883 14.535 21385 Z= 0.439 Chirality : 0.050 0.405 2484 Planarity : 0.007 0.063 2596 Dihedral : 9.039 86.191 5770 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.15), residues: 1799 helix: -4.37 (0.08), residues: 537 sheet: -2.48 (0.20), residues: 494 loop : -2.39 (0.19), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.732 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.3447 time to fit residues: 221.2075 Evaluate side-chains 273 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 ASN E 421 ASN A 308 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 113 ASN B 217 ASN B 303 ASN B 421 ASN C 80 GLN C 128 ASN C 323 ASN D 56 HIS D 151 HIS G 111 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15744 Z= 0.197 Angle : 0.561 7.943 21385 Z= 0.294 Chirality : 0.043 0.304 2484 Planarity : 0.005 0.044 2596 Dihedral : 7.843 89.578 2368 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.18), residues: 1799 helix: -1.98 (0.18), residues: 520 sheet: -1.90 (0.22), residues: 482 loop : -1.82 (0.21), residues: 797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 1.732 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 309 average time/residue: 0.2895 time to fit residues: 129.9697 Evaluate side-chains 274 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1376 time to fit residues: 6.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 ASN E 303 ASN A 190 GLN A 308 ASN A 387 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 152 GLN C 182 GLN D 56 HIS G 111 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15744 Z= 0.210 Angle : 0.523 6.675 21385 Z= 0.273 Chirality : 0.042 0.282 2484 Planarity : 0.004 0.038 2596 Dihedral : 7.481 89.409 2368 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1799 helix: -0.82 (0.21), residues: 524 sheet: -1.51 (0.22), residues: 481 loop : -1.51 (0.22), residues: 794 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 1.726 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 281 average time/residue: 0.2975 time to fit residues: 120.7805 Evaluate side-chains 259 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 248 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1531 time to fit residues: 5.8665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 0.0570 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 ASN A 68 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN C 152 GLN C 182 GLN D 56 HIS G 111 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15744 Z= 0.172 Angle : 0.490 6.594 21385 Z= 0.255 Chirality : 0.041 0.278 2484 Planarity : 0.004 0.036 2596 Dihedral : 7.099 88.248 2368 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1799 helix: -0.10 (0.23), residues: 516 sheet: -1.30 (0.22), residues: 482 loop : -1.25 (0.22), residues: 801 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 1.400 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 267 average time/residue: 0.2997 time to fit residues: 115.9450 Evaluate side-chains 253 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1373 time to fit residues: 5.8428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 242 GLN B 41 ASN B 113 ASN C 152 GLN G 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 15744 Z= 0.307 Angle : 0.548 6.956 21385 Z= 0.283 Chirality : 0.044 0.289 2484 Planarity : 0.004 0.046 2596 Dihedral : 7.191 89.879 2368 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1799 helix: 0.11 (0.23), residues: 531 sheet: -1.27 (0.22), residues: 489 loop : -1.14 (0.22), residues: 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 1.785 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 258 average time/residue: 0.3105 time to fit residues: 115.1627 Evaluate side-chains 254 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 241 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1954 time to fit residues: 6.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 172 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 113 ASN C 152 GLN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15744 Z= 0.232 Angle : 0.510 6.770 21385 Z= 0.265 Chirality : 0.042 0.281 2484 Planarity : 0.004 0.039 2596 Dihedral : 6.938 88.570 2368 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1799 helix: 0.45 (0.23), residues: 524 sheet: -1.08 (0.23), residues: 480 loop : -1.11 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 1.797 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 257 average time/residue: 0.3102 time to fit residues: 114.3550 Evaluate side-chains 246 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 236 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1304 time to fit residues: 4.7904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 97 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 148 GLN C 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15744 Z= 0.160 Angle : 0.488 7.352 21385 Z= 0.252 Chirality : 0.041 0.272 2484 Planarity : 0.003 0.034 2596 Dihedral : 6.670 87.457 2368 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1799 helix: 0.68 (0.23), residues: 524 sheet: -0.89 (0.23), residues: 473 loop : -1.04 (0.22), residues: 802 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 1.761 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 255 average time/residue: 0.3057 time to fit residues: 112.0250 Evaluate side-chains 240 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1685 time to fit residues: 3.3655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7246 > 50: distance: 34 - 57: 8.226 distance: 52 - 57: 6.723 distance: 57 - 58: 3.762 distance: 58 - 59: 11.982 distance: 58 - 61: 25.923 distance: 59 - 60: 18.916 distance: 59 - 65: 15.338 distance: 61 - 62: 16.633 distance: 62 - 63: 15.326 distance: 62 - 64: 24.978 distance: 65 - 66: 12.101 distance: 66 - 67: 4.237 distance: 66 - 69: 13.194 distance: 67 - 68: 11.175 distance: 67 - 74: 16.340 distance: 69 - 70: 16.209 distance: 70 - 71: 3.486 distance: 71 - 72: 10.452 distance: 72 - 73: 6.588 distance: 74 - 75: 7.767 distance: 75 - 76: 4.595 distance: 75 - 78: 6.159 distance: 76 - 77: 13.552 distance: 76 - 82: 4.205 distance: 78 - 79: 15.482 distance: 79 - 80: 13.767 distance: 79 - 81: 31.377 distance: 82 - 83: 10.674 distance: 83 - 84: 7.139 distance: 83 - 86: 6.659 distance: 84 - 85: 15.494 distance: 84 - 90: 19.843 distance: 86 - 87: 13.208 distance: 87 - 88: 14.953 distance: 87 - 89: 8.564 distance: 91 - 92: 5.791 distance: 91 - 94: 6.426 distance: 92 - 93: 12.922 distance: 92 - 99: 4.588 distance: 95 - 96: 3.842 distance: 96 - 97: 3.633 distance: 97 - 98: 6.308 distance: 99 - 100: 7.461 distance: 100 - 101: 4.429 distance: 101 - 102: 8.867 distance: 101 - 103: 7.341 distance: 103 - 104: 4.177 distance: 104 - 107: 5.500 distance: 105 - 106: 6.424 distance: 115 - 116: 9.542 distance: 116 - 117: 8.093 distance: 116 - 119: 5.364 distance: 117 - 118: 17.467 distance: 117 - 123: 10.076 distance: 119 - 120: 5.899 distance: 120 - 121: 5.767 distance: 120 - 122: 11.791 distance: 123 - 124: 8.621 distance: 124 - 125: 24.361 distance: 124 - 127: 14.528 distance: 125 - 126: 15.564 distance: 125 - 131: 19.521 distance: 127 - 128: 20.659 distance: 127 - 129: 24.351 distance: 128 - 130: 22.507 distance: 131 - 132: 8.941 distance: 132 - 133: 14.827 distance: 132 - 135: 25.309 distance: 133 - 134: 23.916 distance: 133 - 142: 19.975 distance: 135 - 136: 17.005 distance: 136 - 137: 5.595 distance: 137 - 138: 6.091 distance: 138 - 139: 4.720 distance: 139 - 140: 4.730 distance: 139 - 141: 5.018