Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 18:55:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_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_4411/10_2023/6i53_4411_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i53_4411/10_2023/6i53_4411_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-1.21rc1-5097/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 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 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 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 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: 8.40, per 1000 atoms: 0.55 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: 6.33 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: 2.33 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: 4.64 Time building geometry restraints manager: 6.74 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: 8733 17.24 - 34.48: 202 34.48 - 51.71: 51 51.71 - 68.95: 7 68.95 - 86.19: 7 Dihedral angle restraints: 9000 sinusoidal: 3640 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 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2234 0.081 - 0.162: 236 0.162 - 0.243: 9 0.243 - 0.324: 4 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=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+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 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: 1.360 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: 4.250 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.030 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.007 0.144 15744 Z= 0.433 Angle : 0.903 14.535 21385 Z= 0.440 Chirality : 0.051 0.405 2484 Planarity : 0.007 0.063 2596 Dihedral : 9.125 86.191 5536 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 % Allowed : 0.68 % Favored : 99.32 % 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 : 1.816 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.3487 time to fit residues: 223.1846 Evaluate side-chains 273 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3235 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7380 ------------------------------------------------------------------------------- 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: 0.6755 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15744 Z= 0.196 Angle : 0.563 7.920 21385 Z= 0.295 Chirality : 0.042 0.236 2484 Planarity : 0.005 0.044 2596 Dihedral : 7.961 89.284 2134 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 8.01 % Favored : 90.14 % 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: -3.00 (0.18), residues: 1799 helix: -2.03 (0.18), residues: 520 sheet: -1.91 (0.22), residues: 480 loop : -1.83 (0.21), residues: 799 *********************** 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 325 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 295 time to evaluate : 1.781 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 310 average time/residue: 0.2997 time to fit residues: 134.5017 Evaluate side-chains 272 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1548 time to fit residues: 6.1614 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 387 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN 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: 0.6802 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15744 Z= 0.406 Angle : 0.632 7.517 21385 Z= 0.326 Chirality : 0.045 0.191 2484 Planarity : 0.005 0.051 2596 Dihedral : 7.949 88.048 2134 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.85 % Allowed : 9.93 % Favored : 88.22 % 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: -2.21 (0.19), residues: 1799 helix: -0.96 (0.21), residues: 526 sheet: -1.74 (0.22), residues: 490 loop : -1.46 (0.22), residues: 783 *********************** 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: 30 poor density : 259 time to evaluate : 1.667 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 275 average time/residue: 0.3116 time to fit residues: 122.9038 Evaluate side-chains 256 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1406 time to fit residues: 7.0961 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 0.0970 chunk 154 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 G 39 GLN G 111 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15744 Z= 0.173 Angle : 0.511 6.457 21385 Z= 0.265 Chirality : 0.041 0.203 2484 Planarity : 0.004 0.037 2596 Dihedral : 7.452 88.223 2134 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.17 % Allowed : 12.21 % Favored : 86.62 % 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: -1.62 (0.19), residues: 1799 helix: -0.29 (0.22), residues: 526 sheet: -1.29 (0.23), residues: 462 loop : -1.36 (0.22), residues: 811 *********************** 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 270 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 251 time to evaluate : 1.729 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 259 average time/residue: 0.3199 time to fit residues: 117.4150 Evaluate side-chains 239 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1394 time to fit residues: 5.2502 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.3980 chunk 128 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 41 ASN B 113 ASN C 152 GLN G 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15744 Z= 0.226 Angle : 0.518 6.676 21385 Z= 0.267 Chirality : 0.042 0.194 2484 Planarity : 0.004 0.040 2596 Dihedral : 7.274 88.965 2134 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.68 % Allowed : 12.95 % Favored : 86.37 % 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: -1.30 (0.20), residues: 1799 helix: 0.11 (0.23), residues: 520 sheet: -1.18 (0.23), residues: 469 loop : -1.20 (0.22), residues: 810 *********************** 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 259 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 248 time to evaluate : 1.862 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 254 average time/residue: 0.3369 time to fit residues: 123.8543 Evaluate side-chains 243 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1647 time to fit residues: 3.9088 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15744 Z= 0.197 Angle : 0.500 6.663 21385 Z= 0.258 Chirality : 0.041 0.193 2484 Planarity : 0.004 0.046 2596 Dihedral : 7.114 88.175 2134 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.74 % Allowed : 13.44 % Favored : 85.82 % 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: -1.04 (0.20), residues: 1799 helix: 0.44 (0.23), residues: 525 sheet: -1.04 (0.23), residues: 470 loop : -1.14 (0.22), residues: 804 *********************** 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 265 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 1.768 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 260 average time/residue: 0.3067 time to fit residues: 114.2348 Evaluate side-chains 242 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1431 time to fit residues: 4.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 53.8544 > 50: distance: 18 - 197: 7.334 distance: 21 - 194: 4.795 distance: 101 - 186: 16.584 distance: 104 - 183: 18.035 distance: 118 - 167: 31.584 distance: 120 - 125: 27.906 distance: 121 - 164: 16.769 distance: 125 - 126: 3.499 distance: 126 - 127: 22.585 distance: 126 - 129: 38.452 distance: 127 - 128: 22.438 distance: 127 - 132: 24.346 distance: 129 - 130: 26.892 distance: 129 - 131: 30.638 distance: 132 - 133: 11.959 distance: 133 - 134: 10.283 distance: 133 - 136: 14.480 distance: 134 - 135: 12.272 distance: 134 - 143: 16.727 distance: 136 - 137: 4.656 distance: 137 - 138: 9.218 distance: 137 - 139: 7.731 distance: 138 - 140: 10.252 distance: 139 - 141: 4.916 distance: 140 - 142: 12.579 distance: 141 - 142: 16.307 distance: 143 - 144: 7.207 distance: 144 - 145: 7.239 distance: 144 - 147: 11.121 distance: 145 - 146: 9.435 distance: 145 - 148: 7.420 distance: 148 - 149: 7.826 distance: 149 - 152: 4.292 distance: 150 - 151: 6.450 distance: 150 - 155: 7.819 distance: 152 - 153: 8.650 distance: 152 - 154: 4.035 distance: 155 - 156: 14.488 distance: 156 - 157: 26.133 distance: 157 - 158: 14.195 distance: 157 - 159: 32.202 distance: 159 - 160: 28.011 distance: 160 - 161: 23.352 distance: 160 - 163: 32.596 distance: 161 - 162: 23.673 distance: 161 - 164: 9.265 distance: 164 - 165: 8.010 distance: 165 - 166: 27.312 distance: 165 - 168: 23.033 distance: 166 - 167: 24.657 distance: 166 - 176: 23.586 distance: 168 - 169: 17.513 distance: 169 - 170: 14.220 distance: 169 - 171: 12.299 distance: 170 - 172: 9.728 distance: 171 - 173: 6.715 distance: 172 - 174: 18.595 distance: 173 - 174: 23.340 distance: 174 - 175: 8.018 distance: 176 - 177: 20.472 distance: 176 - 182: 20.372 distance: 177 - 178: 13.364 distance: 177 - 180: 21.295 distance: 178 - 179: 15.476 distance: 178 - 183: 14.554 distance: 181 - 182: 29.389 distance: 183 - 184: 16.631 distance: 184 - 185: 9.907 distance: 184 - 187: 12.747 distance: 185 - 186: 9.604 distance: 185 - 194: 5.539 distance: 187 - 188: 16.827 distance: 189 - 190: 8.339 distance: 190 - 191: 11.407 distance: 191 - 192: 12.412 distance: 191 - 193: 19.991 distance: 194 - 195: 11.600 distance: 195 - 196: 8.549 distance: 195 - 198: 12.540 distance: 196 - 202: 8.482 distance: 198 - 199: 13.245 distance: 199 - 200: 7.020 distance: 199 - 201: 22.721