Starting phenix.real_space_refine on Fri Nov 17 18:33:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/11_2023/6pv8_20488.pdb" } resolution = 3.87 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= 0.003 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 127 5.16 5 Na 1 4.78 5 C 13107 2.51 5 N 3094 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 20051 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3126 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" 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: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'P1M': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'P1M': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.67, per 1000 atoms: 0.53 Number of scatterers: 20051 At special positions: 0 Unit cell: (115.92, 112.56, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 127 16.00 Na 1 11.00 O 3720 8.00 N 3094 7.00 C 13107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 132 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.04 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS I 109 " distance=2.04 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 K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG B 701 " - " ASN B 15 " " NAG B 702 " - " ASN B 72 " " NAG C 701 " - " ASN C 15 " " NAG C 702 " - " ASN C 72 " " NAG E 701 " - " ASN E 15 " " NAG E 702 " - " ASN E 72 " " NAG J 1 " - " ASN A 24 " " NAG K 1 " - " ASN A 141 " " NAG L 1 " - " ASN B 117 " " NAG M 1 " - " ASN B 145 " " NAG N 1 " - " ASN C 117 " " NAG O 1 " - " ASN C 145 " " NAG P 1 " - " ASN D 24 " " NAG Q 1 " - " ASN D 141 " " NAG R 1 " - " ASN E 117 " " NAG S 1 " - " ASN E 145 " Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 3.4 seconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 31 sheets defined 33.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.771A pdb=" N PHE A 12 " --> pdb=" O PHE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 227 through 228 No H-bonds generated for 'chain 'A' and resid 227 through 228' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.726A pdb=" N PHE A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.799A pdb=" N LEU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.888A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.858A pdb=" N THR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 463 removed outlier: 3.559A pdb=" N ALA A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.649A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 14 " --> pdb=" O MET B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 5.534A pdb=" N ILE B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 241 through 264 removed outlier: 3.867A pdb=" N LEU B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.715A pdb=" N VAL B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 401 through 457 removed outlier: 4.036A pdb=" N GLU B 405 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.593A pdb=" N LEU C 9 " --> pdb=" O ALA C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.588A pdb=" N ILE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.553A pdb=" N ASN C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.758A pdb=" N LEU C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 298 removed outlier: 3.822A pdb=" N CYS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 401 through 457 removed outlier: 4.495A pdb=" N GLU C 405 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.756A pdb=" N PHE D 12 " --> pdb=" O PHE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.589A pdb=" N ASP D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.699A pdb=" N TYR D 233 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 263 removed outlier: 3.852A pdb=" N LEU D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 299 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.943A pdb=" N THR D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.687A pdb=" N ARG D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 464 removed outlier: 3.555A pdb=" N ALA D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.626A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.621A pdb=" N LYS E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.569A pdb=" N ARG E 88 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 211 through 218 removed outlier: 3.606A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 230 removed outlier: 4.145A pdb=" N ILE E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 264 removed outlier: 3.872A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 298 removed outlier: 3.896A pdb=" N VAL E 298 " --> pdb=" O CYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.705A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 324 removed outlier: 3.851A pdb=" N THR E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 457 removed outlier: 3.789A pdb=" N GLU E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.596A pdb=" N ASP F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 110' Processing helix chain 'H' and resid 81 through 84 removed outlier: 4.113A pdb=" N LYS H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.532A pdb=" N ASP H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'I' and resid 100 through 104 removed outlier: 4.116A pdb=" N ALA I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.562A pdb=" N VAL A 80 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.562A pdb=" N VAL A 80 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 49 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN A 53 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN A 61 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 30 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 146 removed outlier: 7.281A pdb=" N TYR A 205 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 146 Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.476A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 126 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.476A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 46 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASN B 57 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 44 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP B 59 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA B 42 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LYS B 61 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER B 40 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU B 63 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLN B 38 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR B 65 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LYS B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96 removed outlier: 7.593A pdb=" N ILE B 206 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 114 removed outlier: 5.201A pdb=" N THR C 65 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER C 34 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 163 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 35 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.358A pdb=" N LEU C 44 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN C 57 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 46 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 96 removed outlier: 7.278A pdb=" N ILE C 206 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 110 Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 110 removed outlier: 7.075A pdb=" N ILE D 49 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN D 53 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 147 removed outlier: 7.192A pdb=" N TYR D 205 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 147 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.966A pdb=" N ALA E 126 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.689A pdb=" N SER E 46 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 57 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 44 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N TRP E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA E 42 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS E 61 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER E 40 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLU E 63 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN E 38 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR E 65 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N LYS E 36 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 33 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL E 163 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 35 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.445A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE E 206 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.445A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AC4, first strand: chain 'F' and resid 29 through 30 removed outlier: 6.824A pdb=" N LEU F 53 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 69 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AC6, first strand: chain 'G' and resid 27 through 29 Processing sheet with id=AC7, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.536A pdb=" N MET G 33 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 126 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN G 58 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG G 67 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC9, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.720A pdb=" N LEU H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 29 through 30 Processing sheet with id=AD2, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AD3, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.061A pdb=" N GLN I 58 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG I 67 " --> pdb=" O GLN I 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 32 through 34 removed outlier: 3.566A pdb=" N THR I 118 " --> pdb=" O GLN I 111 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2703 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: 6.97 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5951 1.36 - 1.50: 5903 1.50 - 1.64: 8509 1.64 - 1.78: 1 1.78 - 1.92: 207 Bond restraints: 20571 Sorted by residual: bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.332 1.583 -0.252 1.34e-02 5.57e+03 3.52e+02 bond pdb=" C3 P1M D 701 " pdb=" N8 P1M D 701 " ideal model delta sigma weight residual 1.457 1.530 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C3 P1M A 701 " pdb=" N8 P1M A 701 " ideal model delta sigma weight residual 1.457 1.529 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ASN C 117 " pdb=" CA ASN C 117 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.18e-02 7.18e+03 1.23e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.96e+00 ... (remaining 20566 not shown) Histogram of bond angle deviations from ideal: 98.75 - 106.06: 581 106.06 - 113.37: 11902 113.37 - 120.68: 8652 120.68 - 128.00: 6723 128.00 - 135.31: 223 Bond angle restraints: 28081 Sorted by residual: angle pdb=" O LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 121.31 109.06 12.25 8.50e-01 1.38e+00 2.08e+02 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.78 133.05 -13.27 1.03e+00 9.43e-01 1.66e+02 angle pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 119.19 130.10 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" N TYR H 122 " pdb=" CA TYR H 122 " pdb=" C TYR H 122 " ideal model delta sigma weight residual 109.81 120.06 -10.25 2.21e+00 2.05e-01 2.15e+01 angle pdb=" N TYR F 122 " pdb=" CA TYR F 122 " pdb=" C TYR F 122 " ideal model delta sigma weight residual 109.81 120.01 -10.20 2.21e+00 2.05e-01 2.13e+01 ... (remaining 28076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 11037 14.34 - 28.69: 576 28.69 - 43.03: 170 43.03 - 57.38: 15 57.38 - 71.72: 7 Dihedral angle restraints: 11805 sinusoidal: 4751 harmonic: 7054 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual 93.00 48.72 44.28 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 11802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3207 0.133 - 0.265: 155 0.265 - 0.398: 23 0.398 - 0.530: 9 0.530 - 0.663: 1 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.52e+01 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.26 0.14 2.00e-02 2.50e+03 4.94e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.62e+01 ... (remaining 3392 not shown) Planarity restraints: 3335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " -0.269 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" C7 NAG C 702 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.187 2.00e-02 2.50e+03 1.55e-01 3.01e+02 pdb=" C7 NAG N 2 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.253 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.024 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C LEU A 234 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A 235 " 0.022 2.00e-02 2.50e+03 ... (remaining 3332 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 141 2.63 - 3.19: 15928 3.19 - 3.76: 28623 3.76 - 4.33: 38330 4.33 - 4.90: 64291 Nonbonded interactions: 147313 Sorted by model distance: nonbonded pdb=" O GLY D 239 " pdb=" OE2 GLU E 241 " model vdw 2.057 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.109 2.440 nonbonded pdb=" NH1 ARG E 188 " pdb=" OD2 ASP E 204 " model vdw 2.113 2.520 nonbonded pdb=" OE2 GLU C 159 " pdb=" NH1 ARG D 79 " model vdw 2.237 2.520 nonbonded pdb=" OD1 ASP I 103 " pdb=" OH TYR I 107 " model vdw 2.306 2.440 ... (remaining 147308 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 4 through 459 or resid 701 through 712)) selection = chain 'C' selection = (chain 'E' and (resid 4 through 459 or resid 701 through 712)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } 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 group one per residue 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: 1.630 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: 0.020 Extract box with map and model: 6.740 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 55.080 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.230 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.252 20571 Z= 0.400 Angle : 1.067 13.271 28081 Z= 0.540 Chirality : 0.071 0.663 3395 Planarity : 0.009 0.226 3319 Dihedral : 9.812 71.720 7202 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.69 % Allowed : 3.45 % Favored : 95.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -2.83 (0.15), residues: 2351 helix: -1.69 (0.15), residues: 747 sheet: -0.68 (0.21), residues: 568 loop : -2.69 (0.16), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 645 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 658 average time/residue: 0.3343 time to fit residues: 334.6712 Evaluate side-chains 377 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 371 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2514 time to fit residues: 5.6170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 0.0770 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 427 GLN A 428 ASN B 98 ASN B 144 GLN C 4 ASN C 111 ASN C 143 GLN C 416 HIS D 16 ASN D 191 ASN D 317 ASN E 43 GLN F 25 GLN F 78 ASN H 25 GLN H 76 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20571 Z= 0.195 Angle : 0.667 9.492 28081 Z= 0.327 Chirality : 0.045 0.360 3395 Planarity : 0.005 0.052 3319 Dihedral : 5.630 59.033 2663 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 12.83 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -1.33 (0.17), residues: 2351 helix: 0.57 (0.19), residues: 734 sheet: -0.34 (0.21), residues: 581 loop : -2.33 (0.17), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 399 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 46 residues processed: 438 average time/residue: 0.2889 time to fit residues: 201.9230 Evaluate side-chains 387 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 341 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1761 time to fit residues: 18.5022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 428 ASN B 416 HIS C 4 ASN C 20 ASN D 47 ASN D 298 HIS F 22 GLN H 58 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20571 Z= 0.436 Angle : 0.810 11.427 28081 Z= 0.397 Chirality : 0.050 0.391 3395 Planarity : 0.006 0.056 3319 Dihedral : 5.885 54.934 2663 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.42 % Allowed : 14.67 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -1.12 (0.17), residues: 2351 helix: 1.09 (0.19), residues: 727 sheet: -0.68 (0.21), residues: 608 loop : -2.19 (0.18), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 348 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 63 residues processed: 417 average time/residue: 0.2884 time to fit residues: 190.6303 Evaluate side-chains 381 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 318 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.1784 time to fit residues: 24.4090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN C 20 ASN E 4 ASN E 416 HIS F 22 GLN H 24 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20571 Z= 0.168 Angle : 0.615 9.394 28081 Z= 0.299 Chirality : 0.043 0.280 3395 Planarity : 0.004 0.047 3319 Dihedral : 5.373 56.025 2663 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.79 % Allowed : 16.88 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -0.56 (0.17), residues: 2351 helix: 1.75 (0.20), residues: 731 sheet: -0.38 (0.22), residues: 586 loop : -2.00 (0.18), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 373 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 395 average time/residue: 0.2935 time to fit residues: 183.0315 Evaluate side-chains 351 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 328 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1832 time to fit residues: 11.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 9.9990 chunk 127 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 0.0270 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 299 HIS F 22 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20571 Z= 0.249 Angle : 0.651 9.715 28081 Z= 0.314 Chirality : 0.044 0.296 3395 Planarity : 0.004 0.050 3319 Dihedral : 5.381 56.840 2663 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.30 % Allowed : 18.45 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -0.41 (0.18), residues: 2351 helix: 1.89 (0.20), residues: 731 sheet: -0.29 (0.22), residues: 596 loop : -1.93 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 323 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 350 average time/residue: 0.3146 time to fit residues: 173.9553 Evaluate side-chains 344 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1789 time to fit residues: 13.3785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN H 24 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20571 Z= 0.217 Angle : 0.623 9.423 28081 Z= 0.300 Chirality : 0.044 0.275 3395 Planarity : 0.004 0.052 3319 Dihedral : 5.301 56.593 2663 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.79 % Allowed : 18.77 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -0.32 (0.18), residues: 2351 helix: 2.05 (0.20), residues: 732 sheet: -0.30 (0.22), residues: 592 loop : -1.91 (0.18), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 329 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 352 average time/residue: 0.2876 time to fit residues: 161.5231 Evaluate side-chains 331 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 310 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1861 time to fit residues: 10.7894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20571 Z= 0.161 Angle : 0.597 12.085 28081 Z= 0.287 Chirality : 0.042 0.264 3395 Planarity : 0.004 0.049 3319 Dihedral : 5.112 58.064 2663 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 20.19 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % 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: -0.11 (0.18), residues: 2351 helix: 2.26 (0.20), residues: 731 sheet: -0.19 (0.22), residues: 596 loop : -1.81 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 328 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 337 average time/residue: 0.2864 time to fit residues: 153.5486 Evaluate side-chains 318 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 309 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1957 time to fit residues: 6.5247 ------------------------------------------------------------------------------- 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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 66.0904 > 50: distance: 15 - 19: 18.457 distance: 19 - 20: 19.226 distance: 20 - 21: 28.089 distance: 20 - 23: 4.375 distance: 21 - 28: 4.290 distance: 23 - 24: 39.017 distance: 24 - 25: 13.351 distance: 25 - 26: 15.831 distance: 26 - 27: 14.110 distance: 28 - 29: 16.284 distance: 29 - 30: 14.396 distance: 29 - 32: 19.694 distance: 30 - 31: 5.617 distance: 32 - 33: 33.880 distance: 32 - 34: 23.955 distance: 33 - 35: 31.238 distance: 37 - 38: 6.344 distance: 37 - 40: 9.912 distance: 40 - 41: 42.399 distance: 41 - 42: 39.463 distance: 42 - 43: 29.607 distance: 42 - 44: 7.192 distance: 45 - 46: 13.242 distance: 46 - 47: 4.337 distance: 46 - 49: 25.578 distance: 47 - 48: 28.845 distance: 47 - 52: 7.549 distance: 49 - 50: 28.102 distance: 49 - 51: 34.043 distance: 54 - 61: 22.099 distance: 56 - 57: 33.313 distance: 57 - 58: 4.433 distance: 58 - 59: 32.211 distance: 59 - 60: 19.785 distance: 61 - 62: 18.325 distance: 62 - 63: 52.292 distance: 62 - 65: 26.320 distance: 63 - 64: 8.326 distance: 63 - 73: 31.454 distance: 65 - 66: 29.931 distance: 66 - 67: 14.604 distance: 66 - 68: 40.211 distance: 67 - 69: 13.222 distance: 68 - 70: 20.986 distance: 69 - 71: 37.938 distance: 70 - 71: 9.666 distance: 73 - 74: 31.418 distance: 74 - 75: 50.821 distance: 74 - 77: 15.554 distance: 75 - 76: 40.044 distance: 75 - 84: 9.451 distance: 77 - 78: 26.942 distance: 78 - 80: 4.513 distance: 84 - 85: 27.126 distance: 84 - 90: 24.136 distance: 85 - 86: 24.523 distance: 85 - 88: 17.839 distance: 86 - 87: 38.691 distance: 86 - 91: 7.841 distance: 88 - 89: 28.339 distance: 89 - 90: 47.872 distance: 91 - 92: 3.602 distance: 92 - 93: 29.411 distance: 92 - 95: 31.330 distance: 93 - 94: 26.177 distance: 93 - 102: 38.668 distance: 95 - 96: 47.769 distance: 96 - 97: 24.443 distance: 96 - 98: 43.723 distance: 97 - 99: 12.753 distance: 98 - 100: 39.948 distance: 99 - 101: 28.324 distance: 104 - 110: 35.056 distance: 106 - 107: 27.727 distance: 107 - 108: 13.115 distance: 107 - 109: 13.988