Starting phenix.real_space_refine on Tue Aug 6 19:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/08_2024/8e2l_27842.cif" } resolution = 3.51 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= 0.002 sd= 0.048 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 P 27 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10698 2.51 5 N 3027 2.21 5 O 3281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17092 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3114 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "E" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2145 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2067 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.79, per 1000 atoms: 0.57 Number of scatterers: 17092 At special positions: 0 Unit cell: (100.58, 167.99, 188.32, 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) S 54 16.00 P 27 15.00 Mg 5 11.99 O 3281 8.00 N 3027 7.00 C 10698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 3.3 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4444 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 39.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.632A pdb=" N ALA C 52 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.728A pdb=" N THR C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 263 through 268 removed outlier: 4.048A pdb=" N ALA C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 300 through 314 removed outlier: 3.522A pdb=" N ILE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 373 through 389 removed outlier: 3.605A pdb=" N VAL C 377 " --> pdb=" O ASN C 373 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.569A pdb=" N MET C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.685A pdb=" N THR A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.380A pdb=" N PHE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 removed outlier: 3.778A pdb=" N ARG A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 300 through 314 removed outlier: 3.717A pdb=" N ILE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.633A pdb=" N GLU A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 4.217A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.771A pdb=" N MET A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.685A pdb=" N THR B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 174 through 181 removed outlier: 4.380A pdb=" N PHE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.778A pdb=" N ARG B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.519A pdb=" N VAL B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 268' Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.501A pdb=" N ILE B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 350 through 360 removed outlier: 4.181A pdb=" N GLU B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 removed outlier: 3.574A pdb=" N VAL B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.690A pdb=" N MET B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'D' and resid 66 through 73 removed outlier: 3.836A pdb=" N LYS D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.720A pdb=" N THR D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 174 through 181 removed outlier: 4.084A pdb=" N PHE D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.502A pdb=" N VAL D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 268' Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 300 through 314 removed outlier: 3.514A pdb=" N ILE D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 341 Processing helix chain 'D' and resid 350 through 360 removed outlier: 4.113A pdb=" N GLU D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.540A pdb=" N VAL D 377 " --> pdb=" O ASN D 373 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 413 through 430 Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'E' and resid 249 through 263 removed outlier: 4.025A pdb=" N LEU E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 4.006A pdb=" N ALA E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 300 through 314 removed outlier: 3.525A pdb=" N ILE E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 Processing helix chain 'E' and resid 350 through 360 removed outlier: 4.167A pdb=" N GLU E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 389 removed outlier: 3.550A pdb=" N VAL E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 413 through 430 Processing helix chain 'E' and resid 449 through 453 removed outlier: 4.215A pdb=" N ILE E 453 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.519A pdb=" N ILE F 314 " --> pdb=" O LEU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 343 through 349 removed outlier: 3.571A pdb=" N GLU F 346 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 348 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU F 349 " --> pdb=" O GLU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 360 removed outlier: 4.218A pdb=" N GLU F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 389 removed outlier: 3.609A pdb=" N VAL F 377 " --> pdb=" O ASN F 373 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 379 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 removed outlier: 3.669A pdb=" N MET F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 430 Processing helix chain 'F' and resid 457 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 160 through 161 removed outlier: 6.397A pdb=" N VAL C 141 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 184 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.631A pdb=" N ILE C 436 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 465 through 470 removed outlier: 6.839A pdb=" N VAL C 466 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C 486 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 483 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 502 removed outlier: 3.513A pdb=" N THR C 507 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.902A pdb=" N VAL A 161 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 140 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.647A pdb=" N VAL B 393 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE B 436 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 470 removed outlier: 6.990A pdb=" N VAL A 466 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 486 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 483 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 497 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 500 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.903A pdb=" N VAL B 161 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 140 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 470 removed outlier: 6.875A pdb=" N VAL B 466 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 486 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 483 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 497 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 500 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 507 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.767A pdb=" N LEU D 142 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.505A pdb=" N THR E 319 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET E 366 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP E 321 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 393 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ILE E 436 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE E 395 " --> pdb=" O ILE E 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 290 through 293 Processing sheet with id=AB5, first strand: chain 'D' and resid 465 through 470 removed outlier: 6.885A pdb=" N VAL D 466 " --> pdb=" O THR D 486 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 483 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 501 through 502 removed outlier: 3.553A pdb=" N THR D 507 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 465 through 470 removed outlier: 6.901A pdb=" N VAL E 466 " --> pdb=" O THR E 486 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR E 486 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 483 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 497 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 501 through 502 removed outlier: 3.591A pdb=" N THR E 507 " --> pdb=" O ILE E 502 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.801A pdb=" N VAL F 393 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE F 436 " --> pdb=" O VAL F 393 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 468 through 470 removed outlier: 3.705A pdb=" N LEU F 483 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 497 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP F 500 " --> pdb=" O SER F 509 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1770 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: 4.98 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4895 1.33 - 1.45: 2731 1.45 - 1.57: 9625 1.57 - 1.69: 48 1.69 - 1.81: 90 Bond restraints: 17389 Sorted by residual: bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 ... (remaining 17384 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.43: 565 107.43 - 114.62: 10201 114.62 - 121.82: 8807 121.82 - 129.02: 4048 129.02 - 136.22: 102 Bond angle restraints: 23723 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 119.97 19.90 1.00e+00 1.00e+00 3.96e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 ... (remaining 23718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 9677 23.41 - 46.81: 536 46.81 - 70.22: 109 70.22 - 93.62: 25 93.62 - 117.03: 1 Dihedral angle restraints: 10348 sinusoidal: 3515 harmonic: 6833 Sorted by residual: dihedral pdb=" CA ILE A 240 " pdb=" C ILE A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta harmonic sigma weight residual -180.00 -62.97 -117.03 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA PHE C 250 " pdb=" C PHE C 250 " pdb=" N LYS C 251 " pdb=" CA LYS C 251 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" C ASN B 397 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " pdb=" CB ASN B 397 " ideal model delta harmonic sigma weight residual -122.60 -133.66 11.06 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2512 0.077 - 0.153: 252 0.153 - 0.230: 6 0.230 - 0.306: 4 0.306 - 0.383: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ASN B 397 " pdb=" N ASN B 397 " pdb=" C ASN B 397 " pdb=" CB ASN B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA ASN E 397 " pdb=" N ASN E 397 " pdb=" C ASN E 397 " pdb=" CB ASN E 397 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2773 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 394 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ILE B 394 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE B 394 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 395 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 237 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS A 237 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 237 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 238 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 275 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 276 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.031 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 120 2.60 - 3.18: 14832 3.18 - 3.75: 24950 3.75 - 4.33: 32806 4.33 - 4.90: 54251 Nonbonded interactions: 126959 Sorted by model distance: nonbonded pdb=" O1B ATP D 601 " pdb="MG MG D 602 " model vdw 2.028 2.170 nonbonded pdb=" O3G ATP D 601 " pdb="MG MG D 602 " model vdw 2.030 2.170 nonbonded pdb=" OE1 GLN B 325 " pdb="MG MG B 602 " model vdw 2.038 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.039 2.170 nonbonded pdb=" O1B ATP E 601 " pdb="MG MG E 602 " model vdw 2.065 2.170 ... (remaining 126954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'C' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'D' and (resid 48 through 404 or resid 410 through 512)) } ncs_group { reference = (chain 'E' and (resid 244 through 259 or resid 269 through 512 or resid 601 thro \ ugh 602)) selection = chain 'F' } 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: 2.300 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.020 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.004 0.081 17389 Z= 0.249 Angle : 0.729 20.135 23723 Z= 0.559 Chirality : 0.045 0.383 2776 Planarity : 0.003 0.055 3058 Dihedral : 15.288 117.029 5904 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 0.42 % Allowed : 0.71 % Favored : 98.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.93 (0.18), residues: 2340 helix: 0.79 (0.20), residues: 803 sheet: 0.22 (0.32), residues: 304 loop : -1.88 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 272 HIS 0.004 0.001 HIS D 438 PHE 0.023 0.001 PHE B 358 TYR 0.020 0.001 TYR C 386 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 2.005 Fit side-chains REVERT: C 375 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8822 (tppt) REVERT: C 386 TYR cc_start: 0.8901 (m-80) cc_final: 0.8558 (m-80) REVERT: A 386 TYR cc_start: 0.8718 (m-80) cc_final: 0.8242 (m-80) REVERT: A 438 HIS cc_start: 0.5581 (m90) cc_final: 0.4881 (m-70) REVERT: B 491 ASP cc_start: 0.8427 (m-30) cc_final: 0.8127 (m-30) REVERT: E 464 ASP cc_start: 0.8656 (m-30) cc_final: 0.8285 (m-30) REVERT: F 397 ASN cc_start: 0.8324 (m-40) cc_final: 0.8100 (t0) outliers start: 6 outliers final: 1 residues processed: 151 average time/residue: 0.2801 time to fit residues: 65.4152 Evaluate side-chains 109 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 61 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS D 369 HIS ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 HIS ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17389 Z= 0.339 Angle : 0.573 12.910 23723 Z= 0.312 Chirality : 0.044 0.234 2776 Planarity : 0.004 0.085 3058 Dihedral : 11.060 89.580 2750 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.20 % Allowed : 8.47 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2340 helix: 0.83 (0.19), residues: 837 sheet: -0.24 (0.30), residues: 330 loop : -2.06 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 354 HIS 0.011 0.001 HIS D 369 PHE 0.025 0.002 PHE B 358 TYR 0.019 0.002 TYR C 386 ARG 0.003 0.000 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8342 (tmm) cc_final: 0.8051 (tmm) REVERT: A 386 TYR cc_start: 0.8645 (m-80) cc_final: 0.8187 (m-80) REVERT: A 438 HIS cc_start: 0.6145 (m90) cc_final: 0.5323 (m90) REVERT: B 317 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 491 ASP cc_start: 0.8498 (m-30) cc_final: 0.8222 (m-30) REVERT: D 491 ASP cc_start: 0.8597 (m-30) cc_final: 0.8112 (t0) REVERT: E 402 MET cc_start: 0.7395 (tmm) cc_final: 0.7022 (tmm) REVERT: E 464 ASP cc_start: 0.8758 (m-30) cc_final: 0.8418 (m-30) outliers start: 17 outliers final: 11 residues processed: 127 average time/residue: 0.2538 time to fit residues: 52.1044 Evaluate side-chains 118 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 HIS D 244 HIS F 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17389 Z= 0.227 Angle : 0.497 11.788 23723 Z= 0.272 Chirality : 0.042 0.202 2776 Planarity : 0.003 0.093 3058 Dihedral : 10.889 89.943 2750 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.20 % Allowed : 12.85 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.96 (0.18), residues: 2340 helix: 0.96 (0.19), residues: 838 sheet: -0.32 (0.31), residues: 311 loop : -1.98 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 354 HIS 0.011 0.001 HIS B 383 PHE 0.024 0.001 PHE F 358 TYR 0.015 0.001 TYR A 388 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 HIS cc_start: 0.5957 (m90) cc_final: 0.5054 (m90) REVERT: B 317 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 491 ASP cc_start: 0.8555 (m-30) cc_final: 0.8319 (m-30) REVERT: E 341 MET cc_start: 0.8952 (tpp) cc_final: 0.8727 (tpp) REVERT: E 402 MET cc_start: 0.7467 (tmm) cc_final: 0.7124 (tmm) REVERT: E 464 ASP cc_start: 0.8747 (m-30) cc_final: 0.8424 (m-30) REVERT: F 397 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7322 (t0) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.2454 time to fit residues: 47.6300 Evaluate side-chains 120 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 397 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 144 optimal weight: 50.0000 chunk 215 optimal weight: 0.0470 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN E 488 ASN ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 17389 Z= 0.499 Angle : 0.654 9.318 23723 Z= 0.352 Chirality : 0.047 0.278 2776 Planarity : 0.004 0.090 3058 Dihedral : 11.448 85.947 2750 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.43 % Favored : 89.49 % Rotamer: Outliers : 2.40 % Allowed : 14.41 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -1.34 (0.18), residues: 2340 helix: 0.63 (0.19), residues: 852 sheet: -0.79 (0.30), residues: 319 loop : -2.15 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 354 HIS 0.013 0.002 HIS D 438 PHE 0.025 0.002 PHE B 293 TYR 0.016 0.002 TYR C 258 ARG 0.003 0.001 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6425 (pp20) cc_final: 0.6150 (pp20) REVERT: D 491 ASP cc_start: 0.8629 (m-30) cc_final: 0.8260 (t0) REVERT: E 341 MET cc_start: 0.8941 (tpp) cc_final: 0.8500 (tpp) REVERT: E 464 ASP cc_start: 0.8728 (m-30) cc_final: 0.8404 (m-30) outliers start: 34 outliers final: 20 residues processed: 123 average time/residue: 0.2453 time to fit residues: 49.4008 Evaluate side-chains 116 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 1.9990 chunk 129 optimal weight: 0.0040 chunk 3 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 194 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 57 optimal weight: 40.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17389 Z= 0.171 Angle : 0.480 11.249 23723 Z= 0.263 Chirality : 0.042 0.209 2776 Planarity : 0.003 0.083 3058 Dihedral : 11.130 89.282 2750 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 1.91 % Allowed : 16.88 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.96 (0.18), residues: 2340 helix: 1.10 (0.19), residues: 832 sheet: -0.75 (0.30), residues: 311 loop : -1.95 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 354 HIS 0.010 0.001 HIS B 383 PHE 0.021 0.001 PHE F 358 TYR 0.016 0.001 TYR A 388 ARG 0.002 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 443 GLU cc_start: 0.6625 (pp20) cc_final: 0.6091 (pp20) REVERT: A 438 HIS cc_start: 0.6483 (m-70) cc_final: 0.5330 (m90) REVERT: D 461 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: D 491 ASP cc_start: 0.8594 (m-30) cc_final: 0.8238 (t0) REVERT: E 464 ASP cc_start: 0.8718 (m-30) cc_final: 0.8421 (m-30) REVERT: F 397 ASN cc_start: 0.8020 (t0) cc_final: 0.7452 (t0) REVERT: F 402 MET cc_start: 0.7944 (mmm) cc_final: 0.7716 (mtp) outliers start: 27 outliers final: 13 residues processed: 128 average time/residue: 0.2441 time to fit residues: 51.3029 Evaluate side-chains 118 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 228 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 18 optimal weight: 0.0070 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17389 Z= 0.243 Angle : 0.501 10.946 23723 Z= 0.273 Chirality : 0.042 0.155 2776 Planarity : 0.003 0.089 3058 Dihedral : 11.099 87.433 2750 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 1.98 % Allowed : 18.29 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.96 (0.18), residues: 2340 helix: 1.10 (0.19), residues: 842 sheet: -0.82 (0.29), residues: 321 loop : -1.97 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 354 HIS 0.009 0.001 HIS B 383 PHE 0.025 0.001 PHE B 358 TYR 0.017 0.001 TYR A 388 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: C 247 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 443 GLU cc_start: 0.6605 (pp20) cc_final: 0.6228 (pp20) REVERT: A 438 HIS cc_start: 0.6507 (m-70) cc_final: 0.5269 (m90) REVERT: D 461 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: D 491 ASP cc_start: 0.8628 (m-30) cc_final: 0.8253 (t0) REVERT: E 464 ASP cc_start: 0.8669 (m-30) cc_final: 0.8360 (m-30) REVERT: F 397 ASN cc_start: 0.8043 (t0) cc_final: 0.7506 (t0) REVERT: F 402 MET cc_start: 0.7992 (mmm) cc_final: 0.7755 (mtp) outliers start: 28 outliers final: 19 residues processed: 123 average time/residue: 0.2291 time to fit residues: 46.8159 Evaluate side-chains 123 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 57.9169 > 50: distance: 52 - 73: 6.976 distance: 56 - 81: 6.187 distance: 60 - 65: 3.524 distance: 66 - 67: 4.087 distance: 67 - 73: 3.064 distance: 69 - 70: 5.880 distance: 70 - 71: 9.100 distance: 70 - 72: 4.433 distance: 74 - 75: 6.826 distance: 74 - 77: 3.926 distance: 75 - 76: 9.131 distance: 75 - 81: 11.150 distance: 77 - 78: 9.641 distance: 78 - 79: 7.822 distance: 78 - 80: 6.262 distance: 81 - 82: 4.731 distance: 82 - 83: 4.341 distance: 82 - 85: 5.152 distance: 83 - 84: 3.384 distance: 83 - 87: 7.295 distance: 85 - 86: 13.783 distance: 87 - 88: 6.701 distance: 88 - 89: 5.862 distance: 88 - 91: 4.915 distance: 89 - 90: 9.009 distance: 89 - 95: 7.025 distance: 91 - 92: 7.576 distance: 91 - 93: 9.663 distance: 92 - 94: 8.696 distance: 95 - 96: 5.550 distance: 96 - 97: 15.107 distance: 96 - 99: 16.194 distance: 97 - 98: 9.238 distance: 97 - 104: 5.011 distance: 99 - 100: 6.607 distance: 100 - 101: 8.982 distance: 101 - 102: 9.111 distance: 101 - 103: 5.772 distance: 104 - 105: 18.500 distance: 105 - 106: 25.880 distance: 106 - 107: 10.098 distance: 106 - 108: 30.713 distance: 108 - 109: 12.887 distance: 109 - 110: 22.023 distance: 109 - 112: 20.336 distance: 110 - 111: 40.285 distance: 110 - 115: 3.617 distance: 112 - 113: 13.724 distance: 112 - 114: 21.912 distance: 115 - 116: 13.164 distance: 116 - 117: 25.238 distance: 116 - 119: 34.527 distance: 117 - 118: 26.302 distance: 117 - 123: 14.052 distance: 119 - 120: 10.383 distance: 120 - 121: 40.754 distance: 120 - 122: 9.805 distance: 123 - 124: 15.493 distance: 124 - 125: 10.282 distance: 124 - 127: 11.860 distance: 125 - 126: 17.265 distance: 125 - 130: 14.215 distance: 127 - 128: 25.975 distance: 127 - 129: 18.355 distance: 130 - 131: 7.222 distance: 130 - 206: 5.190 distance: 131 - 132: 3.784 distance: 131 - 134: 7.152 distance: 132 - 133: 5.159 distance: 132 - 138: 4.592 distance: 133 - 218: 6.763 distance: 134 - 135: 7.729 distance: 135 - 136: 8.256 distance: 135 - 137: 8.437