Starting phenix.real_space_refine on Wed May 21 22:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.map" model { file = "/net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev7_19993/05_2025/9ev7_19993.cif" } resolution = 2.74 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= 0.035 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 14303 2.51 5 N 3641 2.21 5 O 4199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4688 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4641 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3471 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4705 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4690 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 12.54, per 1000 atoms: 0.56 Number of scatterers: 22195 At special positions: 0 Unit cell: (139.656, 146.427, 157.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 4199 8.00 N 3641 7.00 C 14303 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 - 3.00 Amino acid : True - 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: 5.01 Conformation dependent library (CDL) restraints added in 3.1 seconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 28 sheets defined 29.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.942A pdb=" N SER A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.864A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.838A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.708A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.983A pdb=" N SER B 314 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.769A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.508A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 605 through 636 Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.102A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.835A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.827A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.511A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.925A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.099A pdb=" N SER D 314 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.865A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.844A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.503A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.710A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.062A pdb=" N SER E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.800A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.517A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 605 through 637 Proline residue: E 621 - end of helix removed outlier: 3.921A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.994A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.226A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.323A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.319A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.085A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.193A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.426A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.313A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.067A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 212 removed outlier: 4.269A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.245A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.198A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.039A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.110A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.521A pdb=" N ASP D 287 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.278A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.125A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.684A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.330A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.448A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.229A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 397 through 399 removed outlier: 4.964A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2880 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: 8.76 Time building geometry restraints manager: 5.92 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: 4656 1.33 - 1.45: 5390 1.45 - 1.57: 12589 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 22709 Sorted by residual: bond pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.62e+01 bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.61e+01 bond pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.59e+01 bond pdb=" CA GLU B 103 " pdb=" C GLU B 103 " ideal model delta sigma weight residual 1.526 1.490 0.037 9.20e-03 1.18e+04 1.58e+01 ... (remaining 22704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 30423 1.75 - 3.50: 428 3.50 - 5.25: 55 5.25 - 7.01: 18 7.01 - 8.76: 13 Bond angle restraints: 30937 Sorted by residual: angle pdb=" N TYR B 620 " pdb=" CA TYR B 620 " pdb=" C TYR B 620 " ideal model delta sigma weight residual 113.25 119.40 -6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" N GLU D 103 " pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 110.56 101.80 8.76 1.94e+00 2.66e-01 2.04e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.88 8.68 1.94e+00 2.66e-01 2.00e+01 angle pdb=" N GLU B 103 " pdb=" CA GLU B 103 " pdb=" C GLU B 103 " ideal model delta sigma weight residual 110.56 101.88 8.68 1.94e+00 2.66e-01 2.00e+01 ... (remaining 30932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 12716 14.37 - 28.74: 445 28.74 - 43.12: 139 43.12 - 57.49: 22 57.49 - 71.86: 10 Dihedral angle restraints: 13332 sinusoidal: 5160 harmonic: 8172 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE E 522 " pdb=" C ILE E 522 " pdb=" N PHE E 523 " pdb=" CA PHE E 523 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2970 0.056 - 0.112: 464 0.112 - 0.168: 84 0.168 - 0.224: 1 0.224 - 0.279: 9 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 620 " pdb=" N TYR A 620 " pdb=" C TYR A 620 " pdb=" CB TYR A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3525 not shown) Planarity restraints: 4019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 197 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C LEU B 197 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 197 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU B 198 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 200 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO B 201 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 199 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C ILE D 199 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE D 199 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 200 " 0.015 2.00e-02 2.50e+03 ... (remaining 4016 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1465 2.74 - 3.28: 20634 3.28 - 3.82: 34427 3.82 - 4.36: 40215 4.36 - 4.90: 72656 Nonbonded interactions: 169397 Sorted by model distance: nonbonded pdb=" OG SER E 367 " pdb=" OD1 ASP E 369 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.243 3.040 nonbonded pdb=" CB HIS B 222 " pdb=" CD1 LEU B 325 " model vdw 2.246 3.860 ... (remaining 169392 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' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 123 or (resid 124 and (name N or n \ ame CA or name C or name O or name CB )) or resid 125 through 195 or (resid 196 \ through 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 or (resid 202 through 203 and (name N or name CA or name C or name O or name C \ B )) or resid 204 through 205 or (resid 206 through 208 and (name N or name CA o \ r name C or name O or name CB )) or resid 209 through 240 or (resid 241 through \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throug \ h 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 292 or (resid 293 and (name N or name CA or name C or name O o \ r name CB )) or resid 294 through 311 or (resid 312 through 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 or (resid \ 321 through 322 and (name N or name CA or name C or name O or name CB )) or resi \ d 323 through 637)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 or (resid 107 and (name N \ or name CA or name C or name O or name CB )) or resid 108 through 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB )) or resid 125 throug \ h 637)) selection = (chain 'D' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB )) or resid 125 through 195 or (resid 196 through 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 or (resid 202 through 203 and (n \ ame N or name CA or name C or name O or name CB )) or resid 204 through 205 or ( \ resid 206 through 208 and (name N or name CA or name C or name O or name CB )) o \ r resid 209 through 240 or (resid 241 through 242 and (name N or name CA or name \ C or name O or name CB )) or resid 243 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 289 or (resid 29 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 291 or (resi \ d 292 through 293 and (name N or name CA or name C or name O or name CB )) or re \ sid 294 through 311 or (resid 312 through 313 and (name N or name CA or name C o \ r name O or name CB )) or resid 314 through 318 or (resid 319 and (name N or nam \ e CA or name C or name O or name CB )) or resid 320 or (resid 321 through 322 an \ d (name N or name CA or name C or name O or name CB )) or resid 323 through 637) \ ) selection = (chain 'E' and (resid 37 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 97 or (resid 98 through 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 104 or ( \ resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 \ or (resid 107 and (name N or name CA or name C or name O or name CB )) or resid \ 108 through 195 or (resid 196 through 200 and (name N or name CA or name C or na \ me O or name CB )) or resid 201 through 205 or (resid 206 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 through 240 or (resi \ d 241 through 242 and (name N or name CA or name C or name O or name CB )) or re \ sid 243 through 263 or (resid 264 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 291 or (resid 292 through 293 and (name N or nam \ e CA or name C or name O or name CB )) or resid 294 through 311 or (resid 312 th \ rough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 320 or (resid 321 through 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 637)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.660 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.003 0.052 22709 Z= 0.217 Angle : 0.552 8.758 30937 Z= 0.315 Chirality : 0.044 0.279 3528 Planarity : 0.004 0.064 4019 Dihedral : 8.721 71.862 8094 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 0.58 % Allowed : 3.11 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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: 0.94 (0.16), residues: 2830 helix: 1.93 (0.21), residues: 677 sheet: 0.91 (0.16), residues: 959 loop : -0.33 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 534 HIS 0.004 0.001 HIS C 285 PHE 0.011 0.001 PHE A 561 TYR 0.008 0.001 TYR B 517 ARG 0.002 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.19264 ( 1045) hydrogen bonds : angle 6.36311 ( 2880) covalent geometry : bond 0.00315 (22709) covalent geometry : angle 0.55226 (30937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 580 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8489 (mt0) cc_final: 0.8261 (mt0) REVERT: A 414 PHE cc_start: 0.7611 (p90) cc_final: 0.7205 (p90) REVERT: A 597 GLN cc_start: 0.8131 (mt0) cc_final: 0.7919 (mt0) REVERT: A 632 TYR cc_start: 0.8339 (t80) cc_final: 0.8129 (t80) REVERT: B 249 LEU cc_start: 0.8411 (tp) cc_final: 0.8201 (tt) REVERT: B 354 THR cc_start: 0.8578 (m) cc_final: 0.8376 (p) REVERT: C 206 GLN cc_start: 0.6854 (tt0) cc_final: 0.6607 (tt0) REVERT: C 400 TYR cc_start: 0.8072 (t80) cc_final: 0.7707 (t80) REVERT: C 444 ASP cc_start: 0.8047 (p0) cc_final: 0.7804 (p0) REVERT: C 458 THR cc_start: 0.8287 (t) cc_final: 0.7907 (m) REVERT: C 487 TYR cc_start: 0.8258 (p90) cc_final: 0.7926 (p90) REVERT: C 517 TYR cc_start: 0.8378 (t80) cc_final: 0.8161 (t80) REVERT: D 517 TYR cc_start: 0.8422 (t80) cc_final: 0.8149 (t80) REVERT: D 560 ASN cc_start: 0.7884 (t0) cc_final: 0.7670 (t0) REVERT: E 277 GLN cc_start: 0.7399 (mp10) cc_final: 0.6771 (mp-120) REVERT: E 304 VAL cc_start: 0.8198 (p) cc_final: 0.7976 (m) REVERT: E 354 THR cc_start: 0.8334 (m) cc_final: 0.8121 (p) REVERT: E 411 GLN cc_start: 0.8213 (tt0) cc_final: 0.7988 (tt0) REVERT: E 599 ARG cc_start: 0.8417 (tpt170) cc_final: 0.8188 (tpt170) outliers start: 14 outliers final: 3 residues processed: 590 average time/residue: 1.4443 time to fit residues: 973.3537 Evaluate side-chains 500 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 497 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 255 LYS Chi-restraints excluded: chain E residue 328 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 256 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 206 GLN A 221 GLN A 611 GLN B 233 HIS B 307 ASN B 410 ASN B 411 GLN B 432 GLN C 307 ASN C 344 GLN C 552 ASN D 221 GLN D 344 GLN D 409 GLN D 411 GLN E 338 GLN E 344 GLN E 360 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134122 restraints weight = 32375.537| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.38 r_work: 0.3541 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22709 Z= 0.222 Angle : 0.634 8.032 30937 Z= 0.340 Chirality : 0.048 0.189 3528 Planarity : 0.005 0.043 4019 Dihedral : 4.877 45.293 3072 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.33 % Allowed : 11.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.79 % 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: 0.93 (0.16), residues: 2830 helix: 1.85 (0.20), residues: 718 sheet: 1.00 (0.17), residues: 900 loop : -0.40 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 121 HIS 0.006 0.002 HIS D 144 PHE 0.022 0.002 PHE B 505 TYR 0.025 0.002 TYR B 53 ARG 0.009 0.001 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.07278 ( 1045) hydrogen bonds : angle 4.93674 ( 2880) covalent geometry : bond 0.00517 (22709) covalent geometry : angle 0.63440 (30937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 512 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8079 (t0) cc_final: 0.7861 (t70) REVERT: A 345 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7933 (mtp85) REVERT: A 414 PHE cc_start: 0.8284 (p90) cc_final: 0.7829 (p90) REVERT: A 479 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7246 (mt-10) REVERT: A 521 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: A 599 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8402 (tpt170) REVERT: B 405 ASN cc_start: 0.8329 (m110) cc_final: 0.8078 (m-40) REVERT: B 560 ASN cc_start: 0.8383 (t0) cc_final: 0.8177 (t0) REVERT: B 620 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: C 414 PHE cc_start: 0.8233 (p90) cc_final: 0.7974 (p90) REVERT: C 458 THR cc_start: 0.8460 (t) cc_final: 0.8116 (m) REVERT: C 473 VAL cc_start: 0.8434 (m) cc_final: 0.8159 (t) REVERT: C 620 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: D 143 TYR cc_start: 0.6402 (m-80) cc_final: 0.6153 (m-80) REVERT: D 163 TYR cc_start: 0.7964 (m-80) cc_final: 0.7588 (m-80) REVERT: D 327 SER cc_start: 0.7932 (p) cc_final: 0.7560 (t) REVERT: D 363 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8619 (mtpp) REVERT: D 414 PHE cc_start: 0.8469 (p90) cc_final: 0.8141 (p90) REVERT: D 425 GLU cc_start: 0.8349 (tt0) cc_final: 0.7320 (tm-30) REVERT: D 481 GLU cc_start: 0.7902 (tt0) cc_final: 0.7453 (tt0) REVERT: D 515 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8345 (mp) REVERT: E 303 LEU cc_start: 0.7703 (tp) cc_final: 0.7491 (tp) REVERT: E 403 GLN cc_start: 0.7917 (tp40) cc_final: 0.7434 (tp-100) REVERT: E 480 GLU cc_start: 0.7620 (mp0) cc_final: 0.7232 (mp0) REVERT: E 599 ARG cc_start: 0.8722 (tpt170) cc_final: 0.8434 (tpt90) outliers start: 56 outliers final: 26 residues processed: 538 average time/residue: 1.4055 time to fit residues: 851.4614 Evaluate side-chains 503 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 474 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 514 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1116 > 50: distance: 1 - 18: 3.004 distance: 34 - 38: 29.722 distance: 38 - 39: 4.002 distance: 39 - 40: 50.825 distance: 39 - 42: 24.519 distance: 40 - 41: 16.890 distance: 40 - 49: 3.666 distance: 42 - 43: 21.486 distance: 43 - 44: 20.427 distance: 43 - 45: 12.041 distance: 44 - 46: 23.271 distance: 45 - 47: 24.043 distance: 46 - 48: 13.069 distance: 47 - 48: 10.548 distance: 49 - 50: 37.805 distance: 50 - 51: 24.900 distance: 50 - 53: 39.863 distance: 51 - 52: 41.957 distance: 51 - 57: 42.511 distance: 53 - 54: 26.710 distance: 54 - 55: 29.837 distance: 54 - 56: 14.659 distance: 57 - 58: 27.202 distance: 58 - 59: 12.965 distance: 58 - 61: 12.898 distance: 59 - 68: 57.562 distance: 61 - 62: 25.075 distance: 62 - 63: 26.100 distance: 62 - 64: 37.837 distance: 63 - 65: 25.186 distance: 64 - 66: 40.358 distance: 65 - 67: 55.832 distance: 66 - 67: 57.809 distance: 68 - 69: 40.177 distance: 69 - 70: 38.845 distance: 69 - 72: 40.874 distance: 70 - 76: 40.101 distance: 72 - 73: 58.033 distance: 73 - 74: 9.977 distance: 73 - 75: 28.467 distance: 76 - 77: 18.987 distance: 77 - 78: 19.961 distance: 77 - 80: 48.606 distance: 78 - 79: 39.979 distance: 78 - 81: 56.447 distance: 81 - 82: 39.471 distance: 82 - 83: 67.808 distance: 82 - 85: 56.716 distance: 83 - 84: 42.703 distance: 83 - 93: 40.073 distance: 85 - 86: 29.311 distance: 86 - 87: 50.775 distance: 86 - 88: 41.433 distance: 87 - 89: 18.573 distance: 88 - 90: 48.983 distance: 90 - 91: 26.102 distance: 91 - 92: 39.739 distance: 93 - 94: 40.350 distance: 94 - 95: 39.923 distance: 94 - 97: 38.800 distance: 95 - 96: 41.872 distance: 95 - 100: 55.241 distance: 97 - 98: 56.555 distance: 98 - 99: 57.372 distance: 100 - 101: 39.173 distance: 102 - 103: 36.868 distance: 102 - 111: 57.248 distance: 104 - 105: 15.281 distance: 105 - 106: 38.869 distance: 105 - 107: 4.466 distance: 106 - 108: 37.843 distance: 107 - 109: 37.339 distance: 108 - 110: 21.133 distance: 109 - 110: 31.426 distance: 111 - 112: 11.302 distance: 112 - 113: 18.335 distance: 112 - 115: 37.631 distance: 113 - 114: 43.094 distance: 113 - 119: 24.268 distance: 115 - 116: 28.390 distance: 116 - 117: 41.887 distance: 116 - 118: 53.847 distance: 119 - 120: 48.317 distance: 120 - 121: 34.364 distance: 120 - 123: 36.148 distance: 121 - 122: 42.228 distance: 121 - 130: 27.999 distance: 123 - 124: 40.719 distance: 124 - 125: 48.982 distance: 125 - 126: 41.102 distance: 127 - 128: 18.473 distance: 127 - 129: 23.976