Starting phenix.real_space_refine on Tue Mar 19 10:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr8_24655/03_2024/7rr8_24655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr8_24655/03_2024/7rr8_24655.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/7rr8_24655/03_2024/7rr8_24655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr8_24655/03_2024/7rr8_24655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr8_24655/03_2024/7rr8_24655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr8_24655/03_2024/7rr8_24655_updated.pdb" } 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= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 132 5.16 5 C 15482 2.51 5 N 3861 2.21 5 O 4441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 602": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7779 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 7804 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 981} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7780 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 218 Unusual residues: {'D12': 4, 'PTY': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 182 Unusual residues: {'D12': 4, 'PTY': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 166 Unusual residues: {'D12': 5, 'PTY': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 12.65, per 1000 atoms: 0.53 Number of scatterers: 23929 At special positions: 0 Unit cell: (120.7, 115.6, 143.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 13 15.00 O 4441 8.00 N 3861 7.00 C 15482 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: 9.61 Conformation dependent library (CDL) restraints added in 4.6 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 24 sheets defined 53.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.884A pdb=" N GLN A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.987A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.589A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 358 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.840A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 removed outlier: 4.585A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 4.152A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 457 removed outlier: 3.891A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 462 through 486 removed outlier: 3.967A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 511 through 536 removed outlier: 3.871A pdb=" N TRP A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.505A pdb=" N LEU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 692 through 708 removed outlier: 3.607A pdb=" N LYS A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.584A pdb=" N TRP A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 801 through 803 No H-bonds generated for 'chain 'A' and resid 801 through 803' Processing helix chain 'A' and resid 837 through 849 removed outlier: 3.541A pdb=" N GLN A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 874 through 892 removed outlier: 3.527A pdb=" N TYR A 892 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 918 removed outlier: 3.859A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Proline residue: A 906 - end of helix removed outlier: 3.522A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 953 Processing helix chain 'A' and resid 960 through 990 removed outlier: 4.648A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 997 through 1031 removed outlier: 3.579A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 28 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.769A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 3.558A pdb=" N VAL C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Proline residue: C 116 - end of helix Processing helix chain 'C' and resid 120 through 125 removed outlier: 3.961A pdb=" N GLN C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 299 through 312 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 330 through 358 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.736A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.938A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 422 removed outlier: 4.122A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.911A pdb=" N GLN C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 451 removed outlier: 5.154A pdb=" N SER C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.883A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 512 through 536 removed outlier: 3.831A pdb=" N PHE C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 558 Processing helix chain 'C' and resid 584 through 600 Processing helix chain 'C' and resid 644 through 655 Processing helix chain 'C' and resid 692 through 695 No H-bonds generated for 'chain 'C' and resid 692 through 695' Processing helix chain 'C' and resid 699 through 702 No H-bonds generated for 'chain 'C' and resid 699 through 702' Processing helix chain 'C' and resid 706 through 708 No H-bonds generated for 'chain 'C' and resid 706 through 708' Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.646A pdb=" N LEU C 739 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 754 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 783 through 788 Processing helix chain 'C' and resid 801 through 804 Processing helix chain 'C' and resid 839 through 849 Processing helix chain 'C' and resid 861 through 892 removed outlier: 3.519A pdb=" N ALA C 873 " --> pdb=" O SER C 869 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 896 through 902 Processing helix chain 'C' and resid 905 through 919 Processing helix chain 'C' and resid 925 through 954 removed outlier: 3.830A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 991 removed outlier: 5.344A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 997 through 1032 removed outlier: 4.358A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C1019 " --> pdb=" O THR C1015 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C1020 " --> pdb=" O VAL C1016 " (cutoff:3.500A) Proline residue: C1023 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 54 through 68 removed outlier: 5.020A pdb=" N GLN B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 316 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 331 through 358 Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 372 through 385 Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.402A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 456 removed outlier: 4.822A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.844A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 512 through 534 Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 584 through 600 removed outlier: 3.681A pdb=" N VAL B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 644 through 655 removed outlier: 3.601A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 707 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 743 through 754 removed outlier: 3.549A pdb=" N THR B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 837 through 850 removed outlier: 3.747A pdb=" N MET B 841 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.788A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 868 " --> pdb=" O TYR B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 892 Processing helix chain 'B' and resid 897 through 918 removed outlier: 3.610A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Proline residue: B 906 - end of helix removed outlier: 3.971A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 954 Processing helix chain 'B' and resid 960 through 990 removed outlier: 3.655A pdb=" N VAL B 968 " --> pdb=" O THR B 964 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 997 through 1032 removed outlier: 4.090A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.054A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.719A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 607 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N SER A 630 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL A 609 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 628 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 611 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 626 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.404A pdb=" N VAL A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N MET A 184 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS A 770 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A 186 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR A 772 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET A 188 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N MET A 774 " --> pdb=" O MET A 188 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 824 through 830 Processing sheet with id= E, first strand: chain 'A' and resid 723 through 731 Processing sheet with id= F, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= G, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.674A pdb=" N LYS A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 175 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.909A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.362A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 322 through 324 removed outlier: 4.038A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 609 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 628 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA C 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 626 " --> pdb=" O ALA C 611 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN C 613 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR C 624 " --> pdb=" O ASN C 613 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= L, first strand: chain 'C' and resid 681 through 685 removed outlier: 4.626A pdb=" N ASP C 681 " --> pdb=" O THR C 860 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 860 " --> pdb=" O ASP C 681 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 723 through 726 Processing sheet with id= N, first strand: chain 'C' and resid 761 through 763 Processing sheet with id= O, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= P, first strand: chain 'C' and resid 172 through 177 removed outlier: 6.591A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.905A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.699A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.426A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 138 through 143 removed outlier: 4.110A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.577A pdb=" N VAL B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.783A pdb=" N SER B 630 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B 609 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 628 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 611 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 626 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN B 613 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR B 624 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 723 through 731 Processing sheet with id= W, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= X, first strand: chain 'B' and resid 250 through 253 removed outlier: 7.271A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3669 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: 9.53 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3902 1.29 - 1.43: 5744 1.43 - 1.56: 14415 1.56 - 1.69: 27 1.69 - 1.82: 258 Bond restraints: 24346 Sorted by residual: bond pdb=" C ASP B 407 " pdb=" O ASP B 407 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.15e-02 7.56e+03 4.54e+01 bond pdb=" C PRO B 368 " pdb=" O PRO B 368 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.28e-02 6.10e+03 3.01e+01 bond pdb=" C ILE C 474 " pdb=" O ILE C 474 " ideal model delta sigma weight residual 1.240 1.182 0.058 1.18e-02 7.18e+03 2.41e+01 bond pdb=" C ALA B 441 " pdb=" O ALA B 441 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.15e+01 bond pdb=" N THR A 538 " pdb=" CA THR A 538 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.21e-02 6.83e+03 1.39e+01 ... (remaining 24341 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.00: 668 106.00 - 113.02: 13046 113.02 - 120.04: 8595 120.04 - 127.07: 10407 127.07 - 134.09: 208 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C PRO C 800 " pdb=" CA PRO C 800 " pdb=" CB PRO C 800 " ideal model delta sigma weight residual 111.11 123.38 -12.27 1.17e+00 7.31e-01 1.10e+02 angle pdb=" CA PHE A 4 " pdb=" CB PHE A 4 " pdb=" CG PHE A 4 " ideal model delta sigma weight residual 113.80 106.15 7.65 1.00e+00 1.00e+00 5.86e+01 angle pdb=" CA GLY A 639 " pdb=" C GLY A 639 " pdb=" O GLY A 639 " ideal model delta sigma weight residual 122.23 117.72 4.51 6.90e-01 2.10e+00 4.27e+01 angle pdb=" C GLU B 866 " pdb=" CA GLU B 866 " pdb=" CB GLU B 866 " ideal model delta sigma weight residual 110.81 100.97 9.84 1.60e+00 3.91e-01 3.78e+01 angle pdb=" CA PHE B 801 " pdb=" C PHE B 801 " pdb=" O PHE B 801 " ideal model delta sigma weight residual 120.82 114.71 6.11 1.05e+00 9.07e-01 3.39e+01 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 14200 32.10 - 64.19: 411 64.19 - 96.29: 31 96.29 - 128.38: 1 128.38 - 160.48: 5 Dihedral angle restraints: 14648 sinusoidal: 5864 harmonic: 8784 Sorted by residual: dihedral pdb=" CA GLN A 34 " pdb=" C GLN A 34 " pdb=" N TYR A 35 " pdb=" CA TYR A 35 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR B 329 " pdb=" C THR B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C PRO C 800 " pdb=" N PRO C 800 " pdb=" CA PRO C 800 " pdb=" CB PRO C 800 " ideal model delta harmonic sigma weight residual -120.70 -132.20 11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 14645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3455 0.076 - 0.152: 352 0.152 - 0.229: 19 0.229 - 0.305: 4 0.305 - 0.381: 1 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA PRO C 800 " pdb=" N PRO C 800 " pdb=" C PRO C 800 " pdb=" CB PRO C 800 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C6 PTY B1202 " pdb=" C1 PTY B1202 " pdb=" C5 PTY B1202 " pdb=" O7 PTY B1202 " both_signs ideal model delta sigma weight residual False 2.49 2.22 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3828 not shown) Planarity restraints: 4155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.028 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE A 4 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 682 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" C PHE C 682 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE C 682 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C 683 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C GLN A 89 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 90 " -0.016 2.00e-02 2.50e+03 ... (remaining 4152 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2849 2.75 - 3.29: 23877 3.29 - 3.83: 40604 3.83 - 4.36: 48638 4.36 - 4.90: 84580 Nonbonded interactions: 200548 Sorted by model distance: nonbonded pdb=" O ALA A 430 " pdb=" OG SER A 434 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR B 44 " pdb=" OG SER B 132 " model vdw 2.228 2.440 nonbonded pdb=" O ILE A 647 " pdb=" OG1 THR A 648 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 892 " pdb=" O ILE A 943 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP A 153 " pdb=" OH TYR A 182 " model vdw 2.246 2.440 ... (remaining 200543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 499 or resid 511 through 658 or (resid 659 and ( \ name N or name CA or name C or name O or name CB )) or resid 660 through 702 or \ (resid 703 through 704 and (name N or name CA or name C or name O or name CB )) \ or resid 705 through 1034 or (resid 1101 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C2 or name C20 or name C21 or name C22 or name C3 or name C30 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or n \ ame C38 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or n \ ame O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) \ or (resid 1102 and (name C1 or name C11 or name C12 or name C13 or name C14 or n \ ame C15 or name C16 or name C5 or name C6 or name C8 or name N1 or name O10 or n \ ame O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or \ name P1 )) or (resid 1103 and (name C1 or name O11 or name O12 or name O13 or n \ ame O14 or name O30 or name O4 or name P1 )) or (resid 1105 and (name C10 or nam \ e C11 or name C12 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 )) or (resid 1106 and (name C3 or name C4 or name C5 or name C6 or name C7 ) \ ) or (resid 1107 and (name C1 or name C10 or name C2 or name C3 or name C4 or na \ me C5 or name C6 or name C7 or name C8 or name C9 )))) selection = (chain 'B' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 407 or (resid 408 through 409 and (nam \ e N or name CA or name C or name O or name CB )) or resid 410 through 499 or res \ id 511 through 702 or (resid 703 through 704 and (name N or name CA or name C or \ name O or name CB )) or resid 705 through 1034 or (resid 1201 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C \ 3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1202 and (name C1 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C5 or name C6 or name C8 or na \ me N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or (resid 1203 and (name C1 or name O11 or nam \ e O12 or name O13 or name O14 or name O30 or name O4 or name P1 )) or (resid 120 \ 5 and (name C10 or name C11 or name C12 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 )) or (resid 1206 and (name C3 or name C4 or name C5 o \ r name C6 or name C7 )) or resid 1207)) selection = (chain 'C' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 407 or (resid 408 through 409 and (nam \ e N or name CA or name C or name O or name CB )) or resid 410 through 499 or res \ id 511 through 658 or (resid 659 and (name N or name CA or name C or name O or n \ ame CB )) or resid 660 through 1034 or (resid 1101 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C5 or name C6 or name C8 or name N1 or name O10 or nam \ e O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or n \ ame P1 )) or (resid 1102 and (name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1103 and (name C1 or name O11 or name O12 or nam \ e O13 or name O14 or name O30 or name O4 or name P1 )) or resid 1105 or (resid 1 \ 106 and (name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 1107 a \ nd (name C1 or name C10 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name C9 )))) } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.240 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 65.530 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.160 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.077 24346 Z= 0.340 Angle : 0.793 16.059 32924 Z= 0.470 Chirality : 0.046 0.381 3831 Planarity : 0.004 0.036 4155 Dihedral : 14.589 160.476 9014 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.22 % 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: 0.59 (0.16), residues: 3063 helix: 1.30 (0.13), residues: 1634 sheet: -0.52 (0.25), residues: 416 loop : -0.58 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 859 HIS 0.002 0.000 HIS A 709 PHE 0.058 0.001 PHE A 4 TYR 0.024 0.001 TYR A 35 ARG 0.004 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 372 time to evaluate : 2.677 Fit side-chains revert: symmetry clash REVERT: A 410 ILE cc_start: 0.8522 (pt) cc_final: 0.8212 (pt) REVERT: A 414 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6466 (tm-30) REVERT: A 918 PHE cc_start: 0.7039 (t80) cc_final: 0.6822 (t80) REVERT: A 970 MET cc_start: 0.8019 (mtp) cc_final: 0.7718 (mtt) REVERT: C 438 ILE cc_start: 0.8706 (tp) cc_final: 0.8490 (tp) REVERT: C 948 PHE cc_start: 0.8303 (t80) cc_final: 0.8048 (t80) REVERT: B 664 PHE cc_start: 0.7508 (t80) cc_final: 0.7280 (t80) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.3608 time to fit residues: 214.2090 Evaluate side-chains 303 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 862 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 737 GLN A1000 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24346 Z= 0.225 Angle : 0.513 6.900 32924 Z= 0.262 Chirality : 0.041 0.152 3831 Planarity : 0.004 0.036 4155 Dihedral : 11.920 133.297 3686 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.16 % Allowed : 6.60 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.80 (0.16), residues: 3063 helix: 1.48 (0.13), residues: 1638 sheet: -0.54 (0.25), residues: 429 loop : -0.46 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 515 HIS 0.002 0.000 HIS A 709 PHE 0.025 0.001 PHE A 4 TYR 0.019 0.001 TYR A 49 ARG 0.004 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 317 time to evaluate : 2.670 Fit side-chains REVERT: A 414 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6485 (tm-30) REVERT: A 918 PHE cc_start: 0.7060 (t80) cc_final: 0.6834 (t80) REVERT: A 970 MET cc_start: 0.8016 (mtp) cc_final: 0.7713 (mtt) REVERT: C 438 ILE cc_start: 0.8702 (tp) cc_final: 0.8441 (tp) REVERT: C 948 PHE cc_start: 0.8341 (t80) cc_final: 0.8101 (t80) REVERT: B 89 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7591 (mm-40) REVERT: B 664 PHE cc_start: 0.7510 (t80) cc_final: 0.7239 (t80) outliers start: 29 outliers final: 14 residues processed: 335 average time/residue: 0.3587 time to fit residues: 194.5410 Evaluate side-chains 312 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 231 optimal weight: 0.0470 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 276 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 526 HIS A 737 GLN A1000 GLN C 81 ASN C 231 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24346 Z= 0.155 Angle : 0.477 7.520 32924 Z= 0.241 Chirality : 0.040 0.149 3831 Planarity : 0.003 0.050 4155 Dihedral : 11.064 117.157 3683 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.16 % Allowed : 8.68 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.99 (0.16), residues: 3063 helix: 1.63 (0.13), residues: 1640 sheet: -0.53 (0.24), residues: 444 loop : -0.32 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 754 HIS 0.005 0.000 HIS A 526 PHE 0.015 0.001 PHE A 352 TYR 0.011 0.001 TYR C 49 ARG 0.009 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 323 time to evaluate : 2.739 Fit side-chains REVERT: A 414 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6423 (tm-30) REVERT: A 862 MET cc_start: 0.7081 (pmm) cc_final: 0.6710 (pmm) REVERT: A 918 PHE cc_start: 0.7064 (t80) cc_final: 0.6829 (t80) REVERT: A 970 MET cc_start: 0.7905 (mtp) cc_final: 0.7661 (mtt) REVERT: C 335 ILE cc_start: 0.9059 (tp) cc_final: 0.8829 (mm) REVERT: C 438 ILE cc_start: 0.8604 (tp) cc_final: 0.8357 (tp) REVERT: C 712 MET cc_start: 0.8207 (tpt) cc_final: 0.8004 (tpt) REVERT: B 664 PHE cc_start: 0.7465 (t80) cc_final: 0.7231 (t80) REVERT: B 866 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6844 (tm-30) outliers start: 29 outliers final: 21 residues processed: 339 average time/residue: 0.3563 time to fit residues: 196.9917 Evaluate side-chains 321 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 835 LYS Chi-restraints excluded: chain B residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 58.0394 > 50: distance: 12 - 147: 25.048 distance: 15 - 144: 13.003 distance: 62 - 83: 20.032 distance: 68 - 91: 25.020 distance: 73 - 96: 22.582 distance: 76 - 83: 20.806 distance: 83 - 84: 19.990 distance: 84 - 85: 27.546 distance: 84 - 87: 31.973 distance: 85 - 86: 40.937 distance: 85 - 91: 18.342 distance: 87 - 88: 22.771 distance: 88 - 89: 44.867 distance: 88 - 90: 22.706 distance: 91 - 92: 14.062 distance: 92 - 93: 21.688 distance: 92 - 95: 22.061 distance: 93 - 94: 34.339 distance: 93 - 96: 10.140 distance: 96 - 97: 7.511 distance: 97 - 98: 18.880 distance: 97 - 100: 35.439 distance: 98 - 99: 27.569 distance: 98 - 102: 23.359 distance: 100 - 101: 39.635 distance: 102 - 103: 19.308 distance: 103 - 104: 26.869 distance: 103 - 106: 14.709 distance: 104 - 105: 7.531 distance: 104 - 111: 31.774 distance: 106 - 107: 29.371 distance: 107 - 108: 5.166 distance: 108 - 109: 31.446 distance: 109 - 110: 11.294 distance: 111 - 112: 19.472 distance: 112 - 113: 25.598 distance: 112 - 115: 45.610 distance: 113 - 114: 19.693 distance: 113 - 119: 33.635 distance: 115 - 116: 13.646 distance: 116 - 117: 36.944 distance: 116 - 118: 28.391 distance: 119 - 120: 19.186 distance: 119 - 125: 29.336 distance: 120 - 121: 12.595 distance: 120 - 123: 10.344 distance: 121 - 122: 23.898 distance: 121 - 126: 33.007 distance: 123 - 124: 43.789 distance: 124 - 125: 5.528 distance: 126 - 127: 42.418 distance: 127 - 128: 36.813 distance: 127 - 130: 41.167 distance: 128 - 129: 41.900 distance: 128 - 133: 14.692 distance: 130 - 131: 33.144 distance: 130 - 132: 46.608 distance: 133 - 134: 50.784 distance: 134 - 135: 34.894 distance: 135 - 136: 27.847 distance: 135 - 137: 13.527 distance: 137 - 138: 24.817 distance: 138 - 139: 25.675 distance: 138 - 141: 15.856 distance: 139 - 140: 15.296 distance: 139 - 144: 11.920 distance: 141 - 142: 21.924 distance: 141 - 143: 5.376 distance: 145 - 146: 19.265 distance: 146 - 147: 19.868 distance: 146 - 148: 23.164