Starting phenix.real_space_refine on Thu Aug 8 21:03:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjl_40093/08_2024/8gjl_40093.cif" } resolution = 3.44 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= 0.021 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 S 84 5.16 5 C 15512 2.51 5 N 3856 2.21 5 O 4463 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B GLU 956": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C ASP 807": "OD1" <-> "OD2" Residue "C GLU 839": "OE1" <-> "OE2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C GLU 941": "OE1" <-> "OE2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C GLU 956": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23916 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7932 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7978 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7982 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 41, 'TRANS': 990} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CPF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.47, per 1000 atoms: 0.52 Number of scatterers: 23916 At special positions: 0 Unit cell: (114.49, 123.05, 147.66, 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 84 16.00 F 1 9.00 O 4463 8.00 N 3856 7.00 C 15512 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: 9.42 Conformation dependent library (CDL) restraints added in 4.3 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 26 sheets defined 60.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'B' and resid 1 through 9 removed outlier: 3.548A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 99 through 118 removed outlier: 4.263A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.778A pdb=" N ILE B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.530A pdb=" N LYS B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 removed outlier: 3.518A pdb=" N VAL B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 299 through 316 Processing helix chain 'B' and resid 329 through 360 removed outlier: 4.545A pdb=" N PHE B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 388 Proline residue: B 369 - end of helix removed outlier: 3.595A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix removed outlier: 3.603A pdb=" N THR B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 424 removed outlier: 5.218A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 460 removed outlier: 5.267A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix removed outlier: 4.103A pdb=" N PHE B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 498 removed outlier: 3.821A pdb=" N ILE B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 507 through 534 Processing helix chain 'B' and resid 535 through 556 Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.538A pdb=" N THR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET B 598 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 685 through 702 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 769 through 775 removed outlier: 3.632A pdb=" N ARG B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 779 removed outlier: 4.536A pdb=" N LEU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 855 through 863 Processing helix chain 'B' and resid 867 through 887 removed outlier: 3.631A pdb=" N PHE B 871 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 899 removed outlier: 4.205A pdb=" N VAL B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 914 removed outlier: 4.046A pdb=" N VAL B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 950 Processing helix chain 'B' and resid 953 through 985 removed outlier: 4.505A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix Processing helix chain 'B' and resid 990 through 1032 removed outlier: 3.677A pdb=" N GLY B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1014 " --> pdb=" O THR B1010 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.734A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.518A pdb=" N ALA A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 71 removed outlier: 4.248A pdb=" N THR A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 123 removed outlier: 4.114A pdb=" N VAL A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 4.267A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASP A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.777A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 360 Processing helix chain 'A' and resid 362 through 388 Proline residue: A 369 - end of helix Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 393 through 424 removed outlier: 4.253A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 461 removed outlier: 5.174A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Proline residue: A 457 - end of helix removed outlier: 3.906A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 499 removed outlier: 3.620A pdb=" N ILE A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 507 through 534 removed outlier: 3.652A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.664A pdb=" N PHE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.597A pdb=" N THR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 598 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 685 through 703 removed outlier: 3.648A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 770 through 776 removed outlier: 5.779A pdb=" N THR A 775 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A 776 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.011A pdb=" N ASN A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 845 Processing helix chain 'A' and resid 854 through 864 Processing helix chain 'A' and resid 865 through 887 Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.801A pdb=" N ALA A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 914 removed outlier: 3.662A pdb=" N ALA A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 950 removed outlier: 4.070A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 986 removed outlier: 4.869A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix removed outlier: 3.570A pdb=" N PHE A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1032 removed outlier: 3.919A pdb=" N ARG A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 9 removed outlier: 3.674A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 Processing helix chain 'C' and resid 54 through 71 removed outlier: 4.111A pdb=" N THR C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.965A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 299 through 315 Processing helix chain 'C' and resid 329 through 361 removed outlier: 4.231A pdb=" N PHE C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 388 removed outlier: 3.889A pdb=" N MET C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 392 through 424 removed outlier: 4.145A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 Processing helix chain 'C' and resid 440 through 461 removed outlier: 3.748A pdb=" N VAL C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Proline residue: C 457 - end of helix removed outlier: 3.851A pdb=" N PHE C 460 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 489 removed outlier: 3.568A pdb=" N GLY C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 498 removed outlier: 3.924A pdb=" N SER C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 534 Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.753A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 685 through 703 removed outlier: 3.583A pdb=" N THR C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 735 through 747 Processing helix chain 'C' and resid 769 through 774 removed outlier: 3.680A pdb=" N ARG C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 774 " --> pdb=" O GLY C 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 769 through 774' Processing helix chain 'C' and resid 777 through 781 Processing helix chain 'C' and resid 829 through 845 Processing helix chain 'C' and resid 854 through 863 Processing helix chain 'C' and resid 865 through 887 removed outlier: 3.965A pdb=" N TYR C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 898 removed outlier: 3.901A pdb=" N VAL C 895 " --> pdb=" O MET C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 914 removed outlier: 4.258A pdb=" N ALA C 902 " --> pdb=" O ALA C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 949 Processing helix chain 'C' and resid 953 through 986 removed outlier: 4.507A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 3.787A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 removed outlier: 4.198A pdb=" N ALA C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.876A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B 810 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN B 708 " --> pdb=" O ASP B 823 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.876A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B 810 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 675 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.658A pdb=" N VAL B 172 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN B 295 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 286 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 144 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 288 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 294 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE B 136 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.658A pdb=" N VAL B 172 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN B 295 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 280 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ALA B 621 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP B 611 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N GLU B 619 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 267 through 273 removed outlier: 7.656A pdb=" N TYR B 183 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 763 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN B 753 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 766 " --> pdb=" O TYR B 751 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR B 751 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 220 removed outlier: 4.072A pdb=" N SER B 234 " --> pdb=" O PRO C 718 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 254 removed outlier: 3.609A pdb=" N ARG B 253 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 798 through 805 removed outlier: 3.980A pdb=" N SER A 234 " --> pdb=" O PRO B 718 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AB2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.432A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 823 " --> pdb=" O ASN A 708 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN A 708 " --> pdb=" O ASP A 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.432A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 818 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.770A pdb=" N GLU A 138 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU A 294 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 136 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU A 137 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP A 329 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 139 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.796A pdb=" N GLY A 280 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 267 through 273 removed outlier: 7.242A pdb=" N TYR A 183 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN A 765 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N MET A 185 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ARG A 767 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE A 187 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.686A pdb=" N LEU A 261 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 798 through 804 removed outlier: 3.954A pdb=" N SER C 234 " --> pdb=" O PRO A 718 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.654A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 810 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 819 " --> pdb=" O THR C 711 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR C 711 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN C 821 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 709 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.654A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 810 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 818 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 822 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 322 through 325 removed outlier: 6.708A pdb=" N ILE C 292 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 139 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE C 290 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C 141 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 288 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 143 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 286 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AC6, first strand: chain 'C' and resid 267 through 269 removed outlier: 4.010A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 251 through 254 removed outlier: 3.557A pdb=" N ARG C 253 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 783 through 785 1663 hydrogen bonds defined for protein. 4851 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: 10.07 Time building geometry restraints manager: 10.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3941 1.32 - 1.44: 6191 1.44 - 1.57: 14084 1.57 - 1.69: 1 1.69 - 1.82: 162 Bond restraints: 24379 Sorted by residual: bond pdb=" C10 CPF C1101 " pdb=" C5 CPF C1101 " ideal model delta sigma weight residual 1.399 1.483 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C VAL A 407 " pdb=" O VAL A 407 " ideal model delta sigma weight residual 1.238 1.191 0.047 1.18e-02 7.18e+03 1.58e+01 bond pdb=" C7 CPF C1101 " pdb=" C8 CPF C1101 " ideal model delta sigma weight residual 1.410 1.483 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C CYS A 452 " pdb=" O CYS A 452 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.22e-02 6.72e+03 8.90e+00 bond pdb=" C SER A 973 " pdb=" O SER A 973 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.16e-02 7.43e+03 8.47e+00 ... (remaining 24374 not shown) Histogram of bond angle deviations from ideal: 59.89 - 74.73: 3 74.73 - 89.57: 0 89.57 - 104.41: 342 104.41 - 119.25: 20049 119.25 - 134.09: 12731 Bond angle restraints: 33125 Sorted by residual: angle pdb=" CB PRO B 562 " pdb=" CG PRO B 562 " pdb=" CD PRO B 562 " ideal model delta sigma weight residual 106.10 89.90 16.20 3.20e+00 9.77e-02 2.56e+01 angle pdb=" N ILE A 929 " pdb=" CA ILE A 929 " pdb=" C ILE A 929 " ideal model delta sigma weight residual 110.42 105.70 4.72 9.60e-01 1.09e+00 2.42e+01 angle pdb=" N LEU C 137 " pdb=" CA LEU C 137 " pdb=" C LEU C 137 " ideal model delta sigma weight residual 113.88 107.86 6.02 1.23e+00 6.61e-01 2.40e+01 angle pdb=" N LEU A 928 " pdb=" CA LEU A 928 " pdb=" C LEU A 928 " ideal model delta sigma weight residual 112.23 106.07 6.16 1.26e+00 6.30e-01 2.39e+01 angle pdb=" C ILE A 939 " pdb=" CA ILE A 939 " pdb=" CB ILE A 939 " ideal model delta sigma weight residual 112.24 105.99 6.25 1.34e+00 5.57e-01 2.17e+01 ... (remaining 33120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 13733 23.61 - 47.23: 847 47.23 - 70.84: 70 70.84 - 94.46: 12 94.46 - 118.07: 1 Dihedral angle restraints: 14663 sinusoidal: 5625 harmonic: 9038 Sorted by residual: dihedral pdb=" CA PHE B 976 " pdb=" C PHE B 976 " pdb=" N THR B 977 " pdb=" CA THR B 977 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C15 CPF C1101 " pdb=" C16 CPF C1101 " pdb=" N3 CPF C1101 " pdb=" C17 CPF C1101 " ideal model delta sinusoidal sigma weight residual -60.38 57.69 -118.07 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CA TYR B 828 " pdb=" C TYR B 828 " pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3438 0.063 - 0.126: 455 0.126 - 0.188: 40 0.188 - 0.251: 7 0.251 - 0.314: 2 Chirality restraints: 3942 Sorted by residual: chirality pdb=" CA ILE A 929 " pdb=" N ILE A 929 " pdb=" C ILE A 929 " pdb=" CB ILE A 929 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 CPF C1101 " pdb=" C12 CPF C1101 " pdb=" C13 CPF C1101 " pdb=" N1 CPF C1101 " both_signs ideal model delta sigma weight residual True 2.29 2.60 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU C 938 " pdb=" N LEU C 938 " pdb=" C LEU C 938 " pdb=" CB LEU C 938 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3939 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 118 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 119 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 288 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.08e+00 pdb=" N PRO C 289 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 289 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 289 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 901 " -0.017 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" CG PHE C 901 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 901 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 901 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 901 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 901 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 901 " 0.003 2.00e-02 2.50e+03 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 258 2.64 - 3.21: 24016 3.21 - 3.77: 37706 3.77 - 4.34: 51855 4.34 - 4.90: 86315 Nonbonded interactions: 200150 Sorted by model distance: nonbonded pdb=" OD1 ASP A 611 " pdb=" OG1 THR A 614 " model vdw 2.075 3.040 nonbonded pdb=" OE1 GLN A 312 " pdb=" OH TYR A 324 " model vdw 2.109 3.040 nonbonded pdb=" OG1 THR A 43 " pdb=" O VAL A 92 " model vdw 2.121 3.040 nonbonded pdb=" OG SER B 132 " pdb=" OD1 ASP B 174 " model vdw 2.127 3.040 nonbonded pdb=" O ASN C 212 " pdb=" ND2 ASN C 753 " model vdw 2.159 3.120 ... (remaining 200145 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 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 through 221 or (resid 222 and (na \ me N or name CA or name C or name O or name CB )) or resid 223 through 255 or (r \ esid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 t \ hrough 418 or (resid 419 and (name N or name CA or name C or name O or name CB ) \ ) or resid 420 through 507 or (resid 508 and (name N or name CA or name C or nam \ e O or name CB )) or resid 509 through 536 or (resid 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throu \ gh 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or \ resid 704 through 1032)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 through 221 or (resid 222 and (na \ me N or name CA or name C or name O or name CB )) or resid 223 through 255 or (r \ esid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 t \ hrough 418 or (resid 419 and (name N or name CA or name C or name O or name CB ) \ ) or resid 420 through 507 or (resid 508 and (name N or name CA or name C or nam \ e O or name CB )) or resid 509 through 536 or (resid 537 and (name N or name CA \ or name C or name O or name CB )) or resid 538 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throu \ gh 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or \ resid 704 through 1031 or (resid 1032 and (name N or name CA or name C or name \ O or name CB )))) } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 63.170 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 24379 Z= 0.257 Angle : 0.692 16.199 33125 Z= 0.394 Chirality : 0.044 0.314 3942 Planarity : 0.005 0.077 4197 Dihedral : 14.151 118.073 8819 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.65 % Allowed : 15.53 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 3090 helix: 1.93 (0.12), residues: 1713 sheet: -0.04 (0.24), residues: 437 loop : -0.29 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 889 HIS 0.003 0.001 HIS B 995 PHE 0.042 0.001 PHE C 901 TYR 0.022 0.001 TYR B 530 ARG 0.012 0.001 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 495 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 430 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: B 540 LEU cc_start: 0.8799 (mm) cc_final: 0.8580 (mm) REVERT: B 676 MET cc_start: 0.8783 (tmm) cc_final: 0.8105 (tmm) REVERT: B 904 PHE cc_start: 0.8272 (t80) cc_final: 0.8068 (t80) REVERT: B 908 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9126 (pp) REVERT: B 913 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7761 (mmm-85) REVERT: B 965 ARG cc_start: 0.8798 (mmm160) cc_final: 0.7887 (mmm160) REVERT: A 22 ILE cc_start: 0.9612 (mp) cc_final: 0.9388 (mp) REVERT: A 381 PHE cc_start: 0.8910 (m-80) cc_final: 0.8665 (m-80) REVERT: A 928 LEU cc_start: 0.8874 (mt) cc_final: 0.8661 (mt) REVERT: C 109 ASN cc_start: 0.8124 (m-40) cc_final: 0.7753 (m-40) REVERT: C 185 MET cc_start: 0.9002 (tpp) cc_final: 0.8623 (tpp) REVERT: C 415 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7815 (tt0) REVERT: C 438 ASN cc_start: 0.8070 (m-40) cc_final: 0.7862 (m-40) outliers start: 17 outliers final: 5 residues processed: 502 average time/residue: 0.3035 time to fit residues: 250.9551 Evaluate side-chains 422 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 415 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 0.0050 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 109 ASN B 302 ASN B 594 ASN A 299 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN C 514 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24379 Z= 0.221 Angle : 0.634 9.760 33125 Z= 0.328 Chirality : 0.044 0.292 3942 Planarity : 0.005 0.060 4197 Dihedral : 5.226 84.201 3327 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.52 % Allowed : 16.45 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3090 helix: 1.87 (0.12), residues: 1728 sheet: -0.07 (0.24), residues: 436 loop : -0.16 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 853 HIS 0.011 0.002 HIS B 995 PHE 0.025 0.001 PHE C 901 TYR 0.027 0.002 TYR B 849 ARG 0.005 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 481 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 PHE cc_start: 0.8936 (m-10) cc_final: 0.8666 (m-10) REVERT: B 470 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8393 (ttm110) REVERT: B 540 LEU cc_start: 0.8754 (mm) cc_final: 0.8522 (mm) REVERT: B 676 MET cc_start: 0.8733 (tmm) cc_final: 0.8318 (tmm) REVERT: B 904 PHE cc_start: 0.8290 (t80) cc_final: 0.7994 (t80) REVERT: B 913 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7690 (mmm-85) REVERT: B 1005 MET cc_start: 0.6759 (tmm) cc_final: 0.6450 (ttp) REVERT: A 381 PHE cc_start: 0.8894 (m-80) cc_final: 0.8570 (m-80) REVERT: C 109 ASN cc_start: 0.8232 (m-40) cc_final: 0.7792 (m-40) REVERT: C 356 MET cc_start: 0.8890 (ttm) cc_final: 0.8653 (mtp) REVERT: C 415 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7756 (tm-30) REVERT: C 437 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8332 (tpp) REVERT: C 438 ASN cc_start: 0.8049 (m-40) cc_final: 0.7847 (m-40) REVERT: C 717 PHE cc_start: 0.8618 (m-80) cc_final: 0.8181 (m-80) REVERT: C 807 ASP cc_start: 0.8443 (p0) cc_final: 0.8056 (p0) REVERT: C 934 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8074 (ttpt) outliers start: 66 outliers final: 32 residues processed: 515 average time/residue: 0.2748 time to fit residues: 237.7213 Evaluate side-chains 460 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 427 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 976 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 851 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 281 optimal weight: 0.0570 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: