Starting phenix.real_space_refine (version: dev) on Tue Feb 21 13:32:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tj5_8409/02_2023/5tj5_8409_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.011 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14976 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3391 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'CIS': 16, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 542} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 947 Unresolved non-hydrogen angles: 1317 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 6, 'TYR:plan': 4, 'UNK:plan-1': 250, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 449 Chain: "B" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1266 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 914 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 139} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 823 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 885 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 869 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 145} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 895 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 922 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 866 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 4, 'TRANS': 145} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "L" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 411 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 52} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 949 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "N" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 978 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 270 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'UNK:plan-1': 54} Unresolved non-hydrogen planarities: 54 Chain: "P" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1537 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'CIS': 4, 'PTRANS': 3, 'TRANS': 261} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'UNK:plan-1': 61, 'TYR:plan': 6, 'ASN:plan1': 15, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 364 Time building chain proxies: 8.66, per 1000 atoms: 0.58 Number of scatterers: 14976 At special positions: 0 Unit cell: (119.658, 130.536, 114.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2710 8.00 N 2600 7.00 C 9625 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: 7.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 96.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 6 through 34 removed outlier: 4.030A pdb=" N UNK A 34 " --> pdb=" O UNK A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 96 removed outlier: 4.148A pdb=" N UNK A 78 " --> pdb=" O UNK A 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N UNK A 96 " --> pdb=" O UNK A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 176 removed outlier: 4.271A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N UNK A 131 " --> pdb=" O UNK A 127 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK A 137 " --> pdb=" O UNK A 133 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N UNK A 138 " --> pdb=" O UNK A 134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N UNK A 139 " --> pdb=" O UNK A 135 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK A 140 " --> pdb=" O UNK A 136 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK A 144 " --> pdb=" O UNK A 140 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N UNK A 145 " --> pdb=" O UNK A 141 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N UNK A 146 " --> pdb=" O UNK A 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK A 149 " --> pdb=" O UNK A 145 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N UNK A 156 " --> pdb=" O UNK A 152 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N UNK A 158 " --> pdb=" O UNK A 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK A 159 " --> pdb=" O UNK A 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N UNK A 174 " --> pdb=" O UNK A 170 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N UNK A 176 " --> pdb=" O UNK A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 278 through 295 removed outlier: 4.658A pdb=" N UNK A 283 " --> pdb=" O UNK A 279 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK A 291 " --> pdb=" O UNK A 287 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N UNK A 292 " --> pdb=" O UNK A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 410 through 421 Proline residue: A 416 - end of helix removed outlier: 3.634A pdb=" N ALA A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.224A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 4.094A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.871A pdb=" N MET A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 removed outlier: 3.567A pdb=" N SER A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.884A pdb=" N TYR A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 547 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.524A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 removed outlier: 3.593A pdb=" N MET A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 657 removed outlier: 3.902A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.631A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 711 through 733 removed outlier: 3.607A pdb=" N PHE A 722 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 753 removed outlier: 3.558A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 763 through 792 removed outlier: 3.603A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 removed outlier: 3.915A pdb=" N HIS A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 4.076A pdb=" N ALA A 821 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 removed outlier: 3.852A pdb=" N ASP B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 4.005A pdb=" N LEU B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 91 removed outlier: 3.506A pdb=" N GLY B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 121 removed outlier: 4.285A pdb=" N ILE B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE B 117 " --> pdb=" O TYR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 173 removed outlier: 4.228A pdb=" N TRP B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 removed outlier: 4.208A pdb=" N ILE B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.756A pdb=" N LEU B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 3.918A pdb=" N CYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET D 27 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 84 removed outlier: 3.763A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 130 removed outlier: 4.045A pdb=" N LEU D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 162 removed outlier: 3.729A pdb=" N ILE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 138 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 14 through 37 removed outlier: 3.826A pdb=" N ALA E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 4.641A pdb=" N VAL E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 122 removed outlier: 3.843A pdb=" N GLY E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY E 92 " --> pdb=" O PHE E 88 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.503A pdb=" N MET E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 133 " --> pdb=" O MET E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 154 removed outlier: 3.846A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 13 No H-bonds generated for 'chain 'F' and resid 11 through 13' Processing helix chain 'F' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 Processing helix chain 'F' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE F 89 " --> pdb=" O TYR F 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 44 " --> pdb=" O CYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 54 through 77 removed outlier: 3.664A pdb=" N ILE G 62 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE G 89 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 137 Processing helix chain 'G' and resid 137 through 153 Processing helix chain 'H' and resid 11 through 13 No H-bonds generated for 'chain 'H' and resid 11 through 13' Processing helix chain 'H' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL H 44 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 54 Processing helix chain 'H' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE H 110 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 137 Processing helix chain 'H' and resid 137 through 153 Processing helix chain 'I' and resid 11 through 13 No H-bonds generated for 'chain 'I' and resid 11 through 13' Processing helix chain 'I' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 44 " --> pdb=" O CYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 122 removed outlier: 3.906A pdb=" N ILE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU I 91 " --> pdb=" O GLY I 87 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 110 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 121 " --> pdb=" O ARG I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 137 Processing helix chain 'I' and resid 137 through 153 Processing helix chain 'J' and resid 11 through 13 No H-bonds generated for 'chain 'J' and resid 11 through 13' Processing helix chain 'J' and resid 14 through 44 removed outlier: 4.273A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 44 " --> pdb=" O CYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 54 through 77 removed outlier: 3.664A pdb=" N ILE J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 137 Processing helix chain 'J' and resid 137 through 153 Processing helix chain 'L' and resid 7 through 16 removed outlier: 3.741A pdb=" N PHE L 11 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA L 16 " --> pdb=" O ILE L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 19 No H-bonds generated for 'chain 'L' and resid 17 through 19' Processing helix chain 'L' and resid 29 through 47 removed outlier: 4.214A pdb=" N VAL L 37 " --> pdb=" O TRP L 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA L 42 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 13 No H-bonds generated for 'chain 'M' and resid 11 through 13' Processing helix chain 'M' and resid 14 through 44 removed outlier: 4.274A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL M 44 " --> pdb=" O CYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 54 Processing helix chain 'M' and resid 54 through 77 removed outlier: 3.665A pdb=" N ILE M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 67 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE M 110 " --> pdb=" O PHE M 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 137 Processing helix chain 'M' and resid 137 through 153 Processing helix chain 'N' and resid 11 through 13 No H-bonds generated for 'chain 'N' and resid 11 through 13' Processing helix chain 'N' and resid 14 through 44 removed outlier: 4.274A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL N 44 " --> pdb=" O CYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 54 Processing helix chain 'N' and resid 54 through 77 removed outlier: 3.666A pdb=" N ILE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY N 67 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER N 77 " --> pdb=" O LEU N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 122 removed outlier: 3.907A pdb=" N ILE N 89 " --> pdb=" O TYR N 85 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN N 90 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU N 91 " --> pdb=" O GLY N 87 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE N 110 " --> pdb=" O PHE N 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN N 121 " --> pdb=" O ARG N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 137 Processing helix chain 'N' and resid 137 through 153 Processing helix chain 'O' and resid 2 through 25 removed outlier: 4.059A pdb=" N UNK O 6 " --> pdb=" O UNK O 2 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N UNK O 7 " --> pdb=" O UNK O 3 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK O 8 " --> pdb=" O UNK O 4 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK O 12 " --> pdb=" O UNK O 8 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNK O 13 " --> pdb=" O UNK O 9 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK O 18 " --> pdb=" O UNK O 14 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N UNK O 19 " --> pdb=" O UNK O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 100 removed outlier: 4.401A pdb=" N UNK O 91 " --> pdb=" O UNK O 87 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N UNK O 92 " --> pdb=" O UNK O 88 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK O 97 " --> pdb=" O UNK O 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N UNK O 100 " --> pdb=" O UNK O 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 22 removed outlier: 3.775A pdb=" N GLY P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.532A pdb=" N ILE P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 49 removed outlier: 3.764A pdb=" N LYS P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 86 removed outlier: 3.880A pdb=" N LYS P 75 " --> pdb=" O TYR P 71 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN P 81 " --> pdb=" O TYR P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 112 removed outlier: 3.752A pdb=" N LYS P 93 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR P 102 " --> pdb=" O ILE P 98 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP P 105 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN P 106 " --> pdb=" O TYR P 102 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 134 Processing helix chain 'P' and resid 145 through 149 Processing helix chain 'P' and resid 159 through 163 Processing helix chain 'P' and resid 177 through 196 removed outlier: 3.705A pdb=" N ALA P 187 " --> pdb=" O LYS P 183 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE P 192 " --> pdb=" O TYR P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 228 removed outlier: 3.641A pdb=" N UNK P 211 " --> pdb=" O UNK P 207 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N UNK P 218 " --> pdb=" O UNK P 214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N UNK P 220 " --> pdb=" O UNK P 216 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK P 222 " --> pdb=" O UNK P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 242 Processing helix chain 'P' and resid 250 through 257 removed outlier: 3.697A pdb=" N UNK P 254 " --> pdb=" O UNK P 250 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N UNK P 255 " --> pdb=" O UNK P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 300 removed outlier: 3.878A pdb=" N LEU P 291 " --> pdb=" O HIS P 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU P 294 " --> pdb=" O GLN P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 333 removed outlier: 3.840A pdb=" N ALA P 311 " --> pdb=" O SER P 307 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3542 1.33 - 1.45: 3287 1.45 - 1.57: 8273 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 15170 Sorted by residual: bond pdb=" C LEU A 530 " pdb=" N PHE A 531 " ideal model delta sigma weight residual 1.334 1.275 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" CB TRP L 48 " pdb=" CG TRP L 48 " ideal model delta sigma weight residual 1.498 1.393 0.105 3.10e-02 1.04e+03 1.15e+01 bond pdb=" CA ILE A 569 " pdb=" CB ILE A 569 " ideal model delta sigma weight residual 1.538 1.506 0.032 9.80e-03 1.04e+04 1.10e+01 bond pdb=" CA PHE I 88 " pdb=" C PHE I 88 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.27e+00 bond pdb=" CA PHE J 88 " pdb=" C PHE J 88 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.34e-02 5.57e+03 9.21e+00 ... (remaining 15165 not shown) Histogram of bond angle deviations from ideal: 90.71 - 100.95: 35 100.95 - 111.19: 6914 111.19 - 121.43: 10744 121.43 - 131.67: 3096 131.67 - 141.92: 22 Bond angle restraints: 20811 Sorted by residual: angle pdb=" N GLY A 570 " pdb=" CA GLY A 570 " pdb=" C GLY A 570 " ideal model delta sigma weight residual 112.17 90.71 21.46 1.40e+00 5.10e-01 2.35e+02 angle pdb=" C UNK A 36 " pdb=" N UNK A 37 " pdb=" CA UNK A 37 " ideal model delta sigma weight residual 121.70 137.58 -15.88 1.80e+00 3.09e-01 7.78e+01 angle pdb=" N PHE F 88 " pdb=" CA PHE F 88 " pdb=" C PHE F 88 " ideal model delta sigma weight residual 110.80 92.89 17.91 2.13e+00 2.20e-01 7.07e+01 angle pdb=" N PHE G 88 " pdb=" CA PHE G 88 " pdb=" C PHE G 88 " ideal model delta sigma weight residual 110.80 92.91 17.89 2.13e+00 2.20e-01 7.06e+01 angle pdb=" N PHE N 88 " pdb=" CA PHE N 88 " pdb=" C PHE N 88 " ideal model delta sigma weight residual 110.80 92.91 17.89 2.13e+00 2.20e-01 7.06e+01 ... (remaining 20806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 8280 16.61 - 33.23: 179 33.23 - 49.84: 45 49.84 - 66.45: 3 66.45 - 83.07: 2 Dihedral angle restraints: 8509 sinusoidal: 1581 harmonic: 6928 Sorted by residual: dihedral pdb=" CA ILE A 569 " pdb=" C ILE A 569 " pdb=" N GLY A 570 " pdb=" CA GLY A 570 " ideal model delta harmonic sigma weight residual -180.00 -125.71 -54.29 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA GLY H 87 " pdb=" C GLY H 87 " pdb=" N PHE H 88 " pdb=" CA PHE H 88 " ideal model delta harmonic sigma weight residual 180.00 134.76 45.24 0 5.00e+00 4.00e-02 8.19e+01 dihedral pdb=" CA GLY M 87 " pdb=" C GLY M 87 " pdb=" N PHE M 88 " pdb=" CA PHE M 88 " ideal model delta harmonic sigma weight residual 180.00 134.80 45.20 0 5.00e+00 4.00e-02 8.17e+01 ... (remaining 8506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2350 0.077 - 0.153: 254 0.153 - 0.230: 24 0.230 - 0.306: 3 0.306 - 0.383: 4 Chirality restraints: 2635 Sorted by residual: chirality pdb=" CA PRO I 10 " pdb=" N PRO I 10 " pdb=" C PRO I 10 " pdb=" CB PRO I 10 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE B 117 " pdb=" CA ILE B 117 " pdb=" CG1 ILE B 117 " pdb=" CG2 ILE B 117 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA PRO L 58 " pdb=" N PRO L 58 " pdb=" C PRO L 58 " pdb=" CB PRO L 58 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2632 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 88 " -0.025 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE N 88 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE N 88 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE N 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE N 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 88 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE N 88 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS P 126 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO P 127 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO P 127 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 127 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 570 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLY A 570 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 570 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 571 " 0.017 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 256 2.58 - 3.36: 24985 3.36 - 4.13: 33348 4.13 - 4.90: 60341 Nonbonded interactions: 118931 Sorted by model distance: nonbonded pdb=" O ASN B 46 " pdb=" CA GLY B 48 " model vdw 1.040 3.440 nonbonded pdb=" C ASN B 46 " pdb=" CA GLY B 48 " model vdw 1.963 3.670 nonbonded pdb=" O GLY A 408 " pdb=" OG1 THR A 411 " model vdw 2.070 2.440 nonbonded pdb=" O ASN B 46 " pdb=" C GLY B 48 " model vdw 2.072 3.270 nonbonded pdb=" O TYR D 90 " pdb=" N ASN D 94 " model vdw 2.101 2.520 ... (remaining 118926 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 'E' and (resid 11 through 18 or (resid 19 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 52 or (res \ id 53 through 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 62 or (resid 63 through 65 and (name N or name CA or name C or nam \ e O or name CB )) or resid 66 through 68 or (resid 69 through 75 and (name N or \ name CA or name C or name O or name CB )) or resid 76 through 84 or (resid 85 th \ rough 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or \ (resid 88 through 91 and (name N or name CA or name C or name O or name CB )) o \ r resid 92 through 96 or (resid 97 and (name N or name CA or name C or name O or \ name CB )) or (resid 98 through 100 and (name N or name CA or name C or name O \ or name CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or n \ ame C or name O or name CB )) or resid 105 or (resid 106 through 108 and (name N \ or name CA or name C or name O or name CB )) or resid 109 or (resid 110 through \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 or (r \ esid 113 through 114 and (name N or name CA or name C or name O or name CB )) or \ (resid 115 through 117 and (name N or name CA or name C or name O or name CB )) \ or (resid 118 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 144 or (resid 145 through 149 and ( \ name N or name CA or name C or name O or name CB )) or resid 150 or (resid 151 t \ hrough 158 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 37 or resid 50 through \ 62 or (resid 63 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 66 through 68 or (resid 69 through 75 and (name N or name CA or nam \ e C or name O or name CB )) or resid 76 through 84 or (resid 85 through 86 and ( \ name N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 thr \ ough 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 or (resid 99 through 100 and (name N or name CA or name C or name O or \ name CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 105 through 108 and (name N or name CA or \ name C or name O or name CB )) or resid 109 or (resid 110 through 111 and (name \ N or name CA or name C or name O or name CB )) or (resid 112 through 127 and (na \ me N or name CA or name C or name O or name CB )) or (resid 128 through 136 and \ (name N or name CA or name C or name O or name CB )) or resid 137 through 138 or \ (resid 139 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 0 through 144 or (resid 145 through 149 and (name N or name CA or name C or name \ O or name CB )) or resid 150 through 152 or (resid 153 through 158 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 through \ 37 or (resid 50 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 58 or (resid 59 through 60 and (name N or name CA or na \ me C or name O or name CB )) or (resid 61 through 65 and (name N or name CA or n \ ame C or name O or name CB )) or resid 66 through 69 or (resid 70 through 75 and \ (name N or name CA or name C or name O or name CB )) or resid 76 through 85 or \ (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 o \ r (resid 88 through 91 and (name N or name CA or name C or name O or name CB )) \ or resid 92 through 95 or (resid 96 through 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name \ CA or name C or name O or name CB )) or (resid 101 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or (resid 112 through 1 \ 17 and (name N or name CA or name C or name O or name CB )) or (resid 118 throug \ h 127 and (name N or name CA or name C or name O or name CB )) or (resid 128 thr \ ough 136 and (name N or name CA or name C or name O or name CB )) or resid 137 o \ r (resid 138 through 139 and (name N or name CA or name C or name O or name CB ) \ ) or resid 140 through 145 or (resid 146 through 149 and (name N or name CA or n \ ame C or name O or name CB )) or resid 150 through 158)) selection = (chain 'H' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or (resid 50 thro \ ugh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thro \ ugh 58 or (resid 59 through 60 and (name N or name CA or name C or name O or nam \ e CB )) or resid 61 or (resid 62 through 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 67 or (resid 68 through 75 and (name N \ or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 \ and (name N or name CA or name C or name O or name CB )) or (resid 79 through 8 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resid \ 88 through 91 and (name N or name CA or name C or name O or name CB )) or resid \ 92 through 96 or (resid 97 and (name N or name CA or name C or name O or name C \ B )) or (resid 98 through 108 and (name N or name CA or name C or name O or name \ CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or name C o \ r name O or name CB )) or (resid 112 through 117 and (name N or name CA or name \ C or name O or name CB )) or (resid 118 through 127 and (name N or name CA or na \ me C or name O or name CB )) or (resid 128 through 136 and (name N or name CA or \ name C or name O or name CB )) or resid 137 or (resid 138 through 139 and (name \ N or name CA or name C or name O or name CB )) or resid 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB )) or resid 142 through 143 or \ (resid 144 through 149 and (name N or name CA or name C or name O or name CB )) \ or resid 150 through 151 or (resid 152 through 158 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'I' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 33 or (res \ id 34 through 35 and (name N or name CA or name C or name O or name CB )) or res \ id 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or ( \ resid 50 through 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 or (resid 57 through 60 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 61 through 65 and (name N or name CA or name C or name O or \ name CB )) or resid 66 through 68 or (resid 69 through 75 and (name N or name CA \ or name C or name O or name CB )) or resid 76 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 87 through 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or name C o \ r name O or name CB )) or (resid 105 through 114 and (name N or name CA or name \ C or name O or name CB )) or resid 115 or (resid 116 through 117 and (name N or \ name CA or name C or name O or name CB )) or (resid 118 through 127 and (name N \ or name CA or name C or name O or name CB )) or (resid 128 through 136 and (name \ N or name CA or name C or name O or name CB )) or resid 137 or (resid 138 throu \ gh 139 and (name N or name CA or name C or name O or name CB )) or resid 140 or \ (resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 143 or (resid 144 through 149 and (name N or name CA or name C or name \ O or name CB )) or resid 150 or (resid 151 through 158 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'J' and (resid 11 through 24 or (resid 25 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 33 or (resid 34 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 through \ 37 or (resid 50 through 55 and (name N or name CA or name C or name O or name C \ B )) or resid 56 through 72 or (resid 73 through 75 and (name N or name CA or na \ me C or name O or name CB )) or resid 76 through 84 or (resid 85 through 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 th \ rough 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) \ or resid 101 or (resid 102 through 104 and (name N or name CA or name C or name \ O or name CB )) or resid 105 or (resid 106 through 108 and (name N or name CA or \ name C or name O or name CB )) or (resid 109 through 114 and (name N or name CA \ or name C or name O or name CB )) or resid 115 or (resid 116 through 117 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 118 through 127 and \ (name N or name CA or name C or name O or name CB )) or (resid 128 through 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 or (resid \ 138 through 139 and (name N or name CA or name C or name O or name CB )) or resi \ d 140 through 144 or (resid 145 through 149 and (name N or name CA or name C or \ name O or name CB )) or resid 150 or (resid 151 through 158 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 11 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 through 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 through 33 or (res \ id 34 through 35 and (name N or name CA or name C or name O or name CB )) or res \ id 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or ( \ resid 50 through 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 through 60 and (name N or name CA or name C or \ name O or name CB )) or resid 61 or (resid 62 through 65 and (name N or name CA \ or name C or name O or name CB )) or resid 66 through 67 or (resid 68 through 75 \ and (name N or name CA or name C or name O or name CB )) or resid 76 through 77 \ or (resid 78 and (name N or name CA or name C or name O or name CB )) or (resid \ 79 through 86 and (name N or name CA or name C or name O or name CB )) or resid \ 87 or (resid 88 through 91 and (name N or name CA or name C or name O or name C \ B )) or resid 92 through 96 or (resid 97 and (name N or name CA or name C or nam \ e O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA or \ name C or name O or name CB )) or resid 101 or (resid 102 through 104 and (name \ N or name CA or name C or name O or name CB )) or (resid 105 through 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 or (resid 110 th \ rough 111 and (name N or name CA or name C or name O or name CB )) or resid 112 \ or (resid 113 through 114 and (name N or name CA or name C or name O or name CB \ )) or resid 115 or (resid 116 through 117 and (name N or name CA or name C or na \ me O or name CB )) or (resid 118 through 127 and (name N or name CA or name C or \ name O or name CB )) or (resid 128 through 136 and (name N or name CA or name C \ or name O or name CB )) or resid 137 or (resid 138 through 139 and (name N or n \ ame CA or name C or name O or name CB )) or resid 140 or (resid 141 and (name N \ or name CA or name C or name O or name CB )) or resid 142 through 143 or (resid \ 144 through 149 and (name N or name CA or name C or name O or name CB )) or resi \ d 150 or (resid 151 through 158 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'N' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 16 or (resid 17 through 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 or (resid 24 through 26 and (name N or na \ me CA or name C or name O or name CB )) or resid 27 through 33 or (resid 34 thro \ ugh 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or (resid 50 t \ hrough 55 and (name N or name CA or name C or name O or name CB )) or resid 56 o \ r (resid 57 through 60 and (name N or name CA or name C or name O or name CB )) \ or resid 61 or (resid 62 through 65 and (name N or name CA or name C or name O o \ r name CB )) or resid 66 through 67 or (resid 68 through 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 78 and (na \ me N or name CA or name C or name O or name CB )) or (resid 79 through 86 and (n \ ame N or name CA or name C or name O or name CB )) or resid 87 or (resid 88 thro \ ugh 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thro \ ugh 98 or (resid 99 through 100 and (name N or name CA or name C or name O or na \ me CB )) or resid 101 or (resid 102 through 104 and (name N or name CA or name C \ or name O or name CB )) or resid 105 or (resid 106 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 or (resid \ 113 through 114 and (name N or name CA or name C or name O or name CB )) or resi \ d 115 or (resid 116 through 117 and (name N or name CA or name C or name O or na \ me CB )) or (resid 118 through 127 and (name N or name CA or name C or name O or \ name CB )) or (resid 128 through 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 138 or (resid 139 and (name N or name CA or \ name C or name O or name CB )) or resid 140 or (resid 141 and (name N or name CA \ or name C or name O or name CB )) or resid 142 through 143 or (resid 144 throug \ h 149 and (name N or name CA or name C or name O or name CB )) or resid 150 or ( \ resid 151 through 158 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 9625 2.51 5 N 2600 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.330 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: 3.010 Check model and map are aligned: 0.210 Process input model: 39.890 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 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 : 0.010 0.109 15170 Z= 0.703 Angle : 1.285 21.463 20811 Z= 0.661 Chirality : 0.054 0.383 2635 Planarity : 0.006 0.072 2712 Dihedral : 9.133 83.067 4075 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.38 % Favored : 85.19 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.64 % Twisted Proline : 2.04 % Twisted General : 1.13 % 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: -6.37 (0.11), residues: 2052 helix: -3.99 (0.07), residues: 1462 sheet: None (None), residues: 0 loop : -4.24 (0.20), residues: 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.2058 time to fit residues: 168.3154 Evaluate side-chains 314 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS A 718 HIS A 743 HIS B 46 ASN B 156 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN N 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 15170 Z= 0.278 Angle : 0.920 17.171 20811 Z= 0.464 Chirality : 0.046 0.307 2635 Planarity : 0.005 0.070 2712 Dihedral : 5.839 61.418 2508 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.99 % Favored : 91.62 % Rotamer Outliers : 5.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2052 helix: -0.74 (0.12), residues: 1628 sheet: None (None), residues: 0 loop : -3.52 (0.27), residues: 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 421 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 441 average time/residue: 0.1904 time to fit residues: 136.4000 Evaluate side-chains 361 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 339 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1340 time to fit residues: 7.5156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 142 optimal weight: 0.2980 chunk 154 optimal weight: 8.9990 chunk 127 optimal weight: 0.0040 chunk 141 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 chunk 114 optimal weight: 0.9980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 HIS M 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15170 Z= 0.223 Angle : 0.796 16.655 20811 Z= 0.399 Chirality : 0.041 0.219 2635 Planarity : 0.004 0.065 2712 Dihedral : 4.812 44.714 2508 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.41 % Favored : 92.35 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.49 (0.18), residues: 2052 helix: 0.40 (0.12), residues: 1659 sheet: None (None), residues: 0 loop : -3.28 (0.29), residues: 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 402 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 415 average time/residue: 0.1897 time to fit residues: 128.5636 Evaluate side-chains 344 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1861 time to fit residues: 5.8115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 0.0070 chunk 15 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 15170 Z= 0.211 Angle : 0.777 16.406 20811 Z= 0.379 Chirality : 0.041 0.350 2635 Planarity : 0.004 0.065 2712 Dihedral : 4.452 37.465 2508 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.68 % Favored : 93.08 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.06 (0.19), residues: 2052 helix: 0.74 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -3.38 (0.29), residues: 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 380 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 8 residues processed: 394 average time/residue: 0.2009 time to fit residues: 129.0775 Evaluate side-chains 350 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 342 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1504 time to fit residues: 4.1102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 136 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15170 Z= 0.206 Angle : 0.754 15.930 20811 Z= 0.370 Chirality : 0.041 0.369 2635 Planarity : 0.004 0.065 2712 Dihedral : 4.247 29.658 2508 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.63 % Favored : 93.08 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % 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: 0.22 (0.19), residues: 2052 helix: 0.90 (0.13), residues: 1670 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 372 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 382 average time/residue: 0.1988 time to fit residues: 123.5904 Evaluate side-chains 348 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1741 time to fit residues: 6.5480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 HIS ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 15170 Z= 0.203 Angle : 0.768 15.573 20811 Z= 0.374 Chirality : 0.041 0.373 2635 Planarity : 0.003 0.064 2712 Dihedral : 4.170 24.308 2508 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.53 % Favored : 93.18 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % 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: 0.30 (0.19), residues: 2052 helix: 0.93 (0.13), residues: 1675 sheet: None (None), residues: 0 loop : -3.08 (0.31), residues: 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 368 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 374 average time/residue: 0.1985 time to fit residues: 121.0552 Evaluate side-chains 356 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 342 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1351 time to fit residues: 5.3781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 0.0010 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 15170 Z= 0.195 Angle : 0.767 15.304 20811 Z= 0.372 Chirality : 0.042 0.403 2635 Planarity : 0.004 0.070 2712 Dihedral : 4.036 26.037 2508 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.14 % Favored : 93.62 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2052 helix: 1.01 (0.13), residues: 1670 sheet: None (None), residues: 0 loop : -2.97 (0.31), residues: 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 373 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 378 average time/residue: 0.2012 time to fit residues: 123.1646 Evaluate side-chains 362 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 354 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1486 time to fit residues: 3.8392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN B 46 ASN ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 15170 Z= 0.249 Angle : 0.786 14.907 20811 Z= 0.381 Chirality : 0.043 0.394 2635 Planarity : 0.004 0.063 2712 Dihedral : 4.071 24.177 2508 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.34 % Favored : 93.42 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % 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: 0.44 (0.19), residues: 2052 helix: 1.00 (0.13), residues: 1675 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 1.523 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 365 average time/residue: 0.1984 time to fit residues: 119.1137 Evaluate side-chains 347 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 337 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1411 time to fit residues: 4.5660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15170 Z= 0.219 Angle : 0.807 14.509 20811 Z= 0.385 Chirality : 0.044 0.471 2635 Planarity : 0.004 0.064 2712 Dihedral : 4.040 23.825 2508 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.66 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2052 helix: 0.98 (0.13), residues: 1677 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 363 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 365 average time/residue: 0.1936 time to fit residues: 115.4469 Evaluate side-chains 354 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 347 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1670 time to fit residues: 4.0193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 15170 Z= 0.230 Angle : 0.825 15.264 20811 Z= 0.391 Chirality : 0.045 0.431 2635 Planarity : 0.004 0.063 2712 Dihedral : 4.019 24.826 2508 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.29 % Favored : 93.47 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % 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: 0.44 (0.19), residues: 2052 helix: 1.00 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 1.674 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 362 average time/residue: 0.1967 time to fit residues: 116.5430 Evaluate side-chains 355 residues out of total 1637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 352 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3043 time to fit residues: 3.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.121463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108278 restraints weight = 49952.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110374 restraints weight = 30911.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111865 restraints weight = 21160.296| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15170 Z= 0.210 Angle : 0.840 20.444 20811 Z= 0.391 Chirality : 0.046 0.456 2635 Planarity : 0.003 0.064 2712 Dihedral : 3.950 24.787 2508 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.51 % Favored : 94.30 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.69 % 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: 0.50 (0.19), residues: 2052 helix: 1.06 (0.13), residues: 1667 sheet: None (None), residues: 0 loop : -2.85 (0.31), residues: 385 =============================================================================== Job complete usr+sys time: 2805.24 seconds wall clock time: 51 minutes 9.45 seconds (3069.45 seconds total)