Starting phenix.real_space_refine (version: dev) on Fri Mar 17 13:15:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/03_2023/6o7t_0644.pdb" } resolution = 3.2 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= 0.015 sd= 0.180 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 Residue "a ARG 27": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 403": "NH1" <-> "NH2" Residue "a PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 117": "NH1" <-> "NH2" Residue "g ARG 124": "NH1" <-> "NH2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "h ARG 117": "NH1" <-> "NH2" Residue "h ARG 153": "NH1" <-> "NH2" Residue "i ARG 117": "NH1" <-> "NH2" Residue "i ARG 153": "NH1" <-> "NH2" Residue "j PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 153": "NH1" <-> "NH2" Residue "k ARG 153": "NH1" <-> "NH2" Residue "l ARG 117": "NH1" <-> "NH2" Residue "l ARG 153": "NH1" <-> "NH2" Residue "m ARG 153": "NH1" <-> "NH2" Residue "n ARG 153": "NH1" <-> "NH2" Residue "o TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 125": "NH1" <-> "NH2" Residue "o TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19730 Number of models: 1 Model: "" Number of chains: 15 Chain: "a" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5358 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 365 Chain: "b" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 279 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "c" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1414 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 192} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2181 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 237 Chain: "f" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1080 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "h" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1085 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "i" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1071 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "j" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1035 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1049 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "l" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1025 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1050 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "n" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1034 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "o" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1096 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "e" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.44, per 1000 atoms: 0.58 Number of scatterers: 19730 At special positions: 0 Unit cell: (119.78, 106, 135.68, 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 109 16.00 O 3530 8.00 N 3198 7.00 C 12893 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: 7.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 5 sheets defined 72.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'a' and resid 28 through 35 removed outlier: 3.940A pdb=" N THR a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU a 33 " --> pdb=" O SER a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 58 Processing helix chain 'a' and resid 59 through 79 removed outlier: 3.909A pdb=" N VAL a 65 " --> pdb=" O ARG a 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN a 68 " --> pdb=" O ASN a 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR a 71 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 93 Processing helix chain 'a' and resid 105 through 145 removed outlier: 3.596A pdb=" N ARG a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR a 116 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU a 132 " --> pdb=" O THR a 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN a 134 " --> pdb=" O GLN a 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE a 144 " --> pdb=" O GLN a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 207 removed outlier: 3.590A pdb=" N GLN a 201 " --> pdb=" O ALA a 197 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG a 205 " --> pdb=" O GLN a 201 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU a 207 " --> pdb=" O LEU a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 256 removed outlier: 3.504A pdb=" N LYS a 247 " --> pdb=" O ASP a 243 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 256 " --> pdb=" O ILE a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 304 removed outlier: 3.778A pdb=" N ASP a 283 " --> pdb=" O LYS a 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR a 290 " --> pdb=" O THR a 286 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE a 302 " --> pdb=" O GLU a 298 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS a 304 " --> pdb=" O TYR a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.733A pdb=" N GLN a 311 " --> pdb=" O ASP a 307 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP a 312 " --> pdb=" O SER a 308 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL a 313 " --> pdb=" O TRP a 309 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU a 316 " --> pdb=" O ASP a 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 319 " --> pdb=" O ARG a 315 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE a 320 " --> pdb=" O GLU a 316 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS a 325 " --> pdb=" O GLU a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 359 removed outlier: 3.813A pdb=" N LEU a 349 " --> pdb=" O GLU a 345 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN a 350 " --> pdb=" O LEU a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 387 through 392 Processing helix chain 'a' and resid 410 through 424 Proline residue: a 416 - end of helix removed outlier: 3.659A pdb=" N MET a 422 " --> pdb=" O MET a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 425 through 442 removed outlier: 3.568A pdb=" N MET a 432 " --> pdb=" O HIS a 428 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER a 438 " --> pdb=" O LEU a 434 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 452 through 461 removed outlier: 4.046A pdb=" N MET a 457 " --> pdb=" O GLU a 453 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA a 458 " --> pdb=" O ILE a 454 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY a 461 " --> pdb=" O MET a 457 " (cutoff:3.500A) Processing helix chain 'a' and resid 462 through 479 removed outlier: 3.943A pdb=" N MET a 468 " --> pdb=" O ILE a 464 " (cutoff:3.500A) Processing helix chain 'a' and resid 519 through 523 removed outlier: 3.709A pdb=" N TRP a 522 " --> pdb=" O ASP a 519 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS a 523 " --> pdb=" O TRP a 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 519 through 523' Processing helix chain 'a' and resid 527 through 560 removed outlier: 3.633A pdb=" N PHE a 531 " --> pdb=" O ASN a 527 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS a 547 " --> pdb=" O MET a 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 583 removed outlier: 3.664A pdb=" N ILE a 568 " --> pdb=" O SER a 564 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE a 569 " --> pdb=" O MET a 565 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix Processing helix chain 'a' and resid 583 through 595 removed outlier: 3.672A pdb=" N CYS a 589 " --> pdb=" O TYR a 585 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL a 591 " --> pdb=" O SER a 587 " (cutoff:3.500A) Processing helix chain 'a' and resid 607 through 613 Processing helix chain 'a' and resid 630 through 655 removed outlier: 4.306A pdb=" N PHE a 636 " --> pdb=" O LYS a 632 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU a 638 " --> pdb=" O GLN a 634 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 3.902A pdb=" N LEU a 649 " --> pdb=" O ILE a 645 " (cutoff:3.500A) removed outlier: 4.667A 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 710 through 730 removed outlier: 3.638A pdb=" N HIS a 718 " --> pdb=" O HIS a 714 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE a 720 " --> pdb=" O VAL a 716 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU a 721 " --> pdb=" O ILE a 717 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU a 724 " --> pdb=" O ILE a 720 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN a 725 " --> pdb=" O GLU a 721 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER a 728 " --> pdb=" O LEU a 724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR a 730 " --> pdb=" O CYS a 726 " (cutoff:3.500A) Processing helix chain 'a' and resid 731 through 733 No H-bonds generated for 'chain 'a' and resid 731 through 733' Processing helix chain 'a' and resid 734 through 753 removed outlier: 4.268A pdb=" N LEU a 746 " --> pdb=" O ALA a 742 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR a 752 " --> pdb=" O SER a 748 " (cutoff:3.500A) Processing helix chain 'a' and resid 755 through 759 removed outlier: 3.871A pdb=" N PHE a 759 " --> pdb=" O GLN a 756 " (cutoff:3.500A) Processing helix chain 'a' and resid 765 through 786 removed outlier: 4.304A pdb=" N VAL a 771 " --> pdb=" O VAL a 767 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE a 774 " --> pdb=" O THR a 770 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP a 777 " --> pdb=" O LEU a 773 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA a 779 " --> pdb=" O ALA a 775 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU a 780 " --> pdb=" O MET a 776 " (cutoff:3.500A) Processing helix chain 'a' and resid 787 through 803 removed outlier: 3.771A pdb=" N HIS a 801 " --> pdb=" O SER a 797 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 250 removed outlier: 3.665A pdb=" N LEU b 233 " --> pdb=" O VAL b 229 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU b 234 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA b 240 " --> pdb=" O ILE b 236 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU b 247 " --> pdb=" O TRP b 243 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP b 248 " --> pdb=" O ILE b 244 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 39 removed outlier: 3.599A pdb=" N VAL c 29 " --> pdb=" O VAL c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.699A pdb=" N ILE c 45 " --> pdb=" O GLY c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 89 removed outlier: 3.753A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU c 66 " --> pdb=" O LEU c 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE c 81 " --> pdb=" O TRP c 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER c 84 " --> pdb=" O PHE c 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY c 88 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 97 removed outlier: 3.631A pdb=" N THR c 97 " --> pdb=" O PRO c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 123 removed outlier: 3.652A pdb=" N GLU c 108 " --> pdb=" O ILE c 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA c 118 " --> pdb=" O GLY c 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 168 removed outlier: 3.596A pdb=" N ASN c 156 " --> pdb=" O VAL c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 206 removed outlier: 4.261A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY c 191 " --> pdb=" O ILE c 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU c 204 " --> pdb=" O ILE c 200 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 21 Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.848A pdb=" N ILE d 31 " --> pdb=" O ASN d 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 27 through 32' Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 85 removed outlier: 3.547A pdb=" N ILE d 68 " --> pdb=" O THR d 64 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU d 79 " --> pdb=" O LYS d 75 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP d 85 " --> pdb=" O ASN d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 115 removed outlier: 3.503A pdb=" N THR d 99 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU d 109 " --> pdb=" O ASP d 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE d 111 " --> pdb=" O VAL d 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 127 removed outlier: 3.937A pdb=" N ARG d 126 " --> pdb=" O GLU d 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS d 127 " --> pdb=" O ILE d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 152 removed outlier: 3.795A pdb=" N TYR d 149 " --> pdb=" O LEU d 145 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 194 removed outlier: 3.864A pdb=" N ALA d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 201 through 228 removed outlier: 4.005A pdb=" N GLU d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU d 212 " --> pdb=" O MET d 208 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN d 222 " --> pdb=" O ARG d 218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA d 224 " --> pdb=" O SER d 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 removed outlier: 3.825A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN d 258 " --> pdb=" O PHE d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 269 removed outlier: 3.514A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 298 removed outlier: 3.918A pdb=" N ASP d 298 " --> pdb=" O GLU d 294 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.278A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG d 321 " --> pdb=" O GLU d 317 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR d 324 " --> pdb=" O VAL d 320 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 33 removed outlier: 3.548A pdb=" N VAL f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 70 removed outlier: 4.229A pdb=" N HIS f 53 " --> pdb=" O PRO f 49 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL f 55 " --> pdb=" O VAL f 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 43 removed outlier: 4.206A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA g 41 " --> pdb=" O VAL g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 50 removed outlier: 3.664A pdb=" N LEU g 49 " --> pdb=" O ARG g 46 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU g 50 " --> pdb=" O PRO g 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 46 through 50' Processing helix chain 'g' and resid 54 through 76 removed outlier: 3.760A pdb=" N ILE g 63 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 119 removed outlier: 4.127A pdb=" N SER g 100 " --> pdb=" O SER g 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 152 removed outlier: 4.361A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU g 131 " --> pdb=" O VAL g 127 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 42 removed outlier: 4.357A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER h 35 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR h 42 " --> pdb=" O GLY h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 74 removed outlier: 3.501A pdb=" N ALA h 64 " --> pdb=" O ALA h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 119 removed outlier: 3.740A pdb=" N SER h 100 " --> pdb=" O SER h 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY h 112 " --> pdb=" O ILE h 108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA h 114 " --> pdb=" O ILE h 110 " (cutoff:3.500A) Processing helix chain 'h' and resid 120 through 121 No H-bonds generated for 'chain 'h' and resid 120 through 121' Processing helix chain 'h' and resid 122 through 124 No H-bonds generated for 'chain 'h' and resid 122 through 124' Processing helix chain 'h' and resid 125 through 153 removed outlier: 4.007A pdb=" N LEU h 131 " --> pdb=" O VAL h 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU h 141 " --> pdb=" O GLU h 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU h 149 " --> pdb=" O ILE h 145 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG h 153 " --> pdb=" O LEU h 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 18 removed outlier: 4.431A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 44 removed outlier: 3.592A pdb=" N PHE i 23 " --> pdb=" O SER i 19 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS i 34 " --> pdb=" O TYR i 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL i 44 " --> pdb=" O CYS i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 74 removed outlier: 3.683A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 118 removed outlier: 4.639A pdb=" N GLN i 90 " --> pdb=" O THR i 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE i 110 " --> pdb=" O PHE i 106 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG i 117 " --> pdb=" O ASP i 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 151 removed outlier: 3.504A pdb=" N LEU i 131 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE i 132 " --> pdb=" O GLY i 128 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 37 removed outlier: 3.769A pdb=" N ALA j 20 " --> pdb=" O GLY j 16 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR j 32 " --> pdb=" O ALA j 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS j 34 " --> pdb=" O TYR j 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER j 35 " --> pdb=" O GLY j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 75 removed outlier: 3.569A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 78 No H-bonds generated for 'chain 'j' and resid 76 through 78' Processing helix chain 'j' and resid 83 through 115 removed outlier: 3.602A pdb=" N SER j 100 " --> pdb=" O SER j 96 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA j 103 " --> pdb=" O LEU j 99 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA j 114 " --> pdb=" O ILE j 110 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY j 115 " --> pdb=" O VAL j 111 " (cutoff:3.500A) Processing helix chain 'j' and resid 125 through 156 removed outlier: 3.745A pdb=" N MET j 129 " --> pdb=" O LEU j 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE j 130 " --> pdb=" O PHE j 126 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU j 131 " --> pdb=" O VAL j 127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE j 135 " --> pdb=" O LEU j 131 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA j 136 " --> pdb=" O ILE j 132 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY j 143 " --> pdb=" O LEU j 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU j 144 " --> pdb=" O GLY j 140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL j 146 " --> pdb=" O TYR j 142 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU j 149 " --> pdb=" O ILE j 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN j 156 " --> pdb=" O SER j 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 34 removed outlier: 4.351A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 37 No H-bonds generated for 'chain 'k' and resid 35 through 37' Processing helix chain 'k' and resid 38 through 46 removed outlier: 3.825A pdb=" N LEU k 45 " --> pdb=" O ALA k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 52 removed outlier: 3.638A pdb=" N LEU k 50 " --> pdb=" O PRO k 47 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE k 51 " --> pdb=" O ASP k 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS k 52 " --> pdb=" O LEU k 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 47 through 52' Processing helix chain 'k' and resid 53 through 75 removed outlier: 3.746A pdb=" N VAL k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL k 70 " --> pdb=" O TYR k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 78 No H-bonds generated for 'chain 'k' and resid 76 through 78' Processing helix chain 'k' and resid 84 through 118 removed outlier: 4.810A pdb=" N GLY k 94 " --> pdb=" O GLN k 90 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL k 97 " --> pdb=" O ALA k 93 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP k 113 " --> pdb=" O GLY k 109 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA k 114 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL k 116 " --> pdb=" O GLY k 112 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY k 118 " --> pdb=" O ALA k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 122 Processing helix chain 'k' and resid 127 through 155 removed outlier: 3.546A pdb=" N ILE k 132 " --> pdb=" O GLY k 128 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE k 135 " --> pdb=" O LEU k 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL k 138 " --> pdb=" O ILE k 134 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU k 141 " --> pdb=" O GLU k 137 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 143 " --> pdb=" O LEU k 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL k 146 " --> pdb=" O TYR k 142 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU k 149 " --> pdb=" O ILE k 145 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR k 155 " --> pdb=" O ASN k 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 40 removed outlier: 4.227A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY l 38 " --> pdb=" O LYS l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.654A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU l 50 " --> pdb=" O PRO l 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 46 through 50' Processing helix chain 'l' and resid 54 through 75 removed outlier: 3.889A pdb=" N MET l 59 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE l 65 " --> pdb=" O GLY l 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS l 75 " --> pdb=" O SER l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 78 No H-bonds generated for 'chain 'l' and resid 76 through 78' Processing helix chain 'l' and resid 84 through 119 removed outlier: 4.439A pdb=" N GLN l 90 " --> pdb=" O THR l 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA l 114 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.033A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU l 150 " --> pdb=" O VAL l 146 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG l 153 " --> pdb=" O LEU l 149 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA l 154 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 42 removed outlier: 4.098A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.654A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL m 70 " --> pdb=" O TYR m 66 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 122 removed outlier: 3.531A pdb=" N ILE m 108 " --> pdb=" O ALA m 104 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE m 110 " --> pdb=" O PHE m 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA m 114 " --> pdb=" O ILE m 110 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG m 117 " --> pdb=" O ASP m 113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY m 118 " --> pdb=" O ALA m 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 151 removed outlier: 3.609A pdb=" N LEU m 131 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE m 132 " --> pdb=" O GLY m 128 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY m 143 " --> pdb=" O LEU m 139 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU m 149 " --> pdb=" O ILE m 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 152 through 154 No H-bonds generated for 'chain 'm' and resid 152 through 154' Processing helix chain 'n' and resid 9 through 40 removed outlier: 3.995A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL n 37 " --> pdb=" O ALA n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 78 removed outlier: 3.594A pdb=" N VAL n 70 " --> pdb=" O TYR n 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER n 77 " --> pdb=" O LEU n 73 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 116 removed outlier: 4.482A pdb=" N VAL n 97 " --> pdb=" O ALA n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 117 through 124 removed outlier: 3.686A pdb=" N SER n 120 " --> pdb=" O ARG n 117 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN n 121 " --> pdb=" O GLY n 118 " (cutoff:3.500A) Proline residue: n 123 - end of helix Processing helix chain 'n' and resid 125 through 133 removed outlier: 4.071A pdb=" N ILE n 130 " --> pdb=" O PHE n 126 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU n 131 " --> pdb=" O VAL n 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE n 132 " --> pdb=" O GLY n 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 134 through 151 removed outlier: 3.709A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 154 No H-bonds generated for 'chain 'n' and resid 152 through 154' Processing helix chain 'o' and resid 16 through 46 removed outlier: 3.536A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 80 removed outlier: 3.922A pdb=" N ILE o 68 " --> pdb=" O VAL o 64 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU o 69 " --> pdb=" O MET o 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA o 70 " --> pdb=" O SER o 66 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 124 removed outlier: 3.534A pdb=" N GLY o 95 " --> pdb=" O THR o 91 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL o 124 " --> pdb=" O GLY o 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 162 removed outlier: 3.686A pdb=" N LEU o 139 " --> pdb=" O VAL o 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE o 143 " --> pdb=" O LEU o 139 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU o 149 " --> pdb=" O GLU o 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR o 160 " --> pdb=" O LEU o 156 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 24 removed outlier: 4.149A pdb=" N VAL e 10 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE e 23 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 54 removed outlier: 4.332A pdb=" N SER e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR e 36 " --> pdb=" O VAL e 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'a' and resid 187 through 191 removed outlier: 3.687A pdb=" N PHE a 239 " --> pdb=" O PHE a 212 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE a 212 " --> pdb=" O PHE a 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'a' and resid 506 through 507 1353 hydrogen bonds defined for protein. 4014 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: 6.03 Time building geometry restraints manager: 8.41 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: 4753 1.33 - 1.45: 4541 1.45 - 1.58: 10630 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 20090 Sorted by residual: bond pdb=" CB VAL n 97 " pdb=" CG2 VAL n 97 " ideal model delta sigma weight residual 1.521 1.384 0.137 3.30e-02 9.18e+02 1.72e+01 bond pdb=" CB THR k 24 " pdb=" CG2 THR k 24 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.40e+01 bond pdb=" CG1 ILE n 21 " pdb=" CD1 ILE n 21 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.05e+01 bond pdb=" CB VAL o 105 " pdb=" CG2 VAL o 105 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.87e+00 bond pdb=" CB THR i 24 " pdb=" CG2 THR i 24 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.80e+00 ... (remaining 20085 not shown) Histogram of bond angle deviations from ideal: 93.37 - 101.51: 53 101.51 - 109.65: 2756 109.65 - 117.78: 11677 117.78 - 125.92: 12725 125.92 - 134.06: 221 Bond angle restraints: 27432 Sorted by residual: angle pdb=" C GLN j 156 " pdb=" N ASP j 157 " pdb=" CA ASP j 157 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" CG1 VAL n 97 " pdb=" CB VAL n 97 " pdb=" CG2 VAL n 97 " ideal model delta sigma weight residual 110.80 99.47 11.33 2.20e+00 2.07e-01 2.65e+01 angle pdb=" N ILE k 22 " pdb=" CA ILE k 22 " pdb=" C ILE k 22 " ideal model delta sigma weight residual 110.53 115.29 -4.76 9.40e-01 1.13e+00 2.56e+01 angle pdb=" N VAL a 651 " pdb=" CA VAL a 651 " pdb=" C VAL a 651 " ideal model delta sigma weight residual 110.62 115.72 -5.10 1.02e+00 9.61e-01 2.50e+01 angle pdb=" N LEU k 95 " pdb=" CA LEU k 95 " pdb=" C LEU k 95 " ideal model delta sigma weight residual 111.36 106.07 5.29 1.09e+00 8.42e-01 2.35e+01 ... (remaining 27427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 10643 15.22 - 30.45: 630 30.45 - 45.67: 174 45.67 - 60.90: 24 60.90 - 76.12: 7 Dihedral angle restraints: 11478 sinusoidal: 3487 harmonic: 7991 Sorted by residual: dihedral pdb=" CA ILE a 482 " pdb=" C ILE a 482 " pdb=" N PHE a 483 " pdb=" CA PHE a 483 " ideal model delta harmonic sigma weight residual 180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN m 90 " pdb=" C GLN m 90 " pdb=" N LEU m 91 " pdb=" CA LEU m 91 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASP a 481 " pdb=" C ASP a 481 " pdb=" N ILE a 482 " pdb=" CA ILE a 482 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 11475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 3224 0.137 - 0.275: 156 0.275 - 0.412: 4 0.412 - 0.549: 2 0.549 - 0.687: 4 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CB ILE m 22 " pdb=" CA ILE m 22 " pdb=" CG1 ILE m 22 " pdb=" CG2 ILE m 22 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB ILE k 22 " pdb=" CA ILE k 22 " pdb=" CG1 ILE k 22 " pdb=" CG2 ILE k 22 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB VAL h 138 " pdb=" CA VAL h 138 " pdb=" CG1 VAL h 138 " pdb=" CG2 VAL h 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.61 2.00e-01 2.50e+01 9.45e+00 ... (remaining 3387 not shown) Planarity restraints: 3431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE m 89 " -0.028 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C ILE m 89 " 0.095 2.00e-02 2.50e+03 pdb=" O ILE m 89 " -0.035 2.00e-02 2.50e+03 pdb=" N GLN m 90 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL j 97 " -0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C VAL j 97 " 0.088 2.00e-02 2.50e+03 pdb=" O VAL j 97 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY j 98 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE h 15 " -0.025 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C ILE h 15 " 0.088 2.00e-02 2.50e+03 pdb=" O ILE h 15 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY h 16 " -0.030 2.00e-02 2.50e+03 ... (remaining 3428 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4333 2.77 - 3.30: 18904 3.30 - 3.83: 33285 3.83 - 4.37: 39553 4.37 - 4.90: 66621 Nonbonded interactions: 162696 Sorted by model distance: nonbonded pdb=" O TRP a 777 " pdb=" OG1 THR a 781 " model vdw 2.236 2.440 nonbonded pdb=" O ALA a 407 " pdb=" OG1 THR a 411 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR n 66 " pdb=" OE2 GLU n 137 " model vdw 2.241 2.440 nonbonded pdb=" O LEU c 51 " pdb=" OH TYR c 143 " model vdw 2.250 2.440 nonbonded pdb=" O GLY i 31 " pdb=" OG SER i 35 " model vdw 2.255 2.440 ... (remaining 162691 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 'g' and (resid 2 through 20 or (resid 21 through 22 and (name N or name C \ A 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 or (resi \ d 37 and (name N or name CA or name C or name O or name CB )) or resid 38 or (re \ sid 39 through 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 through 55 or (resid 56 and (name N or name CA or name C or name O or nam \ e CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 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 105 or (resid 106 through \ 107 and (name N or name CA or name C or name O or name CB )) or resid 108 throug \ h 109 or (resid 110 through 111 and (name N or name CA or name C or name O or na \ me 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 n \ ame CA or name C or name O or name CB )) or resid 118 or (resid 119 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 through 144 or (resid 145 and (name N or name CA or name C or name O or na \ me CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'h' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 33 or (resi \ d 34 through 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or re \ sid 38 or (resid 39 through 53 and (name N or name CA or name C or name O or nam \ e CB )) or resid 54 through 55 or (resid 56 and (name N or name CA or name C or \ name O or name CB )) or resid 57 or (resid 58 and (name N or name CA or name C o \ r name O or name CB )) or resid 59 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 105 or (resid \ 106 through 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 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 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 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 through 144 or (resid 145 and (name N or name CA or name C or name O or na \ me CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'i' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 33 or (resi \ d 34 through 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or (r \ esid 38 through 53 and (name N or name CA or name C or name O or name CB )) or r \ esid 54 through 55 or (resid 56 and (name N or name CA or name C or name O or na \ me CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or \ name CB )) or resid 59 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 105 or (resid 106 through \ 107 and (name N or name CA or name C or name O or name CB )) or resid 108 throu \ gh 109 or (resid 110 through 111 and (name N or name CA or name C or name O or n \ ame 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 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 or (resid 129 through \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throug \ h 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 155)) selection = (chain 'j' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 throug \ h 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or (re \ sid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 thro \ ugh 105 or (resid 106 through 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 109 or (resid 110 through 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 or (resid 113 through 114 an \ d (name N or name CA or name C or name O or name CB )) or (resid 115 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or res \ id 133 through 144 or (resid 145 and (name N or name CA or name C or name O or n \ ame CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'k' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 34 or (resid 35 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 36 through 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 55 or (r \ esid 56 and (name N or name CA or name C or name O or name CB )) or resid 57 or \ (resid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 t \ hrough 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 105 or (resid 106 through 107 and (name N or name \ CA or name C or name O or name CB )) or resid 108 through 109 or (resid 110 thr \ ough 111 and (name N or name CA or name C or name O or name CB )) or resid 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 115 through 127 and (name N or name CA or name C or name O or name C \ B )) or resid 128 or (resid 129 through 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 through 144 or (resid 145 and (name N or name \ CA or name C or name O or name CB )) or resid 146 through 154 or (resid 155 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'l' and (resid 2 through 34 or (resid 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 38 through 53 and (name N or name CA or nam \ e C or name O or name CB )) or resid 54 through 55 or (resid 56 and (name N or n \ ame CA or name C or name O or name CB )) or resid 57 through 62 or (resid 63 thr \ ough 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thr \ ough 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 132 and (name N or name CA or name C or nam \ e O or name CB )) or resid 133 through 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 through 154 or (resid 155 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'm' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 34 or (resid 35 and (n \ ame 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 38 through 53 and \ (name N or name CA or name C or name O or name CB )) or resid 54 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB )) or resid 57 o \ r (resid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 \ through 62 or (resid 63 through 65 and (name N or name CA or name C or name O o \ r name CB )) or resid 66 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 109 or (resid 110 t \ hrough 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 through 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 or (resid 129 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 144 or (resid 145 and (name N or nam \ e CA or name C or name O or name CB )) or resid 146 through 154 or (resid 155 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'n' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or re \ sid 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or \ resid 59 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 105 or (resid 106 through 107 and (name \ N or name CA or name C or name O or name CB )) or resid 108 through 109 or (res \ id 110 through 111 and (name N or name CA or name C or name O or name CB )) or ( \ resid 112 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 154 or (resid 155 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 109 5.16 5 C 12893 2.51 5 N 3198 2.21 5 O 3530 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 5.280 Check model and map are aligned: 0.330 Process input model: 51.050 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.009 0.137 20090 Z= 0.604 Angle : 1.251 14.115 27432 Z= 0.670 Chirality : 0.069 0.687 3390 Planarity : 0.011 0.085 3431 Dihedral : 11.380 76.120 6400 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.98 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.13), residues: 2784 helix: -2.45 (0.10), residues: 1954 sheet: -2.27 (0.73), residues: 34 loop : -3.15 (0.17), residues: 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 614 time to evaluate : 2.469 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 623 average time/residue: 0.2819 time to fit residues: 278.0377 Evaluate side-chains 404 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 400 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1787 time to fit residues: 4.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 18 GLN a 68 GLN a 79 HIS a 311 GLN a 480 ASN a 547 HIS a 571 ASN c 132 ASN c 138 ASN d 10 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 222 ASN f 35 HIS g 90 GLN h 90 GLN ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 GLN j 151 ASN k 53 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 151 ASN l 80 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 151 ASN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN o 159 ASN e 55 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20090 Z= 0.206 Angle : 0.660 8.107 27432 Z= 0.347 Chirality : 0.041 0.213 3390 Planarity : 0.005 0.057 3431 Dihedral : 5.130 26.224 2956 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 2784 helix: -1.12 (0.11), residues: 1996 sheet: -2.05 (0.90), residues: 26 loop : -2.65 (0.19), residues: 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 457 time to evaluate : 2.251 Fit side-chains outliers start: 66 outliers final: 36 residues processed: 495 average time/residue: 0.2849 time to fit residues: 226.6016 Evaluate side-chains 432 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 396 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1787 time to fit residues: 15.2106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 571 ASN a 718 HIS a 725 ASN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 GLN k 90 GLN m 82 GLN m 90 GLN m 151 ASN n 80 GLN n 82 GLN n 90 GLN o 98 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 20090 Z= 0.286 Angle : 0.663 9.887 27432 Z= 0.340 Chirality : 0.042 0.201 3390 Planarity : 0.004 0.064 3431 Dihedral : 4.784 25.229 2956 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2784 helix: -0.40 (0.11), residues: 2011 sheet: -1.66 (0.94), residues: 26 loop : -2.42 (0.20), residues: 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 413 time to evaluate : 2.178 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 47 residues processed: 464 average time/residue: 0.2788 time to fit residues: 207.7612 Evaluate side-chains 427 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 380 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.1843 time to fit residues: 19.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 0.0070 chunk 263 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 134 GLN a 374 ASN a 718 HIS c 138 ASN d 7 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 90 GLN j 151 ASN l 151 ASN o 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 20090 Z= 0.177 Angle : 0.577 10.961 27432 Z= 0.296 Chirality : 0.039 0.171 3390 Planarity : 0.004 0.062 3431 Dihedral : 4.483 20.069 2956 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2784 helix: 0.18 (0.12), residues: 1993 sheet: -1.05 (1.03), residues: 26 loop : -2.18 (0.20), residues: 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 416 time to evaluate : 2.238 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 436 average time/residue: 0.2862 time to fit residues: 200.0257 Evaluate side-chains 398 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 376 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2217 time to fit residues: 11.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 381 HIS a 718 HIS c 61 ASN c 132 ASN d 35 GLN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN o 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 20090 Z= 0.390 Angle : 0.678 10.506 27432 Z= 0.345 Chirality : 0.044 0.276 3390 Planarity : 0.004 0.062 3431 Dihedral : 4.606 24.615 2956 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2784 helix: 0.17 (0.11), residues: 1994 sheet: -0.90 (1.03), residues: 26 loop : -2.14 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 378 time to evaluate : 2.296 Fit side-chains outliers start: 61 outliers final: 35 residues processed: 414 average time/residue: 0.3002 time to fit residues: 198.4492 Evaluate side-chains 398 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 363 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1886 time to fit residues: 15.7244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.6980 chunk 237 optimal weight: 0.0270 chunk 52 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 718 HIS c 61 ASN d 35 GLN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 151 ASN o 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3270 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: