Starting phenix.real_space_refine on Sat Dec 9 16:25:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd4_0441/12_2023/6nd4_0441_neut_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 568 5.49 5 C 36360 2.51 5 N 12577 2.21 5 O 14488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63993 Number of models: 1 Model: "" Number of chains: 30 Chain: "0" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 8594 Inner-chain residues flagged as termini: ['pdbres=" N 0 601 "'] Classifications: {'RNA': 408} Modifications used: {'5*END': 1, 'rna2p_pur': 25, 'rna2p_pyr': 29, 'rna3p': 10, 'rna3p_pur': 182, 'rna3p_pyr': 162} Link IDs: {'rna2p': 54, 'rna3p': 353} Chain breaks: 10 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Chain: "1" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 241 Classifications: {'RNA': 15} Modifications used: {'rna3p': 8, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna3p': 14} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3106 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 11, 'rna3p_pur': 58, 'rna3p_pyr': 58} Link IDs: {'rna2p': 29, 'rna3p': 116} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 4132 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 772} Link IDs: {'PTRANS': 22, 'TRANS': 811} Chain breaks: 5 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2665 Unresolved non-hydrogen angles: 3441 Unresolved non-hydrogen dihedrals: 2199 Unresolved non-hydrogen chiralities: 255 Planarities with less than four sites: {'GLN:plan1': 41, 'HIS:plan': 22, 'UNK:plan-1': 14, 'TYR:plan': 24, 'ASN:plan1': 78, 'TRP:plan': 12, 'ASP:plan': 50, 'PHE:plan': 44, 'GLU:plan': 33, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 1439 Chain: "I" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 2427 Classifications: {'peptide': 487} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 475} Link IDs: {'PTRANS': 3, 'TRANS': 483} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1159 Unresolved non-hydrogen angles: 1644 Unresolved non-hydrogen dihedrals: 709 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 7, 'TYR:plan': 3, 'UNK:plan-1': 354, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 588 Chain: "J" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 2441 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 437} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1554 Unresolved non-hydrogen angles: 1995 Unresolved non-hydrogen dihedrals: 1296 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 26, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 15, 'PHE:plan': 19, 'GLU:plan': 22, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 851 Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 612 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'UNK:plan-1': 35, 'TRP:plan': 3, 'HIS:plan': 3, 'ARG:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 172 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 2344 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 427} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 4 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1490 Unresolved non-hydrogen angles: 1925 Unresolved non-hydrogen dihedrals: 1228 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 11, 'TYR:plan': 14, 'ASN:plan1': 33, 'TRP:plan': 9, 'ASP:plan': 29, 'PHE:plan': 16, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 780 Chain: "M" Number of atoms: 2151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 2151 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 11, 'TRANS': 419} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1753 Unresolved non-hydrogen dihedrals: 1128 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 23, 'TYR:plan': 14, 'ASN:plan1': 23, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 24, 'GLU:plan': 24, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 668 Chain: "N" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 3355 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 619} Link IDs: {'PTRANS': 19, 'TRANS': 658} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2126 Unresolved non-hydrogen angles: 2744 Unresolved non-hydrogen dihedrals: 1760 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 11, 'UNK:plan-1': 14, 'TYR:plan': 10, 'ASN:plan1': 53, 'TRP:plan': 17, 'ASP:plan': 45, 'PHE:plan': 31, 'GLU:plan': 27, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1115 Chain: "O" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 4111 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 728} Link IDs: {'PTRANS': 22, 'TRANS': 809} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2656 Unresolved non-hydrogen angles: 3412 Unresolved non-hydrogen dihedrals: 2233 Unresolved non-hydrogen chiralities: 234 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 18, 'TYR:plan': 22, 'ASN:plan1': 45, 'TRP:plan': 13, 'ASP:plan': 52, 'PHE:plan': 59, 'GLU:plan': 41, 'ARG:plan': 44} Unresolved non-hydrogen planarities: 1522 Chain: "P" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 1786 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 5, 'TRANS': 353} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1163 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 932 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'UNK:plan-1': 95, 'TYR:plan': 17, 'ASN:plan1': 24, 'TRP:plan': 4, 'ASP:plan': 12, 'PHE:plan': 14, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 644 Chain: "Q" Number of atoms: 4262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 4262 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 767} Link IDs: {'PTRANS': 19, 'TRANS': 842} Chain breaks: 7 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2719 Unresolved non-hydrogen angles: 3498 Unresolved non-hydrogen dihedrals: 2274 Unresolved non-hydrogen chiralities: 255 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 24, 'UNK:plan-1': 35, 'TYR:plan': 20, 'ASN:plan1': 29, 'TRP:plan': 19, 'ASP:plan': 60, 'PHE:plan': 37, 'GLU:plan': 47, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1399 Chain: "R" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 3604 Classifications: {'peptide': 725} Incomplete info: {'backbone_only': 18, 'truncation_to_alanine': 694} Link IDs: {'PTRANS': 3, 'TRANS': 721} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1686 Unresolved non-hydrogen angles: 2418 Unresolved non-hydrogen dihedrals: 1003 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 11, 'ASN:plan1': 9, 'TYR:plan': 4, 'UNK:plan-1': 567, 'TRP:plan': 2, 'ASP:plan': 9, 'ARG:plan': 8, 'PHE:plan': 5, 'GLU:plan': 16, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 870 Chain: "S" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 2372 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 424} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 460} Chain breaks: 3 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1507 Unresolved non-hydrogen angles: 1945 Unresolved non-hydrogen dihedrals: 1268 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 15, 'TYR:plan': 14, 'ASN:plan1': 32, 'TRP:plan': 10, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 17, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 798 Chain: "T" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 4003 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 710} Link IDs: {'PTRANS': 23, 'TRANS': 788} Chain breaks: 2 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 2515 Unresolved non-hydrogen angles: 3230 Unresolved non-hydrogen dihedrals: 2098 Unresolved non-hydrogen chiralities: 245 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 22, 'TYR:plan': 23, 'ASN:plan1': 39, 'TRP:plan': 10, 'ASP:plan': 52, 'PHE:plan': 46, 'GLU:plan': 35, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1353 Chain: "U" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2014 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 364} Link IDs: {'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1357 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 1157 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 14, 'TYR:plan': 17, 'ASN:plan1': 27, 'TRP:plan': 7, 'ASP:plan': 25, 'PHE:plan': 16, 'GLU:plan': 23, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 774 Chain: "W" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 1895 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 330} Link IDs: {'PTRANS': 21, 'TRANS': 363} Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1209 Unresolved non-hydrogen angles: 1559 Unresolved non-hydrogen dihedrals: 1025 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 21, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 12, 'GLU:plan': 24, 'HIS:plan': 17} Unresolved non-hydrogen planarities: 652 Chain: "Z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 840 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 6, 'TRANS': 162} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 499 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 317 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "a" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 1822 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 320} Link IDs: {'PTRANS': 9, 'TRANS': 358} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1116 Unresolved non-hydrogen angles: 1426 Unresolved non-hydrogen dihedrals: 910 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 6, 'UNK:plan-1': 26, 'TYR:plan': 12, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 19, 'PHE:plan': 16, 'GLU:plan': 26, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 599 Chain: "b" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2109 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 367} Link IDs: {'PTRANS': 6, 'TRANS': 418} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1105 Unresolved non-hydrogen angles: 1457 Unresolved non-hydrogen dihedrals: 820 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 9, 'ASP:plan': 19, 'TYR:plan': 9, 'UNK:plan-1': 124, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 23, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 557 Chain: "c" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1000 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 328 Chain: "d" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1122 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 695 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 577 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 361 Chain: "e" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 601 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 113} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "f" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 601 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 113} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "g" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 1925 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'PTRANS': 12, 'TRANS': 378} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1253 Unresolved non-hydrogen angles: 1599 Unresolved non-hydrogen dihedrals: 1064 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 7, 'ASP:plan': 22, 'PHE:plan': 19, 'GLU:plan': 23, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 677 Chain: "l" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "x" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N HIS J 44 " occ=0.50 ... (3 atoms not shown) pdb=" CB HIS J 44 " occ=0.50 residue: pdb=" N SER J 78 " occ=0.50 ... (3 atoms not shown) pdb=" CB SER J 78 " occ=0.50 residue: pdb=" N ILE J 193 " occ=0.50 ... (3 atoms not shown) pdb=" CB ILE J 193 " occ=0.50 residue: pdb=" N ILE J 226 " occ=0.50 ... (3 atoms not shown) pdb=" CB ILE J 226 " occ=0.50 Time building chain proxies: 27.09, per 1000 atoms: 0.42 Number of scatterers: 63993 At special positions: 0 Unit cell: (291.2, 217.6, 228.8, 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) P 568 15.00 O 14488 8.00 N 12577 7.00 C 36360 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: 22.19 Conformation dependent library (CDL) restraints added in 9.4 seconds 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 241 helices and 147 sheets defined 28.4% alpha, 21.9% beta 128 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 23.83 Creating SS restraints... Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 418 through 426 Processing helix chain 'H' and resid 478 through 480 No H-bonds generated for 'chain 'H' and resid 478 through 480' Processing helix chain 'H' and resid 565 through 568 No H-bonds generated for 'chain 'H' and resid 565 through 568' Processing helix chain 'H' and resid 819 through 830 removed outlier: 4.150A pdb=" N UNK H 826 " --> pdb=" O UNK H 822 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N UNK H 828 " --> pdb=" O UNK H 824 " (cutoff:3.500A) Processing helix chain 'H' and resid 850 through 859 removed outlier: 3.706A pdb=" N ALA H 854 " --> pdb=" O GLU H 850 " (cutoff:3.500A) Processing helix chain 'H' and resid 875 through 878 Processing helix chain 'H' and resid 884 through 895 removed outlier: 3.562A pdb=" N ARG H 890 " --> pdb=" O THR H 886 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 466 Processing helix chain 'I' and resid 477 through 485 Processing helix chain 'I' and resid 497 through 502 Processing helix chain 'I' and resid 510 through 516 removed outlier: 3.739A pdb=" N UNK I 514 " --> pdb=" O UNK I 510 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 529 No H-bonds generated for 'chain 'I' and resid 526 through 529' Processing helix chain 'I' and resid 542 through 544 No H-bonds generated for 'chain 'I' and resid 542 through 544' Processing helix chain 'I' and resid 550 through 557 Processing helix chain 'I' and resid 563 through 571 Processing helix chain 'I' and resid 579 through 589 removed outlier: 3.616A pdb=" N SER I 583 " --> pdb=" O LEU I 579 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE I 584 " --> pdb=" O LEU I 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 598 Processing helix chain 'I' and resid 604 through 616 Processing helix chain 'I' and resid 632 through 645 Processing helix chain 'I' and resid 652 through 677 removed outlier: 3.905A pdb=" N GLU I 674 " --> pdb=" O GLU I 670 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 29 removed outlier: 4.700A pdb=" N GLN J 29 " --> pdb=" O ARG J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 355 through 359 Processing helix chain 'J' and resid 363 through 365 No H-bonds generated for 'chain 'J' and resid 363 through 365' Processing helix chain 'J' and resid 387 through 393 removed outlier: 3.687A pdb=" N ASN J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 397 through 404 Processing helix chain 'J' and resid 411 through 423 Processing helix chain 'J' and resid 429 through 431 No H-bonds generated for 'chain 'J' and resid 429 through 431' Processing helix chain 'J' and resid 436 through 449 Proline residue: J 441 - end of helix removed outlier: 4.455A pdb=" N LYS J 448 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 474 removed outlier: 6.647A pdb=" N ASN J 472 " --> pdb=" O GLU J 468 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR J 473 " --> pdb=" O LEU J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 511 removed outlier: 4.145A pdb=" N LEU J 510 " --> pdb=" O GLY J 506 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU J 511 " --> pdb=" O MET J 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 400 removed outlier: 3.902A pdb=" N UNK K 396 " --> pdb=" O UNK K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 413 removed outlier: 3.620A pdb=" N UNK K 413 " --> pdb=" O UNK K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 425 removed outlier: 3.758A pdb=" N UNK K 424 " --> pdb=" O UNK K 420 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK K 425 " --> pdb=" O UNK K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 443 removed outlier: 4.274A pdb=" N THR K 436 " --> pdb=" O LYS K 432 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS K 439 " --> pdb=" O LEU K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 462 Processing helix chain 'K' and resid 475 through 514 removed outlier: 4.511A pdb=" N SER K 484 " --> pdb=" O LYS K 480 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG K 487 " --> pdb=" O LYS K 483 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER K 488 " --> pdb=" O SER K 484 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER K 489 " --> pdb=" O ALA K 485 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K 490 " --> pdb=" O LEU K 486 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE K 492 " --> pdb=" O SER K 488 " (cutoff:3.500A) Proline residue: K 494 - end of helix removed outlier: 3.812A pdb=" N GLU K 504 " --> pdb=" O GLN K 500 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU K 506 " --> pdb=" O ARG K 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 14 No H-bonds generated for 'chain 'L' and resid 12 through 14' Processing helix chain 'L' and resid 438 through 444 Processing helix chain 'L' and resid 451 through 458 removed outlier: 3.601A pdb=" N VAL L 456 " --> pdb=" O LEU L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 470 Processing helix chain 'L' and resid 476 through 490 removed outlier: 3.669A pdb=" N GLU L 482 " --> pdb=" O VAL L 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 498 Processing helix chain 'L' and resid 500 through 508 removed outlier: 3.639A pdb=" N TRP L 504 " --> pdb=" O VAL L 500 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N CYS L 505 " --> pdb=" O TRP L 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 515 removed outlier: 3.582A pdb=" N SER L 515 " --> pdb=" O GLY L 511 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 554 removed outlier: 4.112A pdb=" N LEU L 536 " --> pdb=" O ARG L 532 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU L 537 " --> pdb=" O ARG L 533 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.818A pdb=" N ALA L 545 " --> pdb=" O LEU L 541 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR L 550 " --> pdb=" O ARG L 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 removed outlier: 3.979A pdb=" N VAL M 11 " --> pdb=" O GLN M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 28 Processing helix chain 'M' and resid 45 through 62 removed outlier: 4.471A pdb=" N GLU M 58 " --> pdb=" O LYS M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 71 removed outlier: 3.818A pdb=" N ILE M 68 " --> pdb=" O LYS M 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE M 69 " --> pdb=" O PHE M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 105 removed outlier: 3.677A pdb=" N ASP M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 112 through 125 removed outlier: 4.297A pdb=" N TRP M 120 " --> pdb=" O HIS M 116 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 138 Processing helix chain 'M' and resid 146 through 153 removed outlier: 3.672A pdb=" N SER M 153 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 166 removed outlier: 3.739A pdb=" N SER M 165 " --> pdb=" O ASN M 162 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN M 166 " --> pdb=" O CYS M 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 162 through 166' Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.525A pdb=" N ILE M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 201 removed outlier: 3.700A pdb=" N GLN M 198 " --> pdb=" O SER M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 223 Processing helix chain 'M' and resid 228 through 232 Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.669A pdb=" N GLU M 240 " --> pdb=" O PRO M 236 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE M 241 " --> pdb=" O ILE M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 267 Processing helix chain 'M' and resid 272 through 285 removed outlier: 3.851A pdb=" N ASN M 285 " --> pdb=" O THR M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 304 removed outlier: 4.546A pdb=" N SER M 294 " --> pdb=" O GLU M 290 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN M 304 " --> pdb=" O CYS M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 326 Processing helix chain 'M' and resid 329 through 335 Processing helix chain 'M' and resid 345 through 358 removed outlier: 4.038A pdb=" N THR M 349 " --> pdb=" O ASP M 345 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER M 350 " --> pdb=" O LYS M 346 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG M 353 " --> pdb=" O THR M 349 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER M 354 " --> pdb=" O SER M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 372 removed outlier: 3.533A pdb=" N LYS M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 392 removed outlier: 3.695A pdb=" N ASP M 386 " --> pdb=" O LEU M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 398 through 409 Processing helix chain 'M' and resid 412 through 421 Processing helix chain 'M' and resid 425 through 429 Processing helix chain 'N' and resid 82 through 85 No H-bonds generated for 'chain 'N' and resid 82 through 85' Processing helix chain 'N' and resid 151 through 153 No H-bonds generated for 'chain 'N' and resid 151 through 153' Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 468 through 472 Processing helix chain 'N' and resid 520 through 524 removed outlier: 3.633A pdb=" N LYS N 524 " --> pdb=" O LYS N 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 520 through 524' Processing helix chain 'N' and resid 526 through 529 removed outlier: 4.335A pdb=" N ASN N 529 " --> pdb=" O PRO N 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 526 through 529' Processing helix chain 'N' and resid 578 through 580 No H-bonds generated for 'chain 'N' and resid 578 through 580' Processing helix chain 'N' and resid 613 through 618 Processing helix chain 'N' and resid 624 through 627 No H-bonds generated for 'chain 'N' and resid 624 through 627' Processing helix chain 'O' and resid 177 through 179 No H-bonds generated for 'chain 'O' and resid 177 through 179' Processing helix chain 'O' and resid 571 through 573 No H-bonds generated for 'chain 'O' and resid 571 through 573' Processing helix chain 'O' and resid 624 through 626 No H-bonds generated for 'chain 'O' and resid 624 through 626' Processing helix chain 'O' and resid 647 through 649 No H-bonds generated for 'chain 'O' and resid 647 through 649' Processing helix chain 'O' and resid 653 through 656 No H-bonds generated for 'chain 'O' and resid 653 through 656' Processing helix chain 'O' and resid 670 through 673 removed outlier: 3.567A pdb=" N ARG O 673 " --> pdb=" O LEU O 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 670 through 673' Processing helix chain 'O' and resid 723 through 731 Processing helix chain 'O' and resid 735 through 743 Processing helix chain 'O' and resid 748 through 755 Processing helix chain 'O' and resid 760 through 769 Proline residue: O 764 - end of helix removed outlier: 3.634A pdb=" N ALA O 767 " --> pdb=" O PRO O 764 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER O 768 " --> pdb=" O LEU O 765 " (cutoff:3.500A) Processing helix chain 'O' and resid 775 through 787 removed outlier: 4.697A pdb=" N ILE O 787 " --> pdb=" O GLY O 783 " (cutoff:3.500A) Processing helix chain 'O' and resid 792 through 812 removed outlier: 6.809A pdb=" N GLY O 808 " --> pdb=" O SER O 804 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR O 809 " --> pdb=" O ALA O 805 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE O 810 " --> pdb=" O SER O 806 " (cutoff:3.500A) Processing helix chain 'O' and resid 818 through 829 removed outlier: 3.517A pdb=" N SER O 823 " --> pdb=" O THR O 819 " (cutoff:3.500A) Processing helix chain 'O' and resid 832 through 851 Processing helix chain 'P' and resid 4 through 20 removed outlier: 3.723A pdb=" N CYS P 11 " --> pdb=" O TYR P 7 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Proline residue: P 13 - end of helix Processing helix chain 'P' and resid 26 through 43 removed outlier: 4.756A pdb=" N LEU P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE P 32 " --> pdb=" O GLU P 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS P 41 " --> pdb=" O THR P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 74 removed outlier: 3.641A pdb=" N ASN P 62 " --> pdb=" O ASN P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 102 removed outlier: 4.529A pdb=" N ILE P 88 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN P 89 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE P 92 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY P 93 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN P 97 " --> pdb=" O GLY P 93 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN P 101 " --> pdb=" O GLN P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 117 Processing helix chain 'P' and resid 126 through 139 removed outlier: 3.675A pdb=" N HIS P 130 " --> pdb=" O TYR P 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE P 132 " --> pdb=" O LYS P 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS P 138 " --> pdb=" O ASN P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 156 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 179 through 206 removed outlier: 3.557A pdb=" N ILE P 193 " --> pdb=" O GLU P 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR P 194 " --> pdb=" O LEU P 190 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS P 195 " --> pdb=" O ASN P 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU P 196 " --> pdb=" O PHE P 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY P 204 " --> pdb=" O ARG P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 287 removed outlier: 3.648A pdb=" N ILE P 269 " --> pdb=" O ARG P 266 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA P 270 " --> pdb=" O GLY P 267 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET P 278 " --> pdb=" O ASP P 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU P 281 " --> pdb=" O MET P 278 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN P 287 " --> pdb=" O HIS P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 325 removed outlier: 3.822A pdb=" N LEU P 309 " --> pdb=" O ASN P 305 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER P 314 " --> pdb=" O ASN P 310 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU P 315 " --> pdb=" O TYR P 311 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P 318 " --> pdb=" O SER P 314 " (cutoff:3.500A) Processing helix chain 'P' and resid 330 through 348 removed outlier: 4.415A pdb=" N UNK P 336 " --> pdb=" O UNK P 332 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N UNK P 337 " --> pdb=" O UNK P 333 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N UNK P 344 " --> pdb=" O UNK P 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK P 347 " --> pdb=" O UNK P 343 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N UNK P 348 " --> pdb=" O UNK P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 removed outlier: 3.597A pdb=" N UNK P 359 " --> pdb=" O UNK P 355 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNK P 360 " --> pdb=" O UNK P 356 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N UNK P 363 " --> pdb=" O UNK P 359 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK P 366 " --> pdb=" O UNK P 362 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 396 removed outlier: 3.746A pdb=" N UNK P 396 " --> pdb=" O UNK P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 414 removed outlier: 3.530A pdb=" N UNK P 404 " --> pdb=" O UNK P 400 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N UNK P 412 " --> pdb=" O UNK P 408 " (cutoff:3.500A) Processing helix chain 'P' and resid 420 through 425 Processing helix chain 'Q' and resid 289 through 303 removed outlier: 3.607A pdb=" N GLY Q 295 " --> pdb=" O GLU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 309 through 315 Processing helix chain 'Q' and resid 322 through 325 No H-bonds generated for 'chain 'Q' and resid 322 through 325' Processing helix chain 'Q' and resid 707 through 727 Processing helix chain 'Q' and resid 745 through 777 removed outlier: 3.808A pdb=" N ARG Q 751 " --> pdb=" O LYS Q 747 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU Q 752 " --> pdb=" O ALA Q 748 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU Q 758 " --> pdb=" O GLU Q 754 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY Q 759 " --> pdb=" O ALA Q 755 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE Q 760 " --> pdb=" O LEU Q 756 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Q 764 " --> pdb=" O ILE Q 760 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY Q 765 " --> pdb=" O ALA Q 761 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR Q 769 " --> pdb=" O GLY Q 765 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS Q 774 " --> pdb=" O ASN Q 770 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU Q 775 " --> pdb=" O ARG Q 771 " (cutoff:3.500A) Processing helix chain 'Q' and resid 792 through 797 Processing helix chain 'Q' and resid 801 through 810 Processing helix chain 'Q' and resid 814 through 817 No H-bonds generated for 'chain 'Q' and resid 814 through 817' Processing helix chain 'Q' and resid 819 through 822 No H-bonds generated for 'chain 'Q' and resid 819 through 822' Processing helix chain 'Q' and resid 826 through 841 removed outlier: 3.612A pdb=" N MET Q 840 " --> pdb=" O ILE Q 836 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN Q 841 " --> pdb=" O ASP Q 837 " (cutoff:3.500A) Processing helix chain 'Q' and resid 843 through 863 Proline residue: Q 851 - end of helix removed outlier: 3.732A pdb=" N PHE Q 859 " --> pdb=" O LYS Q 855 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS Q 862 " --> pdb=" O PHE Q 858 " (cutoff:3.500A) Processing helix chain 'Q' and resid 865 through 868 No H-bonds generated for 'chain 'Q' and resid 865 through 868' Processing helix chain 'Q' and resid 874 through 915 removed outlier: 3.738A pdb=" N ARG Q 882 " --> pdb=" O LEU Q 878 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU Q 886 " --> pdb=" O ARG Q 882 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU Q 898 " --> pdb=" O THR Q 894 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE Q 900 " --> pdb=" O ASP Q 896 " (cutoff:3.500A) Processing helix chain 'R' and resid 650 through 674 removed outlier: 3.949A pdb=" N VAL R 663 " --> pdb=" O ALA R 659 " (cutoff:3.500A) Processing helix chain 'R' and resid 678 through 688 Processing helix chain 'R' and resid 691 through 703 Processing helix chain 'R' and resid 722 through 729 Processing helix chain 'R' and resid 733 through 747 removed outlier: 3.556A pdb=" N ASN R 747 " --> pdb=" O CYS R 743 " (cutoff:3.500A) Processing helix chain 'R' and resid 750 through 765 removed outlier: 3.642A pdb=" N HIS R 753 " --> pdb=" O ALA R 750 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR R 754 " --> pdb=" O LYS R 751 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE R 755 " --> pdb=" O THR R 752 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG R 758 " --> pdb=" O ILE R 755 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET R 765 " --> pdb=" O CYS R 762 " (cutoff:3.500A) Processing helix chain 'R' and resid 769 through 774 removed outlier: 3.501A pdb=" N SER R 773 " --> pdb=" O ILE R 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 778 through 816 removed outlier: 4.423A pdb=" N ALA R 784 " --> pdb=" O LYS R 780 " (cutoff:3.500A) Proline residue: R 787 - end of helix removed outlier: 4.051A pdb=" N TYR R 804 " --> pdb=" O VAL R 800 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE R 805 " --> pdb=" O GLU R 801 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU R 806 " --> pdb=" O GLN R 802 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP R 807 " --> pdb=" O SER R 803 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU R 816 " --> pdb=" O GLU R 812 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 26 removed outlier: 3.574A pdb=" N PHE S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 37 Processing helix chain 'S' and resid 128 through 131 No H-bonds generated for 'chain 'S' and resid 128 through 131' Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'S' and resid 157 through 171 Processing helix chain 'S' and resid 176 through 180 removed outlier: 3.557A pdb=" N ASP S 180 " --> pdb=" O LYS S 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 176 through 180' Processing helix chain 'S' and resid 207 through 213 removed outlier: 3.792A pdb=" N ILE S 211 " --> pdb=" O ALA S 207 " (cutoff:3.500A) Processing helix chain 'S' and resid 473 through 475 No H-bonds generated for 'chain 'S' and resid 473 through 475' Processing helix chain 'S' and resid 499 through 502 No H-bonds generated for 'chain 'S' and resid 499 through 502' Processing helix chain 'T' and resid 657 through 659 No H-bonds generated for 'chain 'T' and resid 657 through 659' Processing helix chain 'T' and resid 730 through 735 Processing helix chain 'T' and resid 816 through 825 Processing helix chain 'T' and resid 831 through 839 removed outlier: 4.144A pdb=" N ALA T 835 " --> pdb=" O SER T 831 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR T 836 " --> pdb=" O SER T 832 " (cutoff:3.500A) Processing helix chain 'T' and resid 845 through 848 No H-bonds generated for 'chain 'T' and resid 845 through 848' Processing helix chain 'T' and resid 859 through 871 Processing helix chain 'T' and resid 878 through 897 removed outlier: 3.762A pdb=" N GLU T 882 " --> pdb=" O PHE T 878 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY T 893 " --> pdb=" O PHE T 889 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP T 894 " --> pdb=" O LYS T 890 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL T 895 " --> pdb=" O ALA T 891 " (cutoff:3.500A) Processing helix chain 'T' and resid 903 through 938 removed outlier: 4.739A pdb=" N LYS T 918 " --> pdb=" O ASP T 914 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU T 919 " --> pdb=" O VAL T 915 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP T 920 " --> pdb=" O HIS T 916 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG T 921 " --> pdb=" O LYS T 917 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU T 922 " --> pdb=" O LYS T 918 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP T 923 " --> pdb=" O GLU T 919 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE T 928 " --> pdb=" O ASP T 924 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 53 Processing helix chain 'U' and resid 190 through 192 No H-bonds generated for 'chain 'U' and resid 190 through 192' Processing helix chain 'U' and resid 388 through 403 Processing helix chain 'U' and resid 408 through 414 removed outlier: 3.928A pdb=" N ILE U 413 " --> pdb=" O GLU U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 421 through 437 Processing helix chain 'W' and resid 88 through 94 removed outlier: 3.629A pdb=" N SER W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER W 94 " --> pdb=" O GLU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 101 Processing helix chain 'W' and resid 358 through 360 No H-bonds generated for 'chain 'W' and resid 358 through 360' Processing helix chain 'W' and resid 422 through 434 removed outlier: 3.669A pdb=" N VAL W 430 " --> pdb=" O GLN W 426 " (cutoff:3.500A) Processing helix chain 'W' and resid 439 through 441 No H-bonds generated for 'chain 'W' and resid 439 through 441' Processing helix chain 'Z' and resid 7 through 10 No H-bonds generated for 'chain 'Z' and resid 7 through 10' Processing helix chain 'Z' and resid 25 through 36 removed outlier: 6.025A pdb=" N ASP Z 29 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR Z 36 " --> pdb=" O MET Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 61 removed outlier: 4.138A pdb=" N ILE Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP Z 53 " --> pdb=" O ARG Z 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS Z 60 " --> pdb=" O ARG Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 84 removed outlier: 3.829A pdb=" N LYS Z 73 " --> pdb=" O PRO Z 69 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS Z 81 " --> pdb=" O LEU Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 99 removed outlier: 3.626A pdb=" N GLU Z 98 " --> pdb=" O SER Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 107 Processing helix chain 'Z' and resid 111 through 118 Processing helix chain 'Z' and resid 124 through 132 Processing helix chain 'A' and resid 428 through 451 Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.277A pdb=" N SER D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 39 removed outlier: 4.027A pdb=" N ASN a 39 " --> pdb=" O GLN a 35 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 44 No H-bonds generated for 'chain 'a' and resid 41 through 44' Processing helix chain 'a' and resid 60 through 69 removed outlier: 3.554A pdb=" N ASP a 68 " --> pdb=" O GLU a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 85 removed outlier: 4.516A pdb=" N LEU a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 112 removed outlier: 4.210A pdb=" N SER a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 133 Processing helix chain 'a' and resid 135 through 139 removed outlier: 4.149A pdb=" N LEU a 138 " --> pdb=" O GLY a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 163 removed outlier: 3.573A pdb=" N LEU a 152 " --> pdb=" O GLU a 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY a 153 " --> pdb=" O ARG a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 203 removed outlier: 4.012A pdb=" N GLN a 183 " --> pdb=" O ALA a 179 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN a 189 " --> pdb=" O ASP a 185 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP a 201 " --> pdb=" O GLU a 197 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS a 202 " --> pdb=" O TRP a 198 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 209 removed outlier: 3.707A pdb=" N LYS a 208 " --> pdb=" O GLU a 205 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 219 Processing helix chain 'a' and resid 243 through 253 removed outlier: 3.544A pdb=" N UNK a 251 " --> pdb=" O UNK a 247 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 299 Processing helix chain 'a' and resid 301 through 306 Processing helix chain 'a' and resid 309 through 318 removed outlier: 3.814A pdb=" N SER a 317 " --> pdb=" O ALA a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 326 removed outlier: 4.153A pdb=" N SER a 326 " --> pdb=" O THR a 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 392 removed outlier: 3.726A pdb=" N SER a 376 " --> pdb=" O LYS a 372 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG a 377 " --> pdb=" O GLY a 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA a 380 " --> pdb=" O SER a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 414 removed outlier: 3.596A pdb=" N GLN a 407 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL a 408 " --> pdb=" O LEU a 404 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG a 411 " --> pdb=" O GLN a 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 28 removed outlier: 4.387A pdb=" N UNK b 27 " --> pdb=" O UNK b 23 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N UNK b 28 " --> pdb=" O UNK b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 41 Processing helix chain 'b' and resid 54 through 66 Processing helix chain 'b' and resid 71 through 77 removed outlier: 4.109A pdb=" N UNK b 76 " --> pdb=" O UNK b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 98 removed outlier: 4.552A pdb=" N UNK b 96 " --> pdb=" O UNK b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 124 Processing helix chain 'b' and resid 134 through 152 removed outlier: 3.643A pdb=" N LYS b 151 " --> pdb=" O ILE b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 186 removed outlier: 4.043A pdb=" N ALA b 166 " --> pdb=" O MET b 162 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA b 168 " --> pdb=" O ILE b 164 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG b 183 " --> pdb=" O THR b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 194 through 198 removed outlier: 4.123A pdb=" N ILE b 198 " --> pdb=" O LEU b 195 " (cutoff:3.500A) Processing helix chain 'b' and resid 202 through 212 removed outlier: 4.085A pdb=" N LEU b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 215 through 220 removed outlier: 3.852A pdb=" N SER b 219 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU b 220 " --> pdb=" O SER b 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 215 through 220' Processing helix chain 'b' and resid 231 through 240 removed outlier: 3.671A pdb=" N GLU b 240 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 253 No H-bonds generated for 'chain 'b' and resid 251 through 253' Processing helix chain 'b' and resid 255 through 283 removed outlier: 3.519A pdb=" N ALA b 259 " --> pdb=" O ILE b 255 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU b 260 " --> pdb=" O ASN b 256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL b 263 " --> pdb=" O ALA b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 303 removed outlier: 4.450A pdb=" N ILE b 300 " --> pdb=" O GLY b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 314 through 318 Processing helix chain 'b' and resid 323 through 330 Processing helix chain 'b' and resid 340 through 344 removed outlier: 3.635A pdb=" N HIS b 344 " --> pdb=" O LEU b 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 375 removed outlier: 3.790A pdb=" N LYS b 358 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE b 359 " --> pdb=" O LYS b 356 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU b 363 " --> pdb=" O ALA b 360 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA b 367 " --> pdb=" O ALA b 364 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU b 371 " --> pdb=" O ALA b 368 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG b 372 " --> pdb=" O VAL b 369 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA b 375 " --> pdb=" O ARG b 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 385 through 401 removed outlier: 3.683A pdb=" N LYS b 393 " --> pdb=" O GLU b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 429 through 431 No H-bonds generated for 'chain 'b' and resid 429 through 431' Processing helix chain 'c' and resid 150 through 157 Processing helix chain 'c' and resid 181 through 188 Processing helix chain 'c' and resid 201 through 210 removed outlier: 3.810A pdb=" N GLU c 206 " --> pdb=" O ARG c 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 Proline residue: c 227 - end of helix Processing helix chain 'c' and resid 249 through 257 removed outlier: 4.360A pdb=" N ASN c 256 " --> pdb=" O ILE c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 273 through 276 No H-bonds generated for 'chain 'c' and resid 273 through 276' Processing helix chain 'c' and resid 282 through 296 removed outlier: 4.310A pdb=" N PHE c 286 " --> pdb=" O ALA c 282 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN c 291 " --> pdb=" O ALA c 287 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU c 296 " --> pdb=" O LYS c 292 " (cutoff:3.500A) Processing helix chain 'd' and resid 150 through 157 Processing helix chain 'd' and resid 176 through 178 No H-bonds generated for 'chain 'd' and resid 176 through 178' Processing helix chain 'd' and resid 181 through 188 Processing helix chain 'd' and resid 204 through 211 Processing helix chain 'd' and resid 227 through 230 Processing helix chain 'd' and resid 247 through 257 removed outlier: 4.709A pdb=" N ALA d 250 " --> pdb=" O PRO d 247 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE d 252 " --> pdb=" O GLN d 249 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE d 253 " --> pdb=" O ALA d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 282 through 296 removed outlier: 3.535A pdb=" N ARG d 288 " --> pdb=" O THR d 284 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU d 295 " --> pdb=" O GLN d 291 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU d 296 " --> pdb=" O LYS d 292 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 27 Processing helix chain 'e' and resid 37 through 45 removed outlier: 3.779A pdb=" N LYS e 42 " --> pdb=" O ASN e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 64 removed outlier: 3.737A pdb=" N LEU e 64 " --> pdb=" O ILE e 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 61 through 64' Processing helix chain 'e' and resid 66 through 73 Processing helix chain 'e' and resid 84 through 90 Processing helix chain 'e' and resid 111 through 124 removed outlier: 3.851A pdb=" N VAL e 117 " --> pdb=" O GLN e 113 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 30 Processing helix chain 'f' and resid 36 through 46 removed outlier: 3.772A pdb=" N LYS f 42 " --> pdb=" O ASN f 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 62 through 64 No H-bonds generated for 'chain 'f' and resid 62 through 64' Processing helix chain 'f' and resid 66 through 73 Processing helix chain 'f' and resid 85 through 91 Processing helix chain 'f' and resid 111 through 124 removed outlier: 4.072A pdb=" N TYR f 115 " --> pdb=" O LYS f 111 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS f 120 " --> pdb=" O ALA f 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 136 through 138 No H-bonds generated for 'chain 'g' and resid 136 through 138' Processing helix chain 'g' and resid 448 through 452 Processing helix chain 'g' and resid 457 through 459 No H-bonds generated for 'chain 'g' and resid 457 through 459' Processing helix chain 'x' and resid 1 through 22 Processing sheet with id= A, first strand: chain 'H' and resid 43 through 47 removed outlier: 5.729A pdb=" N SER H 56 " --> pdb=" O CYS H 62 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N CYS H 62 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 116 through 120 Processing sheet with id= C, first strand: chain 'H' and resid 191 through 193 removed outlier: 4.054A pdb=" N TYR H 151 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR H 156 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU H 141 " --> pdb=" O THR H 156 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 207 through 210 Processing sheet with id= E, first strand: chain 'H' and resid 290 through 294 removed outlier: 5.092A pdb=" N VAL H 279 " --> pdb=" O PHE H 275 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 321 through 325 removed outlier: 3.654A pdb=" N MET H 321 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 330 " --> pdb=" O GLN H 325 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 353 through 358 Processing sheet with id= H, first strand: chain 'H' and resid 449 through 451 removed outlier: 6.346A pdb=" N ASP H 461 " --> pdb=" O GLN H 467 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLN H 467 " --> pdb=" O ASP H 461 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 494 through 500 removed outlier: 6.786A pdb=" N TYR H 510 " --> pdb=" O THR H 496 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU H 498 " --> pdb=" O ILE H 508 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE H 508 " --> pdb=" O LEU H 498 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE H 500 " --> pdb=" O TRP H 506 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TRP H 506 " --> pdb=" O PHE H 500 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR H 545 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR H 533 " --> pdb=" O LEU H 543 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU H 543 " --> pdb=" O THR H 533 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 559 through 563 removed outlier: 4.626A pdb=" N GLY H 572 " --> pdb=" O SER H 563 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 612 through 615 Processing sheet with id= L, first strand: chain 'H' and resid 661 through 663 removed outlier: 3.801A pdb=" N THR H 661 " --> pdb=" O ALA H 673 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN H 682 " --> pdb=" O VAL H 688 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL H 688 " --> pdb=" O ASN H 682 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 712 through 714 removed outlier: 3.500A pdb=" N GLY H 755 " --> pdb=" O ILE H 745 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 766 through 769 Processing sheet with id= O, first strand: chain 'I' and resid 57 through 60 removed outlier: 3.848A pdb=" N UNK I 57 " --> pdb=" O UNK I 71 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 141 through 143 Processing sheet with id= Q, first strand: chain 'I' and resid 186 through 188 removed outlier: 3.860A pdb=" N UNK I 198 " --> pdb=" O UNK I 188 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 218 through 220 removed outlier: 5.704A pdb=" N UNK I 232 " --> pdb=" O UNK I 238 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N UNK I 238 " --> pdb=" O UNK I 232 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 251 through 253 Processing sheet with id= T, first strand: chain 'I' and resid 301 through 306 removed outlier: 3.908A pdb=" N UNK I 310 " --> pdb=" O UNK I 306 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N UNK I 323 " --> pdb=" O UNK I 313 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N UNK I 315 " --> pdb=" O UNK I 321 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N UNK I 321 " --> pdb=" O UNK I 315 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 333 through 336 removed outlier: 3.597A pdb=" N UNK I 30 " --> pdb=" O UNK I 355 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 34 through 37 removed outlier: 3.594A pdb=" N LEU J 326 " --> pdb=" O LEU J 322 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.724A pdb=" N PHE J 55 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG J 62 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER J 67 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL J 73 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 104 through 107 Processing sheet with id= Y, first strand: chain 'J' and resid 130 through 132 Processing sheet with id= Z, first strand: chain 'J' and resid 207 through 209 removed outlier: 3.783A pdb=" N THR J 173 " --> pdb=" O GLY J 187 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 215 through 220 removed outlier: 6.597A pdb=" N CYS J 229 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL J 218 " --> pdb=" O VAL J 227 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL J 227 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA J 220 " --> pdb=" O GLN J 225 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLN J 225 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE J 234 " --> pdb=" O ARG J 248 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR J 246 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP J 238 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS J 244 " --> pdb=" O ASP J 238 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 258 through 262 Processing sheet with id= AC, first strand: chain 'L' and resid 27 through 33 removed outlier: 7.870A pdb=" N VAL L 22 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL L 5 " --> pdb=" O VAL L 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 63 through 65 removed outlier: 3.858A pdb=" N TYR L 97 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER L 89 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL L 95 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 110 through 113 removed outlier: 3.618A pdb=" N GLN L 128 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN L 138 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP L 130 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU L 136 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 150 through 152 Processing sheet with id= AG, first strand: chain 'L' and resid 191 through 196 removed outlier: 6.527A pdb=" N GLY L 205 " --> pdb=" O SER L 192 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU L 194 " --> pdb=" O ILE L 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE L 203 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL L 196 " --> pdb=" O PHE L 201 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE L 201 " --> pdb=" O VAL L 196 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA L 206 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE L 211 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP L 216 " --> pdb=" O THR L 222 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR L 222 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 325 through 330 removed outlier: 6.341A pdb=" N LYS L 278 " --> pdb=" O TYR L 326 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL L 328 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLN L 280 " --> pdb=" O VAL L 328 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE L 330 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL L 282 " --> pdb=" O ILE L 330 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS L 277 " --> pdb=" O ILE L 255 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER L 252 " --> pdb=" O THR L 248 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 295 through 297 removed outlier: 3.539A pdb=" N LEU L 300 " --> pdb=" O ASN L 297 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 46 through 51 removed outlier: 6.067A pdb=" N GLY N 70 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU N 49 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA N 68 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE N 51 " --> pdb=" O ARG N 66 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG N 66 " --> pdb=" O PHE N 51 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN N 80 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN N 87 " --> pdb=" O ASN N 80 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 101 through 105 removed outlier: 3.613A pdb=" N GLY N 101 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU N 114 " --> pdb=" O TRP N 126 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP N 127 " --> pdb=" O PRO N 133 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'N' and resid 144 through 149 removed outlier: 6.624A pdb=" N GLY N 159 " --> pdb=" O TRP N 145 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE N 147 " --> pdb=" O SER N 157 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER N 157 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE N 149 " --> pdb=" O LYS N 155 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS N 155 " --> pdb=" O ILE N 149 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP N 169 " --> pdb=" O HIS N 179 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS N 179 " --> pdb=" O ASP N 169 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 193 through 195 removed outlier: 3.624A pdb=" N HIS N 227 " --> pdb=" O ILE N 212 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER N 214 " --> pdb=" O LEU N 225 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU N 225 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 261 through 263 Processing sheet with id= AO, first strand: chain 'N' and resid 294 through 298 removed outlier: 3.596A pdb=" N SER N 297 " --> pdb=" O PHE N 305 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE N 305 " --> pdb=" O SER N 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER N 324 " --> pdb=" O GLN N 306 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER N 308 " --> pdb=" O ASN N 322 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN N 322 " --> pdb=" O SER N 308 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 335 through 339 Processing sheet with id= AQ, first strand: chain 'N' and resid 382 through 385 removed outlier: 4.223A pdb=" N VAL N 399 " --> pdb=" O LEU N 420 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR N 403 " --> pdb=" O LEU N 416 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU N 416 " --> pdb=" O THR N 403 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 439 through 443 Processing sheet with id= AS, first strand: chain 'N' and resid 495 through 497 removed outlier: 3.980A pdb=" N VAL N 495 " --> pdb=" O VAL N 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 511 " --> pdb=" O VAL N 495 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 534 through 536 Processing sheet with id= AU, first strand: chain 'N' and resid 572 through 576 removed outlier: 3.765A pdb=" N ALA N 572 " --> pdb=" O ILE N 585 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER N 581 " --> pdb=" O ASN N 576 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'N' and resid 645 through 649 Processing sheet with id= AW, first strand: chain 'N' and resid 744 through 746 Processing sheet with id= AX, first strand: chain 'N' and resid 475 through 480 removed outlier: 6.828A pdb=" N CYS N 489 " --> pdb=" O LYS N 476 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL N 478 " --> pdb=" O VAL N 487 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL N 487 " --> pdb=" O VAL N 478 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 28 through 32 Processing sheet with id= AZ, first strand: chain 'O' and resid 58 through 63 removed outlier: 6.731A pdb=" N ILE O 73 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE O 61 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE O 71 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU O 63 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU O 69 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN O 83 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL O 89 " --> pdb=" O ASN O 83 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'O' and resid 102 through 104 removed outlier: 6.073A pdb=" N LYS O 123 " --> pdb=" O ARG O 138 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG O 138 " --> pdb=" O LYS O 123 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'O' and resid 170 through 173 Processing sheet with id= BC, first strand: chain 'O' and resid 194 through 199 removed outlier: 6.887A pdb=" N VAL O 209 " --> pdb=" O MET O 195 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA O 197 " --> pdb=" O TYR O 207 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR O 207 " --> pdb=" O ALA O 197 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE O 199 " --> pdb=" O LYS O 205 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS O 205 " --> pdb=" O PHE O 199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA O 214 " --> pdb=" O SER O 210 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS O 252 " --> pdb=" O VAL O 217 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU O 219 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE O 250 " --> pdb=" O GLU O 219 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'O' and resid 286 through 288 Processing sheet with id= BE, first strand: chain 'O' and resid 283 through 285 Processing sheet with id= BF, first strand: chain 'O' and resid 317 through 321 removed outlier: 5.621A pdb=" N GLU O 331 " --> pdb=" O TYR O 337 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR O 337 " --> pdb=" O GLU O 331 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 351 through 353 Processing sheet with id= BH, first strand: chain 'O' and resid 401 through 405 Processing sheet with id= BI, first strand: chain 'O' and resid 435 through 438 removed outlier: 3.583A pdb=" N ASP O 467 " --> pdb=" O VAL O 457 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'O' and resid 479 through 481 Processing sheet with id= BK, first strand: chain 'O' and resid 529 through 533 removed outlier: 5.955A pdb=" N ASN O 543 " --> pdb=" O GLN O 549 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN O 549 " --> pdb=" O ASN O 543 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'O' and resid 582 through 585 removed outlier: 3.737A pdb=" N LYS O 613 " --> pdb=" O LEU O 603 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP O 605 " --> pdb=" O LEU O 611 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU O 611 " --> pdb=" O ASP O 605 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'O' and resid 6 through 11 removed outlier: 6.597A pdb=" N ILE O 703 " --> pdb=" O SER O 8 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU O 10 " --> pdb=" O LEU O 701 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU O 701 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 683 " --> pdb=" O ALA O 696 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Q' and resid 116 through 118 removed outlier: 3.618A pdb=" N VAL Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Q' and resid 136 through 139 removed outlier: 3.568A pdb=" N VAL Q 147 " --> pdb=" O TYR Q 157 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR Q 157 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP Q 149 " --> pdb=" O GLY Q 155 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY Q 155 " --> pdb=" O ASP Q 149 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 168 through 172 removed outlier: 3.642A pdb=" N TRP Q 176 " --> pdb=" O GLN Q 172 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Q' and resid 216 through 220 Processing sheet with id= BR, first strand: chain 'Q' and resid 256 through 260 removed outlier: 6.887A pdb=" N GLN Q 275 " --> pdb=" O LEU Q 257 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE Q 259 " --> pdb=" O TYR Q 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR Q 273 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR Q 280 " --> pdb=" O ASN Q 276 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG Q 285 " --> pdb=" O PRO Q 328 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Q' and resid 362 through 368 Processing sheet with id= BT, first strand: chain 'Q' and resid 415 through 418 Processing sheet with id= BU, first strand: chain 'Q' and resid 454 through 458 removed outlier: 3.730A pdb=" N THR Q 435 " --> pdb=" O GLY Q 448 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'Q' and resid 527 through 529 removed outlier: 4.328A pdb=" N THR Q 496 " --> pdb=" O SER Q 492 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Q' and resid 500 through 503 Processing sheet with id= BX, first strand: chain 'Q' and resid 537 through 539 Processing sheet with id= BY, first strand: chain 'Q' and resid 576 through 580 removed outlier: 6.971A pdb=" N SER Q 591 " --> pdb=" O LEU Q 577 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE Q 579 " --> pdb=" O ILE Q 589 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE Q 589 " --> pdb=" O ILE Q 579 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR Q 590 " --> pdb=" O LYS Q 598 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS Q 598 " --> pdb=" O THR Q 590 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY Q 601 " --> pdb=" O CYS Q 607 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS Q 607 " --> pdb=" O GLY Q 601 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'Q' and resid 621 through 624 removed outlier: 3.759A pdb=" N LYS Q 622 " --> pdb=" O PHE Q 631 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE Q 631 " --> pdb=" O LYS Q 622 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN Q 629 " --> pdb=" O LEU Q 624 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Q' and resid 663 through 665 removed outlier: 3.789A pdb=" N ALA Q 12 " --> pdb=" O ILE Q 683 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU Q 685 " --> pdb=" O GLN Q 10 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN Q 10 " --> pdb=" O GLU Q 685 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR Q 687 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE Q 8 " --> pdb=" O THR Q 687 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'R' and resid 36 through 41 Processing sheet with id= CC, first strand: chain 'R' and resid 78 through 82 removed outlier: 3.904A pdb=" N UNK R 86 " --> pdb=" O UNK R 82 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'R' and resid 112 through 115 removed outlier: 3.558A pdb=" N UNK R 112 " --> pdb=" O UNK R 125 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'R' and resid 166 through 171 Processing sheet with id= CF, first strand: chain 'R' and resid 200 through 202 Processing sheet with id= CG, first strand: chain 'R' and resid 279 through 281 removed outlier: 4.408A pdb=" N UNK R 279 " --> pdb=" O UNK R 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK R 248 " --> pdb=" O UNK R 261 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'R' and resid 376 through 379 Processing sheet with id= CI, first strand: chain 'R' and resid 429 through 433 removed outlier: 3.772A pdb=" N UNK R 447 " --> pdb=" O UNK R 440 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'R' and resid 500 through 502 removed outlier: 3.684A pdb=" N UNK R 500 " --> pdb=" O UNK R 513 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N UNK R 521 " --> pdb=" O UNK R 532 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK R 532 " --> pdb=" O UNK R 521 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N UNK R 523 " --> pdb=" O UNK R 530 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N UNK R 530 " --> pdb=" O UNK R 523 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'R' and resid 577 through 580 removed outlier: 4.456A pdb=" N UNK R 563 " --> pdb=" O UNK R 559 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N UNK R 559 " --> pdb=" O UNK R 563 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK R 567 " --> pdb=" O UNK R 555 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'S' and resid 134 through 136 Processing sheet with id= CM, first strand: chain 'S' and resid 235 through 237 removed outlier: 4.080A pdb=" N SER S 567 " --> pdb=" O GLY S 580 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'S' and resid 253 through 256 removed outlier: 3.650A pdb=" N THR S 286 " --> pdb=" O ILE S 274 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS S 276 " --> pdb=" O LEU S 284 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU S 284 " --> pdb=" O HIS S 276 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'S' and resid 297 through 300 Processing sheet with id= CP, first strand: chain 'S' and resid 358 through 364 removed outlier: 4.461A pdb=" N ASN S 385 " --> pdb=" O LEU S 377 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET S 396 " --> pdb=" O ILE S 386 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS S 388 " --> pdb=" O TRP S 394 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP S 394 " --> pdb=" O HIS S 388 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'S' and resid 404 through 413 removed outlier: 6.781A pdb=" N VAL S 426 " --> pdb=" O THR S 405 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE S 407 " --> pdb=" O ILE S 424 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE S 424 " --> pdb=" O PHE S 407 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE S 409 " --> pdb=" O ILE S 422 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE S 422 " --> pdb=" O ILE S 409 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR S 411 " --> pdb=" O ARG S 420 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG S 420 " --> pdb=" O TYR S 411 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU S 431 " --> pdb=" O ASN S 427 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG S 445 " --> pdb=" O GLU S 434 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP S 436 " --> pdb=" O VAL S 443 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL S 443 " --> pdb=" O ASP S 436 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'S' and resid 458 through 461 Processing sheet with id= CS, first strand: chain 'S' and resid 529 through 532 Processing sheet with id= CT, first strand: chain 'R' and resid 331 through 336 removed outlier: 7.044A pdb=" N UNK R 346 " --> pdb=" O UNK R 332 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N UNK R 334 " --> pdb=" O UNK R 344 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N UNK R 344 " --> pdb=" O UNK R 334 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'R' and resid 588 through 593 removed outlier: 6.754A pdb=" N UNK R 602 " --> pdb=" O UNK R 589 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N UNK R 591 " --> pdb=" O UNK R 600 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N UNK R 600 " --> pdb=" O UNK R 591 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'T' and resid 40 through 44 removed outlier: 6.051A pdb=" N ASP T 62 " --> pdb=" O LEU T 68 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU T 68 " --> pdb=" O ASP T 62 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'T' and resid 82 through 86 removed outlier: 6.809A pdb=" N LYS T 102 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU T 106 " --> pdb=" O LYS T 102 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'T' and resid 118 through 124 removed outlier: 6.511A pdb=" N SER T 131 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU T 121 " --> pdb=" O CYS T 129 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N CYS T 129 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE T 123 " --> pdb=" O TYR T 127 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N TYR T 127 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS T 141 " --> pdb=" O PHE T 153 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE T 153 " --> pdb=" O LYS T 141 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'T' and resid 167 through 171 removed outlier: 6.852A pdb=" N VAL T 183 " --> pdb=" O VAL T 168 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU T 170 " --> pdb=" O THR T 181 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR T 181 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN T 192 " --> pdb=" O LEU T 198 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU T 198 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'T' and resid 209 through 213 removed outlier: 6.442A pdb=" N GLY T 224 " --> pdb=" O THR T 210 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA T 212 " --> pdb=" O ALA T 222 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA T 222 " --> pdb=" O ALA T 212 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU T 229 " --> pdb=" O THR T 225 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG T 242 " --> pdb=" O MET T 232 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'T' and resid 251 through 257 removed outlier: 6.417A pdb=" N GLY T 267 " --> pdb=" O SER T 252 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU T 254 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER T 265 " --> pdb=" O LEU T 254 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE T 256 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS T 263 " --> pdb=" O PHE T 256 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS T 285 " --> pdb=" O PHE T 275 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP T 277 " --> pdb=" O ARG T 283 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ARG T 283 " --> pdb=" O ASP T 277 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'T' and resid 345 through 347 removed outlier: 4.037A pdb=" N SER T 318 " --> pdb=" O GLY T 314 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'T' and resid 322 through 324 Processing sheet with id= DD, first strand: chain 'T' and resid 375 through 379 Processing sheet with id= DE, first strand: chain 'T' and resid 454 through 456 removed outlier: 7.044A pdb=" N PHE T 439 " --> pdb=" O HIS T 434 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS T 434 " --> pdb=" O PHE T 439 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA T 416 " --> pdb=" O ALA T 433 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'T' and resid 463 through 468 removed outlier: 7.044A pdb=" N GLY T 478 " --> pdb=" O LYS T 464 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL T 466 " --> pdb=" O PHE T 476 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE T 476 " --> pdb=" O VAL T 466 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET T 468 " --> pdb=" O PHE T 474 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE T 474 " --> pdb=" O MET T 468 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER T 483 " --> pdb=" O SER T 479 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS T 496 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN T 488 " --> pdb=" O LEU T 494 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU T 494 " --> pdb=" O ASN T 488 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'T' and resid 505 through 510 removed outlier: 6.200A pdb=" N CYS T 520 " --> pdb=" O THR T 506 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE T 508 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL T 518 " --> pdb=" O ILE T 508 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU T 510 " --> pdb=" O LYS T 516 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS T 516 " --> pdb=" O LEU T 510 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE T 525 " --> pdb=" O GLY T 521 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP T 530 " --> pdb=" O LEU T 536 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU T 536 " --> pdb=" O ASP T 530 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'T' and resid 550 through 552 removed outlier: 3.707A pdb=" N LEU T 557 " --> pdb=" O HIS T 552 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP T 571 " --> pdb=" O VAL T 577 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL T 577 " --> pdb=" O ASP T 571 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'T' and resid 588 through 593 removed outlier: 6.943A pdb=" N ALA T 603 " --> pdb=" O THR T 589 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE T 591 " --> pdb=" O VAL T 601 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL T 601 " --> pdb=" O PHE T 591 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE T 593 " --> pdb=" O TRP T 599 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP T 599 " --> pdb=" O PHE T 593 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR T 608 " --> pdb=" O SER T 604 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP T 613 " --> pdb=" O CYS T 619 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS T 619 " --> pdb=" O ASP T 613 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'T' and resid 24 through 30 removed outlier: 6.743A pdb=" N ILE T 653 " --> pdb=" O PHE T 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE T 29 " --> pdb=" O ILE T 651 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE T 651 " --> pdb=" O ILE T 29 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'U' and resid 70 through 74 removed outlier: 6.892A pdb=" N GLY U 86 " --> pdb=" O TYR U 71 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE U 73 " --> pdb=" O ALA U 84 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA U 84 " --> pdb=" O ILE U 73 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL U 91 " --> pdb=" O SER U 87 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN U 96 " --> pdb=" O GLU U 102 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU U 102 " --> pdb=" O ASN U 96 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'U' and resid 175 through 177 removed outlier: 5.583A pdb=" N THR U 144 " --> pdb=" O SER U 140 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY U 115 " --> pdb=" O CYS U 139 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'U' and resid 184 through 188 Processing sheet with id= DN, first strand: chain 'U' and resid 225 through 227 removed outlier: 3.732A pdb=" N GLN U 256 " --> pdb=" O LEU U 246 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP U 248 " --> pdb=" O PRO U 254 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'U' and resid 267 through 269 Processing sheet with id= DP, first strand: chain 'U' and resid 341 through 343 Processing sheet with id= DQ, first strand: chain 'U' and resid 362 through 365 removed outlier: 4.767A pdb=" N VAL U 372 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY U 60 " --> pdb=" O LEU U 374 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG U 376 " --> pdb=" O PHE U 58 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE U 58 " --> pdb=" O ARG U 376 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'W' and resid 105 through 107 removed outlier: 3.722A pdb=" N ASN W 380 " --> pdb=" O GLY W 393 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'W' and resid 114 through 118 removed outlier: 3.806A pdb=" N HIS W 133 " --> pdb=" O GLY W 129 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP W 138 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU W 144 " --> pdb=" O ASP W 138 " (cutoff:3.500A) Processing sheet with id= DT, first strand: chain 'W' and resid 156 through 159 removed outlier: 3.630A pdb=" N SER W 156 " --> pdb=" O ALA W 169 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'W' and resid 195 through 199 removed outlier: 3.530A pdb=" N SER W 226 " --> pdb=" O TYR W 216 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id= DV, first strand: chain 'W' and resid 237 through 240 removed outlier: 3.526A pdb=" N THR W 255 " --> pdb=" O HIS W 251 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain 'W' and resid 297 through 302 removed outlier: 4.204A pdb=" N SER W 297 " --> pdb=" O GLY W 293 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain 'W' and resid 321 through 324 Processing sheet with id= ), first strand: chain 'Z' and resid 136 through 138 Processing sheet with id= *, first strand: chain 'a' and resid 6 through 10 removed outlier: 6.151A pdb=" N LYS a 19 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU a 50 " --> pdb=" O LYS a 19 " (cutoff:3.500A) Processing sheet with id= +, first strand: chain 'a' and resid 96 through 99 Processing sheet with id= ,, first strand: chain 'b' and resid 86 through 88 removed outlier: 6.508A pdb=" N UNK b 104 " --> pdb=" O UNK b 87 " (cutoff:3.500A) No H-bonds generated for sheet with id= , Processing sheet with id= -, first strand: chain 'c' and resid 122 through 125 Processing sheet with id= ., first strand: chain 'c' and resid 239 through 242 removed outlier: 6.032A pdb=" N VAL c 193 " --> pdb=" O VAL c 170 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR c 172 " --> pdb=" O VAL c 193 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR c 195 " --> pdb=" O TYR c 172 " (cutoff:3.500A) Processing sheet with id= /, first strand: chain 'c' and resid 266 through 272 removed outlier: 6.418A pdb=" N ARG c 319 " --> pdb=" O PRO c 300 " (cutoff:3.500A) Processing sheet with id= 0, first strand: chain 'd' and resid 87 through 90 Processing sheet with id= 1, first strand: chain 'd' and resid 194 through 197 removed outlier: 6.707A pdb=" N VAL d 170 " --> pdb=" O TYR d 195 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL d 197 " --> pdb=" O VAL d 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR d 172 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS d 239 " --> pdb=" O LEU d 171 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU d 173 " --> pdb=" O CYS d 239 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE d 241 " --> pdb=" O LEU d 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'd' and resid 265 through 272 removed outlier: 3.600A pdb=" N GLY d 265 " --> pdb=" O TYR d 320 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS d 313 " --> pdb=" O LEU d 306 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG d 319 " --> pdb=" O PRO d 300 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'e' and resid 33 through 35 Processing sheet with id= 4, first strand: chain 'f' and resid 49 through 54 removed outlier: 6.626A pdb=" N ILE f 102 " --> pdb=" O GLU f 50 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE f 52 " --> pdb=" O ALA f 100 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA f 100 " --> pdb=" O ILE f 52 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'g' and resid 146 through 150 removed outlier: 4.069A pdb=" N ILE g 563 " --> pdb=" O THR g 150 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'g' and resid 157 through 163 removed outlier: 6.990A pdb=" N VAL g 190 " --> pdb=" O THR g 158 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE g 160 " --> pdb=" O TYR g 188 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR g 188 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N CYS g 162 " --> pdb=" O PHE g 186 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE g 186 " --> pdb=" O CYS g 162 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP g 200 " --> pdb=" O LYS g 210 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS g 210 " --> pdb=" O ASP g 200 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'g' and resid 239 through 244 removed outlier: 6.644A pdb=" N GLY g 254 " --> pdb=" O LEU g 240 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL g 242 " --> pdb=" O VAL g 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL g 252 " --> pdb=" O VAL g 242 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA g 244 " --> pdb=" O TYR g 250 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR g 250 " --> pdb=" O ALA g 244 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY g 255 " --> pdb=" O LYS g 259 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS g 259 " --> pdb=" O GLY g 255 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER g 264 " --> pdb=" O PRO g 270 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'g' and resid 285 through 288 removed outlier: 3.748A pdb=" N SER g 285 " --> pdb=" O SER g 298 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU g 316 " --> pdb=" O THR g 306 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER g 308 " --> pdb=" O GLN g 314 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN g 314 " --> pdb=" O SER g 308 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 347 through 350 removed outlier: 4.215A pdb=" N ASP g 327 " --> pdb=" O VAL g 339 " (cutoff:3.500A) Processing sheet with id= :, first strand: chain 'g' and resid 434 through 436 removed outlier: 3.764A pdb=" N VAL g 404 " --> pdb=" O GLY g 416 " (cutoff:3.500A) Processing sheet with id= ;, first strand: chain 'g' and resid 477 through 480 removed outlier: 5.254A pdb=" N LYS g 500 " --> pdb=" O LEU g 510 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU g 510 " --> pdb=" O LYS g 500 " (cutoff:3.500A) 2662 hydrogen bonds defined for protein. 7395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 298 hydrogen bonds 504 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 33.48 Time building geometry restraints manager: 24.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 28542 1.43 - 1.65: 36723 1.65 - 1.88: 5 1.88 - 2.10: 1 2.10 - 2.33: 5 Bond restraints: 65276 Sorted by residual: bond pdb=" C2 G 2 248 " pdb=" N3 G 2 248 " ideal model delta sigma weight residual 1.323 2.317 -0.994 2.00e-02 2.50e+03 2.47e+03 bond pdb=" N3 G 2 248 " pdb=" C4 G 2 248 " ideal model delta sigma weight residual 1.350 2.326 -0.976 2.00e-02 2.50e+03 2.38e+03 bond pdb=" N1 G 2 248 " pdb=" C2 G 2 248 " ideal model delta sigma weight residual 1.373 2.178 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C6 G 2 248 " pdb=" N1 G 2 248 " ideal model delta sigma weight residual 1.391 2.195 -0.804 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C5 G 2 248 " pdb=" C6 G 2 248 " ideal model delta sigma weight residual 1.419 2.161 -0.742 2.00e-02 2.50e+03 1.38e+03 ... (remaining 65271 not shown) Histogram of bond angle deviations from ideal: 81.97 - 94.72: 2 94.72 - 107.46: 5061 107.46 - 120.21: 57681 120.21 - 132.96: 30190 132.96 - 145.70: 35 Bond angle restraints: 92969 Sorted by residual: angle pdb=" O3' U 0 524 " pdb=" P U 0 525 " pdb=" OP1 U 0 525 " ideal model delta sigma weight residual 108.00 81.97 26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" N VAL H 28 " pdb=" CA VAL H 28 " pdb=" C VAL H 28 " ideal model delta sigma weight residual 113.71 105.87 7.84 9.50e-01 1.11e+00 6.81e+01 angle pdb=" C ASN H 769 " pdb=" N TYR H 770 " pdb=" CA TYR H 770 " ideal model delta sigma weight residual 121.18 135.13 -13.95 1.98e+00 2.55e-01 4.97e+01 angle pdb=" N PRO Q 785 " pdb=" CA PRO Q 785 " pdb=" CB PRO Q 785 " ideal model delta sigma weight residual 103.25 110.63 -7.38 1.05e+00 9.07e-01 4.94e+01 angle pdb=" O3' U 0 524 " pdb=" P U 0 525 " pdb=" OP2 U 0 525 " ideal model delta sigma weight residual 108.00 88.25 19.75 3.00e+00 1.11e-01 4.33e+01 ... (remaining 92964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 37048 35.73 - 71.46: 1155 71.46 - 107.19: 146 107.19 - 142.92: 6 142.92 - 178.64: 11 Dihedral angle restraints: 38366 sinusoidal: 7955 harmonic: 30411 Sorted by residual: dihedral pdb=" CA PHE e 9 " pdb=" C PHE e 9 " pdb=" N PRO e 10 " pdb=" CA PRO e 10 " ideal model delta harmonic sigma weight residual -180.00 -116.74 -63.26 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA SER A 453 " pdb=" C SER A 453 " pdb=" N VAL A 454 " pdb=" CA VAL A 454 " ideal model delta harmonic sigma weight residual -180.00 -133.91 -46.09 0 5.00e+00 4.00e-02 8.50e+01 dihedral pdb=" O4' U 0 332 " pdb=" C1' U 0 332 " pdb=" N1 U 0 332 " pdb=" C2 U 0 332 " ideal model delta sinusoidal sigma weight residual -128.00 48.10 -176.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 38363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.449: 12753 0.449 - 0.898: 0 0.898 - 1.346: 0 1.346 - 1.795: 0 1.795 - 2.244: 1 Chirality restraints: 12754 Sorted by residual: chirality pdb=" P U 0 525 " pdb=" OP1 U 0 525 " pdb=" OP2 U 0 525 " pdb=" O5' U 0 525 " both_signs ideal model delta sigma weight residual True 2.41 0.17 2.24 2.00e-01 2.50e+01 1.26e+02 chirality pdb=" C3' C 0 311 " pdb=" C4' C 0 311 " pdb=" O3' C 0 311 " pdb=" C2' C 0 311 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PRO J 17 " pdb=" N PRO J 17 " pdb=" C PRO J 17 " pdb=" CB PRO J 17 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 12751 not shown) Planarity restraints: 10980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' N 0 595 " 0.483 2.00e-02 2.50e+03 6.03e-01 7.27e+03 pdb=" C2' N 0 595 " -0.594 2.00e-02 2.50e+03 pdb=" C3' N 0 595 " -0.219 2.00e-02 2.50e+03 pdb=" C4' N 0 595 " 0.222 2.00e-02 2.50e+03 pdb=" C5' N 0 595 " -0.819 2.00e-02 2.50e+03 pdb=" O2' N 0 595 " -0.593 2.00e-02 2.50e+03 pdb=" O3' N 0 595 " 0.911 2.00e-02 2.50e+03 pdb=" O4' N 0 595 " 0.610 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N 1 1 " -0.511 2.00e-02 2.50e+03 4.48e-01 4.01e+03 pdb=" C2' N 1 1 " -0.390 2.00e-02 2.50e+03 pdb=" C3' N 1 1 " -0.440 2.00e-02 2.50e+03 pdb=" C4' N 1 1 " 0.411 2.00e-02 2.50e+03 pdb=" C5' N 1 1 " 0.171 2.00e-02 2.50e+03 pdb=" O2' N 1 1 " 0.877 2.00e-02 2.50e+03 pdb=" O3' N 1 1 " -0.165 2.00e-02 2.50e+03 pdb=" O4' N 1 1 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N 0 594 " -0.482 2.00e-02 2.50e+03 4.47e-01 3.99e+03 pdb=" C2' N 0 594 " -0.410 2.00e-02 2.50e+03 pdb=" C3' N 0 594 " -0.500 2.00e-02 2.50e+03 pdb=" C4' N 0 594 " 0.385 2.00e-02 2.50e+03 pdb=" C5' N 0 594 " 0.125 2.00e-02 2.50e+03 pdb=" O2' N 0 594 " 0.865 2.00e-02 2.50e+03 pdb=" O3' N 0 594 " -0.120 2.00e-02 2.50e+03 pdb=" O4' N 0 594 " 0.137 2.00e-02 2.50e+03 ... (remaining 10977 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 11934 2.76 - 3.30: 57183 3.30 - 3.83: 103430 3.83 - 4.37: 103180 4.37 - 4.90: 167329 Nonbonded interactions: 443056 Sorted by model distance: nonbonded pdb=" O2' C 0 307 " pdb=" OP1 C 0 311 " model vdw 2.230 2.440 nonbonded pdb=" O2' C 0 296 " pdb=" O LEU T 68 " model vdw 2.271 2.440 nonbonded pdb=" O2 C 0 96 " pdb=" O2' A 0 155 " model vdw 2.279 2.440 nonbonded pdb=" O2' G 0 288 " pdb=" O ALA b 416 " model vdw 2.280 2.440 nonbonded pdb=" N6 A 2 30 " pdb=" O ILE U 342 " model vdw 2.281 2.520 ... (remaining 443051 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 'c' and (resid 115 through 125 or resid 138 through 324)) selection = (chain 'd' and resid 115 through 324) } ncs_group { reference = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.050 Extract box with map and model: 11.640 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 158.580 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 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 0.994 65276 Z= 0.555 Angle : 1.026 26.028 92969 Z= 0.606 Chirality : 0.055 2.244 12754 Planarity : 0.018 0.603 10980 Dihedral : 18.280 178.644 18366 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.16 % 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: -3.63 (0.07), residues: 9093 helix: -2.74 (0.08), residues: 2314 sheet: -1.84 (0.10), residues: 2191 loop : -2.48 (0.08), residues: 4588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4590 time to fit residues: 136.9580 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 747 optimal weight: 10.0000 chunk 670 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 693 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 516 optimal weight: 5.9990 chunk 803 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 65276 Z= 0.324 Angle : 0.881 26.314 92969 Z= 0.507 Chirality : 0.048 2.011 12754 Planarity : 0.006 0.123 10980 Dihedral : 17.494 179.285 18366 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.01 % 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 (0.08), residues: 9093 helix: -1.03 (0.09), residues: 2413 sheet: -1.52 (0.10), residues: 2364 loop : -2.00 (0.09), residues: 4316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.495 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5147 time to fit residues: 153.0718 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 446 optimal weight: 0.8980 chunk 249 optimal weight: 0.0570 chunk 668 optimal weight: 9.9990 chunk 547 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 805 optimal weight: 0.8980 chunk 869 optimal weight: 5.9990 chunk 717 optimal weight: 6.9990 chunk 798 optimal weight: 30.0000 chunk 274 optimal weight: 0.5980 chunk 645 optimal weight: 3.9990 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 65276 Z= 0.128 Angle : 0.621 26.657 92969 Z= 0.370 Chirality : 0.044 2.003 12754 Planarity : 0.005 0.115 10980 Dihedral : 16.966 179.323 18366 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % 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: -1.50 (0.09), residues: 9093 helix: 0.37 (0.11), residues: 2443 sheet: -1.19 (0.10), residues: 2329 loop : -1.65 (0.09), residues: 4321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 5.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5363 time to fit residues: 159.3445 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 795 optimal weight: 20.0000 chunk 605 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 540 optimal weight: 9.9990 chunk 808 optimal weight: 30.0000 chunk 855 optimal weight: 40.0000 chunk 422 optimal weight: 4.9990 chunk 765 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 65276 Z= 0.470 Angle : 1.084 26.627 92969 Z= 0.616 Chirality : 0.054 2.002 12754 Planarity : 0.007 0.111 10980 Dihedral : 18.190 179.775 18366 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.21 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % 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: -2.88 (0.08), residues: 9093 helix: -1.29 (0.09), residues: 2368 sheet: -1.64 (0.11), residues: 2224 loop : -2.38 (0.09), residues: 4501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.492 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4623 time to fit residues: 137.9782 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 712 optimal weight: 0.9990 chunk 485 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 636 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 729 optimal weight: 0.9980 chunk 591 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 767 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 65276 Z= 0.256 Angle : 0.758 26.911 92969 Z= 0.442 Chirality : 0.047 1.998 12754 Planarity : 0.005 0.110 10980 Dihedral : 17.601 177.858 18366 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % 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: -2.38 (0.08), residues: 9093 helix: -0.40 (0.10), residues: 2402 sheet: -1.72 (0.11), residues: 2222 loop : -2.16 (0.09), residues: 4469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5274 time to fit residues: 157.6667 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 287 optimal weight: 7.9990 chunk 770 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 502 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 856 optimal weight: 20.0000 chunk 710 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 449 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 65276 Z= 0.407 Angle : 0.927 26.952 92969 Z= 0.533 Chirality : 0.051 2.000 12754 Planarity : 0.006 0.110 10980 Dihedral : 18.119 176.822 18366 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.64 % Favored : 86.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % 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: -2.95 (0.08), residues: 9093 helix: -1.01 (0.10), residues: 2357 sheet: -1.94 (0.11), residues: 2161 loop : -2.49 (0.09), residues: 4575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4718 time to fit residues: 140.4803 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 825 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 487 optimal weight: 4.9990 chunk 625 optimal weight: 0.0020 chunk 484 optimal weight: 7.9990 chunk 720 optimal weight: 7.9990 chunk 478 optimal weight: 20.0000 chunk 852 optimal weight: 0.0570 chunk 533 optimal weight: 10.0000 chunk 520 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 overall best weight: 3.8112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 65276 Z= 0.257 Angle : 0.759 27.122 92969 Z= 0.442 Chirality : 0.047 1.999 12754 Planarity : 0.005 0.110 10980 Dihedral : 17.703 175.575 18366 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % 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: -2.58 (0.09), residues: 9093 helix: -0.33 (0.10), residues: 2358 sheet: -2.00 (0.11), residues: 2180 loop : -2.31 (0.09), residues: 4555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.431 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5000 time to fit residues: 148.2258 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 5.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 527 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 509 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 chunk 167 optimal weight: 0.4980 chunk 165 optimal weight: 20.0000 chunk 542 optimal weight: 1.9990 chunk 581 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 670 optimal weight: 30.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.7745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 65276 Z= 0.201 Angle : 0.692 27.160 92969 Z= 0.406 Chirality : 0.045 1.996 12754 Planarity : 0.005 0.109 10980 Dihedral : 17.355 179.532 18366 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % 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: -2.13 (0.09), residues: 9093 helix: 0.41 (0.11), residues: 2361 sheet: -1.97 (0.11), residues: 2194 loop : -2.14 (0.09), residues: 4538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.532 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4936 time to fit residues: 147.9352 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 775 optimal weight: 5.9990 chunk 817 optimal weight: 9.9990 chunk 745 optimal weight: 0.9980 chunk 794 optimal weight: 30.0000 chunk 816 optimal weight: 20.0000 chunk 478 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 624 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 718 optimal weight: 0.8980 chunk 751 optimal weight: 30.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 65276 Z= 0.320 Angle : 0.823 27.120 92969 Z= 0.476 Chirality : 0.048 1.999 12754 Planarity : 0.006 0.110 10980 Dihedral : 17.806 177.752 18366 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.69 (0.08), residues: 9093 helix: -0.31 (0.10), residues: 2325 sheet: -2.06 (0.11), residues: 2156 loop : -2.45 (0.09), residues: 4612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5023 time to fit residues: 150.0413 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 792 optimal weight: 8.9990 chunk 521 optimal weight: 9.9990 chunk 840 optimal weight: 30.0000 chunk 513 optimal weight: 9.9990 chunk 398 optimal weight: 4.9990 chunk 584 optimal weight: 2.9990 chunk 881 optimal weight: 20.0000 chunk 811 optimal weight: 0.9980 chunk 702 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 542 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 65276 Z= 0.279 Angle : 0.771 27.142 92969 Z= 0.448 Chirality : 0.047 1.998 12754 Planarity : 0.005 0.110 10980 Dihedral : 17.745 177.537 18366 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.00 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.67 (0.09), residues: 9093 helix: -0.18 (0.11), residues: 2335 sheet: -2.12 (0.11), residues: 2088 loop : -2.47 (0.09), residues: 4670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18186 Ramachandran restraints generated. 9093 Oldfield, 0 Emsley, 9093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4982 time to fit residues: 148.0541 Evaluate side-chains 152 residues out of total 8188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 430 optimal weight: 0.0170 chunk 557 optimal weight: 10.0000 chunk 747 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 647 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 703 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 722 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090379 restraints weight = 325333.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084579 restraints weight = 347607.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084047 restraints weight = 415942.435| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.9227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 65276 Z= 0.337 Angle : 0.857 27.119 92969 Z= 0.493 Chirality : 0.049 1.997 12754 Planarity : 0.006 0.110 10980 Dihedral : 18.028 176.346 18366 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 15.13 % Favored : 84.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % 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: -3.06 (0.08), residues: 9093 helix: -0.62 (0.10), residues: 2343 sheet: -2.29 (0.11), residues: 2098 loop : -2.69 (0.09), residues: 4652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP H 193 PHE 0.000 0.000 PHE H 48 TYR 0.000 0.000 TYR H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.69 seconds wall clock time: 119 minutes 3.10 seconds (7143.10 seconds total)