Starting phenix.real_space_refine (version: dev) on Tue Apr 12 09:17:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ztp_11423/04_2022/6ztp_11423_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 sd= 0.076 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "AF TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 172846 Number of models: 1 Model: "" Number of chains: 79 Chain: "AA" Number of atoms: 32909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32909 Classifications: {'RNA': 1533} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 750, 'rna3p_pyr': 568, 'rna2p_pur': 118, 'rna2p_pyr': 86} Link IDs: {'rna3p': 1327, 'rna2p': 205} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "AB" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1765 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "AC" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1640 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "AD" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "AE" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1148 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "AF" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "AG" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1214 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "AH" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "AI" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1031 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "AJ" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 800 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "AK" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AL" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "AN" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "AO" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "AP" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "AQ" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "AR" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "AS" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "AT" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "AU" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "AV" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 572 Classifications: {'RNA': 27} Modifications used: {'rna3p_pyr': 12, 'rna2p_pur': 5, 'rna3p_pur': 8, 'rna2p_pyr': 2} Link IDs: {'rna3p': 20, 'rna2p': 6} Chain breaks: 1 Chain: "AW" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'rna3p': 5, 'rna2p_pyr': 4, 'p5*END': 1, 'rna3p_pur': 31, 'rna3p_pyr': 29, 'rna2p_pur': 8} Link IDs: {'rna3p': 65, 'rna2p': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "AX" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1630 Classifications: {'RNA': 76} Modifications used: {'rna3p': 8, 'rna2p_pyr': 3, 'p5*END': 1, 'rna3p_pur': 31, 'rna2p': 2, 'rna3p_pyr': 26, 'rna2p_pur': 6} Link IDs: {'rna3p': 64, 'rna2p': 11} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3AU%rna3p:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "BA" Number of atoms: 62270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62270 Classifications: {'RNA': 2900} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1379, 'rna3p_pyr': 1057, 'rna2p_pur': 285, 'rna2p_pyr': 154} Link IDs: {'rna3p': 2453, 'rna2p': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 7} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "BC" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2092 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "BD" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BE" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "BF" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "BG" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "BH" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "BK" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "BL" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "BM" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1052 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "BN" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BO" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "BP" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "BQ" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "BR" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "BS" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "BT" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "BU" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 764 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "BV" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "BW" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "BX" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "BY" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "BZ" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B2" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "B3" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 436 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B4" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B5" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B6" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B7" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "CN" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "CT" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 606 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "CA" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 219, 'PCIS': 1} Chain: "CB" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 210, 'PCIS': 1} Chain breaks: 1 Chain: "CC" Number of atoms: 10415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 10415 Classifications: {'peptide': 1320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1264, 'PCIS': 1} Chain breaks: 1 Chain: "CD" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10375 Classifications: {'peptide': 1333} Link IDs: {'PTRANS': 54, 'TRANS': 1277, 'PCIS': 1} Chain breaks: 2 Chain: "CE" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 478 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "AA" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Unusual residues: {' MG': 143} Classifications: {'undetermined': 143} Link IDs: {None: 142} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AX" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'peptide': 1} Link IDs: {None: 1} Chain: "BA" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 317 Unusual residues: {' MG': 317} Classifications: {'undetermined': 317} Link IDs: {None: 316} Chain: "BB" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "BC" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0WDC SG CYSBX 53 119.055 120.288 57.063 1.00 31.76 S ATOM A0Z7G SG CYSB6 11 184.638 174.480 73.640 1.00 44.52 S ATOM A0Z85 SG CYSB6 14 185.279 170.941 73.667 1.00 40.41 S ATOM A0ZB0 SG CYSB6 27 187.713 173.216 74.707 1.00 40.40 S ATOM A0ZH2 SG CYSB7 16 73.625 175.683 65.737 1.00 66.47 S ATOM A1BST SG CYSCD 70 88.760 249.288 136.069 1.00111.48 S ATOM A1BT7 SG CYSCD 72 86.806 247.954 133.330 1.00114.84 S ATOM A1GAV SG CYSCD 814 108.521 312.489 146.880 1.00 70.39 S ATOM A1GQK SG CYSCD 888 106.061 310.629 147.626 1.00 52.47 S ATOM A1GRZ SG CYSCD 895 108.518 310.536 149.691 1.00 59.80 S ATOM A1GSK SG CYSCD 898 106.648 313.219 149.867 1.00 54.18 S Time building chain proxies: 63.14, per 1000 atoms: 0.37 Number of scatterers: 172846 At special positions: 0 Unit cell: (265.104, 375.564, 247.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 258 16.00 P 4793 15.00 Mg 487 11.99 O 45968 8.00 N 31858 7.00 C 89478 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.29 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNB6 101 " pdb="ZN ZNB6 101 " - pdb=" ND1 HISB6 33 " pdb="ZN ZNB6 101 " - pdb=" SG CYSB6 27 " pdb="ZN ZNB6 101 " - pdb=" SG CYSB6 11 " pdb="ZN ZNB6 101 " - pdb=" SG CYSB6 14 " pdb=" ZNB7 100 " pdb="ZN ZNB7 100 " - pdb=" SG CYSB7 16 " pdb=" ZNCD1502 " pdb="ZN ZNCD1502 " - pdb=" SG CYSCD 72 " pdb="ZN ZNCD1502 " - pdb=" SG CYSCD 70 " pdb=" ZNCD1503 " pdb="ZN ZNCD1503 " - pdb=" SG CYSCD 888 " pdb="ZN ZNCD1503 " - pdb=" SG CYSCD 898 " pdb="ZN ZNCD1503 " - pdb=" SG CYSCD 895 " pdb="ZN ZNCD1503 " - pdb=" SG CYSCD 814 " Number of angles added : 9 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16346 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 283 helices and 111 sheets defined 40.4% alpha, 18.0% beta 1667 base pairs and 2496 stacking pairs defined. Time for finding SS restraints: 69.45 Creating SS restraints... Processing helix chain 'AB' and resid 5 through 13 Processing helix chain 'AB' and resid 24 through 32 Proline residue: AB 29 - end of helix removed outlier: 5.992A pdb=" N PHEAB 32 " --> pdb=" O LYSAB 28 " (cutoff:3.500A) Processing helix chain 'AB' and resid 43 through 64 Proline residue: AB 48 - end of helix Processing helix chain 'AB' and resid 73 through 88 removed outlier: 4.614A pdb=" N GLUAB 78 " --> pdb=" O ARGAB 74 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALAAB 79 " --> pdb=" O ALAAB 75 " (cutoff:3.500A) Processing helix chain 'AB' and resid 103 through 123 Processing helix chain 'AB' and resid 130 through 148 removed outlier: 6.348A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) Processing helix chain 'AB' and resid 165 through 170 Processing helix chain 'AB' and resid 171 through 180 Processing helix chain 'AB' and resid 206 through 227 Processing helix chain 'AC' and resid 6 through 12 Processing helix chain 'AC' and resid 28 through 48 Processing helix chain 'AC' and resid 72 through 78 Processing helix chain 'AC' and resid 81 through 96 Processing helix chain 'AC' and resid 108 through 113 removed outlier: 5.797A pdb=" N ALAAC 113 " --> pdb=" O PROAC 109 " (cutoff:3.500A) Processing helix chain 'AC' and resid 114 through 127 Processing helix chain 'AC' and resid 129 through 145 Processing helix chain 'AD' and resid 7 through 16 Processing helix chain 'AD' and resid 27 through 32 Processing helix chain 'AD' and resid 49 through 66 Processing helix chain 'AD' and resid 68 through 83 removed outlier: 5.021A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 Processing helix chain 'AD' and resid 98 through 106 Processing helix chain 'AD' and resid 110 through 121 Processing helix chain 'AD' and resid 146 through 153 removed outlier: 4.603A pdb=" N GLNAD 152 " --> pdb=" O LYSAD 148 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SERAD 153 " --> pdb=" O ALAAD 149 " (cutoff:3.500A) Processing helix chain 'AD' and resid 154 through 166 removed outlier: 4.553A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 5.026A pdb=" N SERAD 192 " --> pdb=" O ARGAD 188 " (cutoff:3.500A) Processing helix chain 'AD' and resid 196 through 206 removed outlier: 3.910A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 71 removed outlier: 4.233A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 Processing helix chain 'AE' and resid 132 through 148 removed outlier: 5.739A pdb=" N ASNAE 148 " --> pdb=" O LEUAE 144 " (cutoff:3.500A) Processing helix chain 'AE' and resid 149 through 158 Processing helix chain 'AE' and resid 160 through 165 removed outlier: 3.513A pdb=" N ILEAE 164 " --> pdb=" O SERAE 160 " (cutoff:3.500A) Processing helix chain 'AF' and resid 14 through 33 removed outlier: 3.917A pdb=" N VALAF 18 " --> pdb=" O GLNAF 14 " (cutoff:3.500A) Proline residue: AF 19 - end of helix Processing helix chain 'AF' and resid 67 through 81 Processing helix chain 'AG' and resid 20 through 31 Processing helix chain 'AG' and resid 35 through 54 Processing helix chain 'AG' and resid 57 through 70 Processing helix chain 'AG' and resid 92 through 111 Processing helix chain 'AG' and resid 115 through 130 Processing helix chain 'AG' and resid 132 through 153 removed outlier: 5.104A pdb=" N ALAAG 150 " --> pdb=" O GLUAG 146 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHEAG 151 " --> pdb=" O ALAAG 147 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALAAG 152 " --> pdb=" O ASNAG 148 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N HISAG 153 " --> pdb=" O LYSAG 149 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 Processing helix chain 'AH' and resid 30 through 44 Processing helix chain 'AH' and resid 112 through 120 Processing helix chain 'AI' and resid 34 through 40 Processing helix chain 'AI' and resid 41 through 56 Proline residue: AI 51 - end of helix removed outlier: 3.627A pdb=" N ASPAI 56 " --> pdb=" O LEUAI 52 " (cutoff:3.500A) Processing helix chain 'AI' and resid 71 through 92 Processing helix chain 'AI' and resid 94 through 102 Processing helix chain 'AJ' and resid 14 through 33 Processing helix chain 'AJ' and resid 80 through 91 removed outlier: 5.451A pdb=" N ASPAJ 91 " --> pdb=" O LEUAJ 87 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 Processing helix chain 'AK' and resid 54 through 59 removed outlier: 4.523A pdb=" N THRAK 59 " --> pdb=" O SERAK 55 " (cutoff:3.500A) Processing helix chain 'AK' and resid 60 through 76 removed outlier: 4.657A pdb=" N GLUAK 76 " --> pdb=" O ASPAK 72 " (cutoff:3.500A) Processing helix chain 'AK' and resid 92 through 104 removed outlier: 5.219A pdb=" N THRAK 96 " --> pdb=" O GLYAK 92 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILEAK 97 " --> pdb=" O ARGAK 93 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 11 Proline residue: AL 11 - end of helix Processing helix chain 'AL' and resid 113 through 118 Processing helix chain 'AM' and resid 14 through 22 removed outlier: 3.705A pdb=" N SERAM 21 " --> pdb=" O ILEAM 17 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILEAM 22 " --> pdb=" O ALAAM 18 " (cutoff:3.500A) Processing helix chain 'AM' and resid 26 through 38 Processing helix chain 'AM' and resid 49 through 64 removed outlier: 3.987A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 Processing helix chain 'AM' and resid 85 through 94 Processing helix chain 'AM' and resid 106 through 111 Processing helix chain 'AN' and resid 3 through 21 Processing helix chain 'AN' and resid 22 through 33 Processing helix chain 'AN' and resid 37 through 52 Proline residue: AN 52 - end of helix Processing helix chain 'AN' and resid 80 through 91 Processing helix chain 'AO' and resid 4 through 16 Processing helix chain 'AO' and resid 24 through 43 removed outlier: 4.317A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AP' and resid 53 through 64 Processing helix chain 'AP' and resid 68 through 82 Processing helix chain 'AR' and resid 11 through 17 removed outlier: 4.675A pdb=" N ALAAR 15 " --> pdb=" O CYSAR 11 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLUAR 16 " --> pdb=" O ARGAR 12 " (cutoff:3.500A) Processing helix chain 'AR' and resid 25 through 34 removed outlier: 4.205A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 Processing helix chain 'AR' and resid 48 through 66 Processing helix chain 'AS' and resid 12 through 26 Processing helix chain 'AS' and resid 70 through 76 Proline residue: AS 76 - end of helix Processing helix chain 'AT' and resid 4 through 41 Processing helix chain 'AT' and resid 44 through 65 Proline residue: AT 56 - end of helix Processing helix chain 'AT' and resid 68 through 87 removed outlier: 5.021A pdb=" N ALAAT 87 " --> pdb=" O ILEAT 83 " (cutoff:3.500A) Processing helix chain 'AU' and resid 11 through 27 Processing helix chain 'AU' and resid 28 through 37 removed outlier: 4.662A pdb=" N PHEAU 37 " --> pdb=" O ARGAU 33 " (cutoff:3.500A) Processing helix chain 'AU' and resid 40 through 64 Processing helix chain 'BC' and resid 10 through 17 removed outlier: 5.444A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VALBC 16 " --> pdb=" O GLYBC 12 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VALBC 17 " --> pdb=" O ARGBC 13 " (cutoff:3.500A) Processing helix chain 'BC' and resid 30 through 35 removed outlier: 3.572A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLUBC 35 " --> pdb=" O ALABC 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 30 through 35' Processing helix chain 'BC' and resid 131 through 136 Proline residue: BC 136 - end of helix Processing helix chain 'BC' and resid 207 through 215 removed outlier: 3.857A pdb=" N ALABC 211 " --> pdb=" O LYSBC 207 " (cutoff:3.500A) Processing helix chain 'BC' and resid 221 through 226 removed outlier: 3.758A pdb=" N METBC 225 " --> pdb=" O ARGBC 221 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASNBC 226 " --> pdb=" O GLYBC 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 221 through 226' Processing helix chain 'BC' and resid 260 through 268 removed outlier: 3.781A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VALBC 268 " --> pdb=" O ASPBC 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 260 through 268' Processing helix chain 'BD' and resid 56 through 61 removed outlier: 5.576A pdb=" N THRBD 61 " --> pdb=" O ALABD 57 " (cutoff:3.500A) Processing helix chain 'BD' and resid 62 through 72 Processing helix chain 'BD' and resid 97 through 103 removed outlier: 4.935A pdb=" N PHEBD 101 " --> pdb=" O SERBD 97 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASPBD 103 " --> pdb=" O GLUBD 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 97 through 103' Processing helix chain 'BD' and resid 120 through 125 Processing helix chain 'BE' and resid 24 through 41 removed outlier: 5.454A pdb=" N GLNBE 41 " --> pdb=" O ALABE 37 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 53 removed outlier: 6.485A pdb=" N THRBE 53 " --> pdb=" O ARGBE 49 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 Processing helix chain 'BE' and resid 130 through 142 Processing helix chain 'BE' and resid 154 through 163 removed outlier: 4.510A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 184 removed outlier: 5.757A pdb=" N ASPBE 184 " --> pdb=" O LEUBE 180 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 Processing helix chain 'BE' and resid 16 through 21 Processing helix chain 'BF' and resid 2 through 21 removed outlier: 5.086A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) Processing helix chain 'BF' and resid 41 through 47 removed outlier: 4.353A pdb=" N ALABF 45 " --> pdb=" O GLYBF 41 " (cutoff:3.500A) Processing helix chain 'BF' and resid 48 through 62 Processing helix chain 'BF' and resid 93 through 112 removed outlier: 4.746A pdb=" N VALBF 108 " --> pdb=" O ILEBF 104 " (cutoff:3.500A) Proline residue: BF 109 - end of helix removed outlier: 5.838A pdb=" N ARGBF 112 " --> pdb=" O VALBF 108 " (cutoff:3.500A) Processing helix chain 'BF' and resid 162 through 174 Processing helix chain 'BF' and resid 134 through 139 removed outlier: 3.826A pdb=" N ILEBF 137 " --> pdb=" O GLUBF 134 " (cutoff:3.500A) Proline residue: BF 139 - end of helix Processing helix chain 'BG' and resid 2 through 8 removed outlier: 4.050A pdb=" N ALABG 7 " --> pdb=" O ARGBG 3 " (cutoff:3.500A) Proline residue: BG 8 - end of helix Processing helix chain 'BG' and resid 60 through 81 Processing helix chain 'BG' and resid 137 through 153 Processing helix chain 'BH' and resid 22 through 28 removed outlier: 3.886A pdb=" N ASNBH 28 " --> pdb=" O GLYBH 24 " (cutoff:3.500A) Processing helix chain 'BH' and resid 29 through 34 removed outlier: 3.534A pdb=" N GLNBH 33 " --> pdb=" O PHEBH 29 " (cutoff:3.500A) Processing helix chain 'BH' and resid 40 through 50 Processing helix chain 'BH' and resid 51 through 74 removed outlier: 3.565A pdb=" N ILEBH 72 " --> pdb=" O ARGBH 68 " (cutoff:3.500A) Processing helix chain 'BH' and resid 95 through 107 removed outlier: 3.537A pdb=" N ALABH 106 " --> pdb=" O ALABH 102 " (cutoff:3.500A) Processing helix chain 'BK' and resid 24 through 38 Processing helix chain 'BK' and resid 88 through 96 Processing helix chain 'BK' and resid 97 through 110 removed outlier: 4.047A pdb=" N ILEBK 101 " --> pdb=" O PROBK 97 " (cutoff:3.500A) Proline residue: BK 110 - end of helix Processing helix chain 'BK' and resid 112 through 123 removed outlier: 3.689A pdb=" N LEUBK 122 " --> pdb=" O METBK 118 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYSBK 123 " --> pdb=" O PHEBK 119 " (cutoff:3.500A) Processing helix chain 'BK' and resid 67 through 72 removed outlier: 4.266A pdb=" N LYSBK 72 " --> pdb=" O ASNBK 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 67 through 72' Processing helix chain 'BL' and resid 104 through 109 removed outlier: 3.895A pdb=" N ARGBL 108 " --> pdb=" O THRBL 104 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SERBL 109 " --> pdb=" O ARGBL 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 104 through 109' Processing helix chain 'BL' and resid 112 through 119 Processing helix chain 'BM' and resid 37 through 42 removed outlier: 3.920A pdb=" N ARGBM 41 " --> pdb=" O GLYBM 37 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SERBM 42 " --> pdb=" O GLNBM 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'BM' and resid 37 through 42' Processing helix chain 'BM' and resid 56 through 62 Proline residue: BM 62 - end of helix Processing helix chain 'BM' and resid 68 through 75 removed outlier: 3.917A pdb=" N ALABM 72 " --> pdb=" O SERBM 68 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILEBM 73 " --> pdb=" O ARGBM 69 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALABM 75 " --> pdb=" O ALABM 71 " (cutoff:3.500A) Processing helix chain 'BM' and resid 78 through 85 Processing helix chain 'BM' and resid 91 through 99 Processing helix chain 'BM' and resid 128 through 139 Processing helix chain 'BN' and resid 42 through 58 Processing helix chain 'BN' and resid 109 through 125 Proline residue: BN 125 - end of helix Processing helix chain 'BO' and resid 13 through 32 Processing helix chain 'BO' and resid 38 through 57 Proline residue: BO 50 - end of helix removed outlier: 4.161A pdb=" N THRBO 57 " --> pdb=" O THRBO 53 " (cutoff:3.500A) Processing helix chain 'BO' and resid 59 through 71 Processing helix chain 'BO' and resid 72 through 88 removed outlier: 4.550A pdb=" N GLYBO 84 " --> pdb=" O PHEBO 80 " (cutoff:3.500A) Proline residue: BO 85 - end of helix Processing helix chain 'BP' and resid 2 through 22 removed outlier: 4.398A pdb=" N ARGBP 13 " --> pdb=" O ARGBP 9 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALABP 14 " --> pdb=" O ARGBP 10 " (cutoff:3.500A) Processing helix chain 'BP' and resid 55 through 63 removed outlier: 5.917A pdb=" N ALABP 59 " --> pdb=" O GLUBP 55 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYSBP 63 " --> pdb=" O ALABP 59 " (cutoff:3.500A) Processing helix chain 'BP' and resid 67 through 86 Processing helix chain 'BP' and resid 101 through 114 Processing helix chain 'BQ' and resid 2 through 13 Processing helix chain 'BQ' and resid 97 through 104 removed outlier: 4.204A pdb=" N ARGBQ 101 " --> pdb=" O LEUBQ 97 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THRBQ 104 " --> pdb=" O LEUBQ 100 " (cutoff:3.500A) Processing helix chain 'BR' and resid 6 through 22 Processing helix chain 'BR' and resid 26 through 31 Processing helix chain 'BR' and resid 32 through 37 Processing helix chain 'BR' and resid 39 through 73 Processing helix chain 'BR' and resid 75 through 87 Processing helix chain 'BR' and resid 91 through 102 Processing helix chain 'BR' and resid 103 through 118 Processing helix chain 'BT' and resid 13 through 25 Processing helix chain 'BT' and resid 28 through 39 Processing helix chain 'BT' and resid 41 through 61 Processing helix chain 'BT' and resid 65 through 70 removed outlier: 3.595A pdb=" N LEUBT 69 " --> pdb=" O ASPBT 65 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYSBT 70 " --> pdb=" O ILEBT 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'BT' and resid 65 through 70' Processing helix chain 'BU' and resid 3 through 11 removed outlier: 4.050A pdb=" N LEUBU 11 " --> pdb=" O LEUBU 7 " (cutoff:3.500A) Processing helix chain 'BU' and resid 17 through 26 Processing helix chain 'BU' and resid 39 through 51 Processing helix chain 'BV' and resid 66 through 71 removed outlier: 3.646A pdb=" N VALBV 70 " --> pdb=" O GLNBV 66 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALABV 71 " --> pdb=" O VALBV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 66 through 71' Processing helix chain 'BW' and resid 13 through 24 Processing helix chain 'BW' and resid 43 through 53 removed outlier: 4.205A pdb=" N LYSBW 53 " --> pdb=" O ASNBW 49 " (cutoff:3.500A) Processing helix chain 'BW' and resid 54 through 59 Processing helix chain 'BY' and resid 52 through 63 Processing helix chain 'BY' and resid 64 through 75 Processing helix chain 'BZ' and resid 2 through 10 removed outlier: 6.548A pdb=" N LEUBZ 6 " --> pdb=" O LYSBZ 2 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SERBZ 10 " --> pdb=" O LEUBZ 6 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 11 through 35 Processing helix chain 'BZ' and resid 39 through 63 removed outlier: 4.645A pdb=" N LEUBZ 43 " --> pdb=" O GLNBZ 39 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYSBZ 44 " --> pdb=" O SERBZ 40 " (cutoff:3.500A) Processing helix chain 'B1' and resid 17 through 28 Processing helix chain 'B1' and resid 41 through 52 Processing helix chain 'B2' and resid 9 through 19 removed outlier: 4.586A pdb=" N HISB2 19 " --> pdb=" O METB2 15 " (cutoff:3.500A) Processing helix chain 'B4' and resid 8 through 16 Processing helix chain 'B4' and resid 17 through 25 removed outlier: 3.948A pdb=" N THRB4 24 " --> pdb=" O ALAB4 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYSB4 25 " --> pdb=" O ARGB4 21 " (cutoff:3.500A) Processing helix chain 'B4' and resid 26 through 38 Processing helix chain 'B5' and resid 7 through 14 Processing helix chain 'B5' and resid 32 through 37 removed outlier: 4.572A pdb=" N LYSB5 36 " --> pdb=" O ILEB5 32 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALAB5 37 " --> pdb=" O LEUB5 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B5' and resid 32 through 37' Processing helix chain 'B5' and resid 38 through 46 Proline residue: B5 46 - end of helix Processing helix chain 'B5' and resid 51 through 63 removed outlier: 4.649A pdb=" N GLYB5 56 " --> pdb=" O LYSB5 52 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEUB5 57 " --> pdb=" O GLYB5 53 " (cutoff:3.500A) Proline residue: B5 63 - end of helix Processing helix chain 'B5' and resid 26 through 31 removed outlier: 4.512A pdb=" N LEUB5 29 " --> pdb=" O HISB5 26 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARGB5 30 " --> pdb=" O ALAB5 27 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HISB5 31 " --> pdb=" O ASNB5 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B5' and resid 26 through 31' Processing helix chain 'B7' and resid 42 through 53 removed outlier: 3.862A pdb=" N THRB7 53 " --> pdb=" O ARGB7 49 " (cutoff:3.500A) Processing helix chain 'B7' and resid 55 through 64 Processing helix chain 'CA' and resid 34 through 50 removed outlier: 3.572A pdb=" N ARGCA 44 " --> pdb=" O GLYCA 40 " (cutoff:3.500A) Processing helix chain 'CA' and resid 77 through 89 removed outlier: 4.249A pdb=" N GLYCA 87 " --> pdb=" O LEUCA 83 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEUCA 88 " --> pdb=" O ASNCA 84 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALACA 89 " --> pdb=" O LEUCA 85 " (cutoff:3.500A) Processing helix chain 'CA' and resid 154 through 163 Processing helix chain 'CA' and resid 212 through 233 removed outlier: 4.522A pdb=" N ARGCA 218 " --> pdb=" O GLUCA 214 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLUCA 229 " --> pdb=" O ALACA 225 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALACA 230 " --> pdb=" O GLUCA 226 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHECA 231 " --> pdb=" O GLNCA 227 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALCA 232 " --> pdb=" O LEUCA 228 " (cutoff:3.500A) Processing helix chain 'CB' and resid 34 through 49 removed outlier: 3.957A pdb=" N ALACB 42 " --> pdb=" O THRCB 38 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERCB 49 " --> pdb=" O ARGCB 45 " (cutoff:3.500A) Processing helix chain 'CB' and resid 77 through 89 removed outlier: 3.559A pdb=" N LEUCB 88 " --> pdb=" O ASNCB 84 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALACB 89 " --> pdb=" O LEUCB 85 " (cutoff:3.500A) Processing helix chain 'CB' and resid 212 through 230 removed outlier: 4.375A pdb=" N ARGCB 218 " --> pdb=" O GLUCB 214 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNCB 227 " --> pdb=" O ILECB 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEUCB 228 " --> pdb=" O LEUCB 224 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALACB 230 " --> pdb=" O GLUCB 226 " (cutoff:3.500A) Processing helix chain 'CC' and resid 4 through 11 removed outlier: 4.771A pdb=" N LYSCC 9 " --> pdb=" O TYRCC 5 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARGCC 10 " --> pdb=" O THRCC 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILECC 11 " --> pdb=" O GLUCC 7 " (cutoff:3.500A) Processing helix chain 'CC' and resid 28 through 40 removed outlier: 3.873A pdb=" N SERCC 34 " --> pdb=" O ILECC 30 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYSCC 37 " --> pdb=" O ASPCC 33 " (cutoff:3.500A) Processing helix chain 'CC' and resid 48 through 57 Processing helix chain 'CC' and resid 81 through 89 Processing helix chain 'CC' and resid 205 through 214 removed outlier: 4.568A pdb=" N ILECC 209 " --> pdb=" O PROCC 205 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEUCC 210 " --> pdb=" O ALACC 206 " (cutoff:3.500A) Processing helix chain 'CC' and resid 216 through 225 Processing helix chain 'CC' and resid 242 through 247 removed outlier: 4.468A pdb=" N LEUCC 246 " --> pdb=" O VALCC 242 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARGCC 247 " --> pdb=" O PROCC 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 242 through 247' Processing helix chain 'CC' and resid 270 through 281 Processing helix chain 'CC' and resid 288 through 296 removed outlier: 3.771A pdb=" N ILECC 292 " --> pdb=" O PROCC 288 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYSCC 295 " --> pdb=" O TYRCC 291 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VALCC 296 " --> pdb=" O ILECC 292 " (cutoff:3.500A) Processing helix chain 'CC' and resid 318 through 329 removed outlier: 3.526A pdb=" N GLYCC 329 " --> pdb=" O LEUCC 325 " (cutoff:3.500A) Processing helix chain 'CC' and resid 345 through 355 Proline residue: CC 355 - end of helix Processing helix chain 'CC' and resid 358 through 371 Processing helix chain 'CC' and resid 378 through 390 removed outlier: 4.411A pdb=" N GLUCC 382 " --> pdb=" O ARGCC 378 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SERCC 383 " --> pdb=" O GLUCC 379 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEUCC 384 " --> pdb=" O ALACC 380 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASNCC 387 " --> pdb=" O SERCC 383 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHECC 389 " --> pdb=" O PHECC 385 " (cutoff:3.500A) Processing helix chain 'CC' and resid 398 through 410 Processing helix chain 'CC' and resid 421 through 438 removed outlier: 3.681A pdb=" N VALCC 428 " --> pdb=" O ASPCC 424 " (cutoff:3.500A) Processing helix chain 'CC' and resid 447 through 452 removed outlier: 6.035A pdb=" N ARGCC 452 " --> pdb=" O LEUCC 448 " (cutoff:3.500A) Processing helix chain 'CC' and resid 455 through 480 removed outlier: 4.479A pdb=" N GLUCC 461 " --> pdb=" O GLYCC 457 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLUCC 477 " --> pdb=" O ARGCC 473 " (cutoff:3.500A) Processing helix chain 'CC' and resid 483 through 488 removed outlier: 6.742A pdb=" N LEUCC 487 " --> pdb=" O ASPCC 483 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N METCC 488 " --> pdb=" O LEUCC 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 483 through 488' Processing helix chain 'CC' and resid 489 through 508 removed outlier: 5.446A pdb=" N ASNCC 494 " --> pdb=" O GLNCC 490 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ALACC 495 " --> pdb=" O ASPCC 491 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N LYSCC 496 " --> pdb=" O METCC 492 " (cutoff:3.500A) Proline residue: CC 497 - end of helix Processing helix chain 'CC' and resid 519 through 529 removed outlier: 3.716A pdb=" N ILECC 524 " --> pdb=" O PROCC 520 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARGCC 529 " --> pdb=" O THRCC 525 " (cutoff:3.500A) Processing helix chain 'CC' and resid 544 through 549 removed outlier: 3.692A pdb=" N ASPCC 549 " --> pdb=" O PHECC 545 " (cutoff:3.500A) Processing helix chain 'CC' and resid 568 through 573 removed outlier: 3.562A pdb=" N ILECC 572 " --> pdb=" O ASNCC 568 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASNCC 573 " --> pdb=" O ILECC 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 568 through 573' Processing helix chain 'CC' and resid 607 through 615 removed outlier: 4.253A pdb=" N GLYCC 612 " --> pdb=" O ALACC 608 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASNCC 613 " --> pdb=" O ILECC 609 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYRCC 614 " --> pdb=" O GLUCC 610 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VALCC 615 " --> pdb=" O GLUCC 611 " (cutoff:3.500A) Processing helix chain 'CC' and resid 662 through 668 removed outlier: 4.924A pdb=" N ILECC 668 " --> pdb=" O GLYCC 664 " (cutoff:3.500A) Processing helix chain 'CC' and resid 670 through 675 removed outlier: 4.285A pdb=" N ASPCC 674 " --> pdb=" O PHECC 670 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASPCC 675 " --> pdb=" O LEUCC 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 670 through 675' Processing helix chain 'CC' and resid 676 through 689 removed outlier: 4.618A pdb=" N ARGCC 687 " --> pdb=" O ALACC 683 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLNCC 688 " --> pdb=" O ASNCC 684 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALACC 689 " --> pdb=" O METCC 685 " (cutoff:3.500A) Processing helix chain 'CC' and resid 703 through 713 removed outlier: 4.813A pdb=" N ALACC 707 " --> pdb=" O GLYCC 703 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VALCC 710 " --> pdb=" O ARGCC 706 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLYCC 713 " --> pdb=" O ALACC 709 " (cutoff:3.500A) Processing helix chain 'CC' and resid 819 through 826 removed outlier: 3.988A pdb=" N VALCC 823 " --> pdb=" O SERCC 819 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASPCC 826 " --> pdb=" O VALCC 822 " (cutoff:3.500A) Processing helix chain 'CC' and resid 858 through 863 Processing helix chain 'CC' and resid 944 through 980 removed outlier: 3.717A pdb=" N ASPCC 959 " --> pdb=" O GLNCC 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLUCC 963 " --> pdb=" O ASPCC 959 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILECC 966 " --> pdb=" O GLUCC 962 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VALCC 978 " --> pdb=" O ARGCC 974 " (cutoff:3.500A) Processing helix chain 'CC' and resid 993 through 1000 removed outlier: 5.503A pdb=" N LEUCC 998 " --> pdb=" O ARGCC 994 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLUCC 999 " --> pdb=" O ASPCC 995 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEUCC1000 " --> pdb=" O ARGCC 996 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1005 through 1038 removed outlier: 3.862A pdb=" N ASNCC1009 " --> pdb=" O GLUCC1005 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHECC1025 " --> pdb=" O LEUCC1021 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLUCC1030 " --> pdb=" O GLUCC1026 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1081 through 1086 removed outlier: 3.757A pdb=" N METCC1085 " --> pdb=" O PROCC1081 " (cutoff:3.500A) Proline residue: CC1086 - end of helix No H-bonds generated for 'chain 'CC' and resid 1081 through 1086' Processing helix chain 'CC' and resid 1100 through 1107 Proline residue: CC1104 - end of helix Processing helix chain 'CC' and resid 1109 through 1135 removed outlier: 3.706A pdb=" N LEUCC1113 " --> pdb=" O ILECC1109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLYCC1125 " --> pdb=" O ALACC1121 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLNCC1135 " --> pdb=" O METCC1131 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1137 through 1151 removed outlier: 3.563A pdb=" N GLUCC1143 " --> pdb=" O ALACC1139 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEUCC1151 " --> pdb=" O ARGCC1147 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1160 through 1165 removed outlier: 4.151A pdb=" N PHECC1164 " --> pdb=" O ASPCC1160 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SERCC1165 " --> pdb=" O LEUCC1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 1160 through 1165' Processing helix chain 'CC' and resid 1166 through 1177 removed outlier: 3.866A pdb=" N ASNCC1175 " --> pdb=" O ARGCC1171 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1191 through 1203 removed outlier: 3.709A pdb=" N GLUCC1197 " --> pdb=" O ALACC1193 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASPCC1203 " --> pdb=" O LEUCC1199 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1238 through 1243 removed outlier: 4.035A pdb=" N LYSCC1242 " --> pdb=" O LEUCC1238 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1271 through 1282 removed outlier: 4.438A pdb=" N GLYCC1282 " --> pdb=" O LEUCC1278 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1283 through 1292 removed outlier: 4.067A pdb=" N LEUCC1287 " --> pdb=" O ALACC1283 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1297 through 1311 removed outlier: 4.457A pdb=" N THRCC1302 " --> pdb=" O VALCC1298 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1320 through 1334 removed outlier: 3.967A pdb=" N LEUCC1333 " --> pdb=" O GLUCC1329 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLYCC1334 " --> pdb=" O ILECC1330 " (cutoff:3.500A) Processing helix chain 'CC' and resid 656 through 661 removed outlier: 4.218A pdb=" N VALCC 660 " --> pdb=" O THRCC 657 " (cutoff:3.500A) Processing helix chain 'CD' and resid 26 through 35 removed outlier: 5.158A pdb=" N PHECD 35 " --> pdb=" O ARGCD 31 " (cutoff:3.500A) Processing helix chain 'CD' and resid 58 through 63 Processing helix chain 'CD' and resid 94 through 101 removed outlier: 4.216A pdb=" N ARGCD 98 " --> pdb=" O GLNCD 94 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARGCD 99 " --> pdb=" O THRCD 95 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLUCD 100 " --> pdb=" O LYSCD 96 " (cutoff:3.500A) Processing helix chain 'CD' and resid 113 through 119 Processing helix chain 'CD' and resid 122 through 129 Processing helix chain 'CD' and resid 131 through 141 removed outlier: 3.982A pdb=" N PHECD 141 " --> pdb=" O ARGCD 137 " (cutoff:3.500A) Processing helix chain 'CD' and resid 161 through 172 removed outlier: 4.016A pdb=" N GLUCD 170 " --> pdb=" O LEUCD 166 " (cutoff:3.500A) Processing helix chain 'CD' and resid 181 through 192 removed outlier: 3.615A pdb=" N ILECD 185 " --> pdb=" O GLYCD 181 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N METCD 192 " --> pdb=" O LEUCD 188 " (cutoff:3.500A) Processing helix chain 'CD' and resid 193 through 208 removed outlier: 3.587A pdb=" N GLUCD 203 " --> pdb=" O GLUCD 199 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASNCD 206 " --> pdb=" O ARGCD 202 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLUCD 207 " --> pdb=" O GLUCD 203 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THRCD 208 " --> pdb=" O GLUCD 204 " (cutoff:3.500A) Processing helix chain 'CD' and resid 211 through 231 removed outlier: 5.210A pdb=" N LYSCD 216 " --> pdb=" O THRCD 212 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLUCD 225 " --> pdb=" O ILECD 221 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLYCD 231 " --> pdb=" O PHECD 227 " (cutoff:3.500A) Processing helix chain 'CD' and resid 233 through 239 removed outlier: 4.534A pdb=" N METCD 237 " --> pdb=" O LYSCD 233 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILECD 238 " --> pdb=" O PROCD 234 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEUCD 239 " --> pdb=" O GLUCD 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 233 through 239' Processing helix chain 'CD' and resid 246 through 251 removed outlier: 4.039A pdb=" N ARGCD 250 " --> pdb=" O PROCD 246 " (cutoff:3.500A) Proline residue: CD 251 - end of helix No H-bonds generated for 'chain 'CD' and resid 246 through 251' Processing helix chain 'CD' and resid 263 through 286 removed outlier: 3.803A pdb=" N ASPCD 267 " --> pdb=" O SERCD 263 " (cutoff:3.500A) Processing helix chain 'CD' and resid 288 through 308 removed outlier: 3.883A pdb=" N ALACD 305 " --> pdb=" O GLUCD 301 " (cutoff:3.500A) Processing helix chain 'CD' and resid 326 through 333 removed outlier: 3.527A pdb=" N LYSCD 332 " --> pdb=" O ALACD 328 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLYCD 333 " --> pdb=" O ASPCD 329 " (cutoff:3.500A) Processing helix chain 'CD' and resid 369 through 378 removed outlier: 3.962A pdb=" N LYSCD 378 " --> pdb=" O LEUCD 374 " (cutoff:3.500A) Processing helix chain 'CD' and resid 379 through 389 removed outlier: 4.234A pdb=" N LEUCD 387 " --> pdb=" O GLYCD 383 " (cutoff:3.500A) Processing helix chain 'CD' and resid 393 through 404 removed outlier: 4.094A pdb=" N LYSCD 399 " --> pdb=" O LYSCD 395 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLUCD 404 " --> pdb=" O METCD 400 " (cutoff:3.500A) Processing helix chain 'CD' and resid 405 through 417 removed outlier: 4.386A pdb=" N TRPCD 409 " --> pdb=" O GLUCD 405 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASPCD 410 " --> pdb=" O ALACD 406 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLUCD 414 " --> pdb=" O ASPCD 410 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARGCD 417 " --> pdb=" O ASPCD 413 " (cutoff:3.500A) Processing helix chain 'CD' and resid 430 through 435 removed outlier: 4.340A pdb=" N ILECD 434 " --> pdb=" O HISCD 430 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLNCD 435 " --> pdb=" O ARGCD 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 430 through 435' Processing helix chain 'CD' and resid 450 through 458 removed outlier: 4.412A pdb=" N ALACD 455 " --> pdb=" O PROCD 451 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALACD 456 " --> pdb=" O LEUCD 452 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYRCD 457 " --> pdb=" O VALCD 453 " (cutoff:3.500A) Processing helix chain 'CD' and resid 473 through 483 Processing helix chain 'CD' and resid 485 through 490 removed outlier: 3.967A pdb=" N ASNCD 489 " --> pdb=" O METCD 485 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILECD 490 " --> pdb=" O SERCD 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 485 through 490' Processing helix chain 'CD' and resid 503 through 515 Processing helix chain 'CD' and resid 529 through 540 removed outlier: 3.741A pdb=" N GLYCD 540 " --> pdb=" O LEUCD 536 " (cutoff:3.500A) Processing helix chain 'CD' and resid 573 through 584 removed outlier: 3.640A pdb=" N METCD 581 " --> pdb=" O ALACD 577 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILECD 582 " --> pdb=" O ILECD 578 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VALCD 583 " --> pdb=" O LEUCD 579 " (cutoff:3.500A) Proline residue: CD 584 - end of helix Processing helix chain 'CD' and resid 588 through 594 removed outlier: 4.582A pdb=" N VALCD 592 " --> pdb=" O PROCD 588 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLNCD 594 " --> pdb=" O SERCD 590 " (cutoff:3.500A) Processing helix chain 'CD' and resid 597 through 612 Processing helix chain 'CD' and resid 614 through 636 removed outlier: 3.783A pdb=" N ILECD 619 " --> pdb=" O LYSCD 615 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLYCD 636 " --> pdb=" O ALACD 632 " (cutoff:3.500A) Processing helix chain 'CD' and resid 640 through 645 removed outlier: 3.831A pdb=" N METCD 644 " --> pdb=" O GLYCD 640 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VALCD 645 " --> pdb=" O ILECD 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 640 through 645' Processing helix chain 'CD' and resid 647 through 671 removed outlier: 4.529A pdb=" N HISCD 651 " --> pdb=" O PROCD 647 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUCD 652 " --> pdb=" O GLUCD 648 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALACD 659 " --> pdb=" O SERCD 655 " (cutoff:3.500A) Processing helix chain 'CD' and resid 674 through 704 removed outlier: 4.001A pdb=" N TYRCD 679 " --> pdb=" O ALACD 675 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASPCD 684 " --> pdb=" O ASNCD 680 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARGCD 692 " --> pdb=" O ALACD 688 " (cutoff:3.500A) Processing helix chain 'CD' and resid 720 through 729 Processing helix chain 'CD' and resid 733 through 741 removed outlier: 3.813A pdb=" N GLNCD 739 " --> pdb=" O ALACD 735 " (cutoff:3.500A) Processing helix chain 'CD' and resid 768 through 805 removed outlier: 3.918A pdb=" N HISCD 777 " --> pdb=" O PHECD 773 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLYCD 778 " --> pdb=" O ILECD 774 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSCD 781 " --> pdb=" O HISCD 777 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALACD 791 " --> pdb=" O ALACD 787 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASNCD 792 " --> pdb=" O LEUCD 788 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLYCD 794 " --> pdb=" O THRCD 790 " (cutoff:3.500A) Processing helix chain 'CD' and resid 834 through 839 removed outlier: 3.812A pdb=" N ARGCD 838 " --> pdb=" O PROCD 834 " (cutoff:3.500A) Processing helix chain 'CD' and resid 865 through 876 removed outlier: 4.671A pdb=" N SERCD 876 " --> pdb=" O LEUCD 872 " (cutoff:3.500A) Processing helix chain 'CD' and resid 895 through 900 Processing helix chain 'CD' and resid 914 through 931 removed outlier: 3.521A pdb=" N ILECD 918 " --> pdb=" O ALACD 914 " (cutoff:3.500A) Proline residue: CD 926 - end of helix removed outlier: 5.422A pdb=" N GLNCD 929 " --> pdb=" O GLUCD 925 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEUCD 930 " --> pdb=" O PROCD 926 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THRCD 931 " --> pdb=" O GLYCD 927 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1063 through 1068 removed outlier: 5.215A pdb=" N THRCD1068 " --> pdb=" O SERCD1064 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1069 through 1075 removed outlier: 6.164A pdb=" N LEUCD1074 " --> pdb=" O GLYCD1070 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARGCD1075 " --> pdb=" O GLYCD1071 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1137 through 1147 removed outlier: 3.839A pdb=" N VALCD1141 " --> pdb=" O GLYCD1137 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEUCD1144 " --> pdb=" O ARGCD1140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALACD1147 " --> pdb=" O ASPCD1143 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1216 through 1224 Processing helix chain 'CD' and resid 1225 through 1245 removed outlier: 4.694A pdb=" N VALCD1240 " --> pdb=" O GLUCD1236 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYRCD1241 " --> pdb=" O VALCD1237 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEUCD1243 " --> pdb=" O ASPCD1239 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1249 through 1262 removed outlier: 4.270A pdb=" N ILECD1253 " --> pdb=" O ASNCD1249 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILECD1256 " --> pdb=" O HISCD1252 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLNCD1259 " --> pdb=" O VALCD1255 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARGCD1262 " --> pdb=" O ARGCD1258 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1281 through 1296 removed outlier: 3.746A pdb=" N GLUCD1291 " --> pdb=" O ILECD1287 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1308 through 1316 removed outlier: 4.742A pdb=" N LEUCD1314 " --> pdb=" O THRCD1310 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THRCD1316 " --> pdb=" O ALACD1312 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1318 through 1326 removed outlier: 3.580A pdb=" N ALACD1322 " --> pdb=" O SERCD1318 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHECD1325 " --> pdb=" O SERCD1321 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLNCD1326 " --> pdb=" O ALACD1322 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1327 through 1339 removed outlier: 3.668A pdb=" N THRCD1333 " --> pdb=" O THRCD1329 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALACD1336 " --> pdb=" O LEUCD1332 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1346 through 1354 removed outlier: 4.121A pdb=" N ASNCD1350 " --> pdb=" O GLYCD1346 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1360 through 1373 removed outlier: 4.649A pdb=" N ARGCD1373 " --> pdb=" O ARGCD1369 " (cutoff:3.500A) Processing helix chain 'CD' and resid 336 through 341 removed outlier: 4.313A pdb=" N ASNCD 341 " --> pdb=" O GLYCD 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'CD' and resid 336 through 341' Processing helix chain 'CE' and resid 6 through 14 removed outlier: 3.798A pdb=" N LYSCE 12 " --> pdb=" O ASPCE 8 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLYCE 14 " --> pdb=" O VALCE 10 " (cutoff:3.500A) Processing helix chain 'CE' and resid 15 through 32 removed outlier: 5.651A pdb=" N LEUCE 19 " --> pdb=" O ASNCE 15 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VALCE 20 " --> pdb=" O ARGCE 16 " (cutoff:3.500A) Processing helix chain 'CE' and resid 45 through 57 removed outlier: 3.645A pdb=" N LEUCE 51 " --> pdb=" O THRCE 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLUCE 55 " --> pdb=" O LEUCE 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLUCE 56 " --> pdb=" O ARGCE 52 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLYCE 57 " --> pdb=" O GLUCE 53 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'AB' and resid 67 through 71 Processing sheet with id= 2, first strand: chain 'AC' and resid 54 through 59 Processing sheet with id= 3, first strand: chain 'AC' and resid 164 through 169 removed outlier: 5.620A pdb=" N ARGAC 164 " --> pdb=" O GLYAC 155 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASPAC 181 " --> pdb=" O LYSAC 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'AD' and resid 141 through 145 removed outlier: 6.560A pdb=" N METAD 178 " --> pdb=" O ILEAD 145 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AE' and resid 12 through 16 removed outlier: 6.920A pdb=" N LEUAE 36 " --> pdb=" O ILEAE 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'AE' and resid 84 through 88 removed outlier: 3.688A pdb=" N ALAAE 99 " --> pdb=" O ASNAE 122 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASNAE 122 " --> pdb=" O ALAAE 99 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AE' and resid 33 through 40 Processing sheet with id= 8, first strand: chain 'AF' and resid 38 through 42 removed outlier: 5.646A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'AF' and resid 43 through 47 removed outlier: 5.896A pdb=" N LEUAF 47 " --> pdb=" O HISAF 55 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N HISAF 55 " --> pdb=" O LEUAF 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AG' and resid 72 through 79 removed outlier: 6.024A pdb=" N THRAG 72 " --> pdb=" O VALAG 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'AH' and resid 23 through 29 removed outlier: 6.531A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'AH' and resid 74 through 77 removed outlier: 3.552A pdb=" N SERAH 74 " --> pdb=" O ALAAH 130 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VALAH 103 " --> pdb=" O ILEAH 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'AI' and resid 5 through 11 Processing sheet with id= 14, first strand: chain 'AJ' and resid 42 through 52 removed outlier: 4.104A pdb=" N LEUAJ 71 " --> pdb=" O PROAJ 43 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'AK' and resid 42 through 45 Processing sheet with id= 16, first strand: chain 'AL' and resid 29 through 32 removed outlier: 5.308A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'AL' and resid 36 through 41 removed outlier: 5.033A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'AP' and resid 4 through 10 Processing sheet with id= 19, first strand: chain 'AQ' and resid 7 through 11 removed outlier: 6.876A pdb=" N GLUAQ 60 " --> pdb=" O VALAQ 76 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'AQ' and resid 19 through 30 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'AS' and resid 30 through 33 Processing sheet with id= 22, first strand: chain 'BC' and resid 80 through 83 removed outlier: 6.701A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLYBC 127 " --> pdb=" O GLNBC 115 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLNBC 117 " --> pdb=" O GLYBC 127 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'BC' and resid 139 through 142 removed outlier: 4.409A pdb=" N SERBC 139 " --> pdb=" O ILEBC 164 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BC' and resid 165 through 168 removed outlier: 3.545A pdb=" N TYRBC 171 " --> pdb=" O ASPBC 168 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BC' and resid 90 through 96 removed outlier: 5.477A pdb=" N ASNBC 90 " --> pdb=" O ALABC 106 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLUBC 100 " --> pdb=" O TYRBC 96 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BD' and resid 3 through 9 removed outlier: 6.647A pdb=" N LYSBD 105 " --> pdb=" O VALBD 177 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BD' and resid 10 through 16 removed outlier: 3.723A pdb=" N GLYBD 10 " --> pdb=" O VALBD 26 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BD' and resid 36 through 39 removed outlier: 3.554A pdb=" N ALABD 47 " --> pdb=" O LYSBD 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BD' and resid 46 through 51 removed outlier: 5.622A pdb=" N ARGBD 46 " --> pdb=" O LEUBD 84 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BE' and resid 1 through 6 removed outlier: 4.256A pdb=" N SERBE 10 " --> pdb=" O LEUBE 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BE' and resid 117 through 120 Processing sheet with id= 32, first strand: chain 'BF' and resid 65 through 69 removed outlier: 7.818A pdb=" N ILEBF 85 " --> pdb=" O VALBF 40 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLYBF 39 " --> pdb=" O GLYBF 151 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLYBF 151 " --> pdb=" O GLYBF 39 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLYBF 126 " --> pdb=" O THRBF 158 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BG' and resid 16 through 19 Processing sheet with id= 34, first strand: chain 'BG' and resid 41 through 45 Processing sheet with id= 35, first strand: chain 'BG' and resid 94 through 98 Processing sheet with id= 36, first strand: chain 'BG' and resid 121 through 125 removed outlier: 5.672A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BH' and resid 16 through 20 removed outlier: 4.608A pdb=" N ASPBH 17 " --> pdb=" O LEUBH 5 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLNBH 2 " --> pdb=" O ALABH 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYSBH 35 " --> pdb=" O LEUBH 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BH' and resid 76 through 81 removed outlier: 5.002A pdb=" N GLUBH 76 " --> pdb=" O LYSBH 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SERBH 131 " --> pdb=" O ARGBH 116 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLUBH 114 " --> pdb=" O GLNBH 133 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BK' and resid 52 through 57 removed outlier: 4.861A pdb=" N ASPBK 19 " --> pdb=" O LEUBK 140 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BK' and resid 74 through 78 removed outlier: 7.680A pdb=" N GLYBK 83 " --> pdb=" O THRBK 78 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BL' and resid 6 through 9 removed outlier: 6.765A pdb=" N LYSBL 40 " --> pdb=" O ILEBL 22 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BL' and resid 8 through 11 Processing sheet with id= 43, first strand: chain 'BN' and resid 37 through 40 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'BN' and resid 62 through 65 removed outlier: 6.467A pdb=" N LEUBN 33 " --> pdb=" O LEUBN 102 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BN' and resid 30 through 36 removed outlier: 8.120A pdb=" N SERBN 30 " --> pdb=" O LYSBN 133 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYSBN 127 " --> pdb=" O VALBN 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BO' and resid 33 through 37 removed outlier: 3.618A pdb=" N ALABO 108 " --> pdb=" O ARGBO 103 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLYBO 101 " --> pdb=" O METBO 110 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BP' and resid 49 through 52 Processing sheet with id= 48, first strand: chain 'BQ' and resid 38 through 45 removed outlier: 6.682A pdb=" N THRBQ 25 " --> pdb=" O LYSBQ 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BQ' and resid 49 through 53 removed outlier: 4.706A pdb=" N ARGBQ 53 " --> pdb=" O HISBQ 56 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SERBQ 57 " --> pdb=" O THRBQ 76 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BS' and resid 11 through 15 Processing sheet with id= 51, first strand: chain 'BS' and resid 18 through 21 removed outlier: 6.676A pdb=" N ASPBS 95 " --> pdb=" O VALBS 64 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYSBS 60 " --> pdb=" O THRBS 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BS' and resid 57 through 60 Processing sheet with id= 53, first strand: chain 'BS' and resid 65 through 68 Processing sheet with id= 54, first strand: chain 'BS' and resid 71 through 78 Processing sheet with id= 55, first strand: chain 'BT' and resid 2 through 8 removed outlier: 4.855A pdb=" N THRBT 100 " --> pdb=" O GLYBT 79 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BT' and resid 81 through 88 removed outlier: 4.010A pdb=" N ARGBT 92 " --> pdb=" O ARGBT 88 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BU' and resid 12 through 15 removed outlier: 5.207A pdb=" N VALBU 31 " --> pdb=" O HISBU 15 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASNBU 28 " --> pdb=" O LEUBU 87 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYSBU 81 " --> pdb=" O VALBU 34 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYSBU 66 " --> pdb=" O ARGBU 77 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASPBU 79 " --> pdb=" O LYSBU 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYSBU 64 " --> pdb=" O ASPBU 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYSBU 81 " --> pdb=" O VALBU 62 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VALBU 62 " --> pdb=" O LYSBU 81 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALABU 83 " --> pdb=" O THRBU 60 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THRBU 60 " --> pdb=" O ALABU 83 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VALBU 85 " --> pdb=" O VALBU 58 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VALBU 58 " --> pdb=" O VALBU 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BV' and resid 40 through 45 removed outlier: 5.332A pdb=" N ASNBV 40 " --> pdb=" O ALABV 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BV' and resid 82 through 87 removed outlier: 7.155A pdb=" N ARGBV 82 " --> pdb=" O LYSBV 97 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ARGBV 94 " --> pdb=" O ILEBV 103 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BW' and resid 39 through 42 removed outlier: 6.663A pdb=" N ALABW 39 " --> pdb=" O ARGBW 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BX' and resid 51 through 54 Processing sheet with id= 62, first strand: chain 'BX' and resid 66 through 71 Processing sheet with id= 63, first strand: chain 'BY' and resid 12 through 19 removed outlier: 3.676A pdb=" N SERBY 19 " --> pdb=" O ASNBY 23 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASNBY 23 " --> pdb=" O SERBY 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'BY' and resid 34 through 41 Processing sheet with id= 65, first strand: chain 'B1' and resid 33 through 39 removed outlier: 7.624A pdb=" N METB1 54 " --> pdb=" O THRB1 10 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'B2' and resid 29 through 32 removed outlier: 4.176A pdb=" N GLUB2 36 " --> pdb=" O ASPB2 31 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'B3' and resid 8 through 13 removed outlier: 6.369A pdb=" N HISB3 19 " --> pdb=" O SERB3 13 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'B3' and resid 34 through 39 removed outlier: 6.160A pdb=" N LEUB3 34 " --> pdb=" O GLUB3 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'B5' and resid 22 through 25 removed outlier: 5.593A pdb=" N PHEB5 22 " --> pdb=" O VALB5 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'B6' and resid 13 through 19 removed outlier: 8.160A pdb=" N ASNB6 13 " --> pdb=" O SERB6 28 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'B7' and resid 20 through 25 removed outlier: 4.868A pdb=" N ASNB7 20 " --> pdb=" O CYSB7 16 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'CA' and resid 15 through 18 removed outlier: 3.607A pdb=" N ASPCA 15 " --> pdb=" O THRCA 27 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THRCA 22 " --> pdb=" O THRCA 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLUCA 188 " --> pdb=" O LYSCA 200 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'CA' and resid 53 through 56 removed outlier: 8.111A pdb=" N SERCA 141 " --> pdb=" O ASPCA 62 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLUCA 60 " --> pdb=" O ARGCA 143 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THRCA 57 " --> pdb=" O VALCA 173 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'CA' and resid 90 through 93 removed outlier: 6.682A pdb=" N ASPCA 120 " --> pdb=" O GLNCA 93 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'CA' and resid 108 through 111 removed outlier: 3.646A pdb=" N CYSCA 131 " --> pdb=" O VALCA 110 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'CA' and resid 96 through 105 removed outlier: 7.497A pdb=" N ASPCA 96 " --> pdb=" O ARGCA 148 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'CB' and resid 22 through 29 removed outlier: 5.257A pdb=" N THRCB 22 " --> pdb=" O THRCB 207 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'CB' and resid 96 through 106 removed outlier: 6.580A pdb=" N ASPCB 96 " --> pdb=" O ARGCB 148 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALACB 138 " --> pdb=" O GLYCB 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLUCB 58 " --> pdb=" O LYSCB 145 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N THRCB 57 " --> pdb=" O VALCB 173 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLYCB 151 " --> pdb=" O TYRCB 177 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'CC' and resid 12 through 15 Processing sheet with id= 80, first strand: chain 'CC' and resid 66 through 71 removed outlier: 6.789A pdb=" N LYSCC 99 " --> pdb=" O VALCC 71 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'CC' and resid 142 through 145 removed outlier: 6.746A pdb=" N GLUCC 142 " --> pdb=" O METCC 515 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'CC' and resid 155 through 159 removed outlier: 5.621A pdb=" N TYRCC 172 " --> pdb=" O PHECC 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASNCC 193 " --> pdb=" O ASPCC 189 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'CC' and resid 236 through 240 removed outlier: 5.265A pdb=" N LYSCC 236 " --> pdb=" O ARGCC 233 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARGCC 233 " --> pdb=" O LYSCC 236 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILECC 229 " --> pdb=" O GLUCC 240 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'CC' and resid 579 through 582 removed outlier: 4.952A pdb=" N PHECC 586 " --> pdb=" O ASNCC 582 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'CC' and resid 632 through 637 removed outlier: 8.147A pdb=" N ASPCC 632 " --> pdb=" O ARGCC 647 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'CC' and resid 725 through 728 removed outlier: 4.808A pdb=" N ARGCC 731 " --> pdb=" O ASPCC 728 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SERCC 730 " --> pdb=" O LEUCC 753 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VALCC 736 " --> pdb=" O GLYCC 747 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLYCC 747 " --> pdb=" O VALCC 736 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'CC' and resid 767 through 770 removed outlier: 7.420A pdb=" N LEUCC 783 " --> pdb=" O CYSCC 770 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'CC' and resid 829 through 841 removed outlier: 8.467A pdb=" N LEUCC1047 " --> pdb=" O ARGCC 936 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASPCC 930 " --> pdb=" O TYRCC1053 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'CC' and resid 848 through 851 removed outlier: 4.300A pdb=" N GLYCC 885 " --> pdb=" O THRCC 851 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'CC' and resid 1072 through 1075 removed outlier: 4.863A pdb=" N ASNCC1072 " --> pdb=" O GLYCC1068 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYSCC1065 " --> pdb=" O LEUCC1235 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THRCC1226 " --> pdb=" O PHECC 804 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'CC' and resid 1212 through 1215 removed outlier: 5.520A pdb=" N LEUCC1212 " --> pdb=" O PHECC1221 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLUCC1219 " --> pdb=" O ASPCC1214 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'CC' and resid 100 through 105 No H-bonds generated for sheet with id= 92 Processing sheet with id= 93, first strand: chain 'CC' and resid 93 through 97 No H-bonds generated for sheet with id= 93 Processing sheet with id= 94, first strand: chain 'CD' and resid 19 through 22 removed outlier: 3.651A pdb=" N LYSCD1340 " --> pdb=" O ILECD 22 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'CD' and resid 82 through 86 removed outlier: 4.404A pdb=" N VALCD 83 " --> pdb=" O VALCD 92 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VALCD 90 " --> pdb=" O CYSCD 85 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'CD' and resid 102 through 107 removed outlier: 3.721A pdb=" N GLYCD 103 " --> pdb=" O VALCD 244 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THRCD 240 " --> pdb=" O LEUCD 107 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'CD' and resid 144 through 147 Processing sheet with id= 98, first strand: chain 'CD' and resid 349 through 354 removed outlier: 6.530A pdb=" N TYRCD 349 " --> pdb=" O VALCD 470 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'CD' and resid 364 through 368 Processing sheet with id=100, first strand: chain 'CD' and resid 525 through 528 removed outlier: 4.496A pdb=" N GLUCD 562 " --> pdb=" O ASPCD 558 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'CD' and resid 706 through 709 removed outlier: 5.343A pdb=" N GLNCD 712 " --> pdb=" O ARGCD 709 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'CD' and resid 819 through 823 Processing sheet with id=103, first strand: chain 'CD' and resid 954 through 957 removed outlier: 5.789A pdb=" N ASNCD 954 " --> pdb=" O GLYCD1013 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLYCD1013 " --> pdb=" O ASNCD 954 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'CD' and resid 964 through 967 removed outlier: 5.237A pdb=" N LYSCD 964 " --> pdb=" O THRCD 976 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'CD' and resid 980 through 985 removed outlier: 4.552A pdb=" N THRCD 980 " --> pdb=" O VALCD 997 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VALCD 997 " --> pdb=" O THRCD 980 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLUCD 993 " --> pdb=" O LEUCD 984 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'CD' and resid 1001 through 1004 removed outlier: 7.266A pdb=" N VALCD1017 " --> pdb=" O ALACD1004 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'CD' and resid 1024 through 1028 removed outlier: 3.650A pdb=" N ALACD1122 " --> pdb=" O VALCD1027 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'CD' and resid 1045 through 1048 removed outlier: 7.165A pdb=" N THRCD1045 " --> pdb=" O LEUCD1062 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALCD1060 " --> pdb=" O THRCD1047 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALACD1105 " --> pdb=" O VALCD1061 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'CD' and resid 1076 through 1080 removed outlier: 5.000A pdb=" N ALACD1097 " --> pdb=" O ILECD1080 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'CD' and resid 1161 through 1166 removed outlier: 6.961A pdb=" N ARGCD1174 " --> pdb=" O GLYCD1166 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYRCD1186 " --> pdb=" O ILECD1177 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'CD' and resid 1263 through 1267 removed outlier: 4.403A pdb=" N LYSCD1263 " --> pdb=" O ASPCD1305 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THRCD1301 " --> pdb=" O VALCD1267 " (cutoff:3.500A) 3003 hydrogen bonds defined for protein. 8862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4199 hydrogen bonds 6624 hydrogen bond angles 0 basepair planarities 1667 basepair parallelities 2496 stacking parallelities Total time for adding SS restraints: 251.79 Time building geometry restraints manager: 60.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 16222 1.28 - 1.41: 67385 1.41 - 1.55: 91952 1.55 - 1.69: 9639 1.69 - 1.82: 452 Bond restraints: 185650 Sorted by residual: bond pdb=" C4 5MUBA1939 " pdb=" C5 5MUBA1939 " ideal model delta sigma weight residual 1.805 1.469 0.336 2.00e-02 2.50e+03 2.83e+02 bond pdb=" C4 5MUBA 747 " pdb=" C5 5MUBA 747 " ideal model delta sigma weight residual 1.805 1.472 0.333 2.00e-02 2.50e+03 2.77e+02 bond pdb=" C4 5MUAX 54 " pdb=" C5 5MUAX 54 " ideal model delta sigma weight residual 1.805 1.477 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" C4 5MUAW 54 " pdb=" C5 5MUAW 54 " ideal model delta sigma weight residual 1.805 1.480 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" N1 5MUBA1939 " pdb=" C6 5MUBA1939 " ideal model delta sigma weight residual 1.638 1.327 0.311 2.00e-02 2.50e+03 2.42e+02 ... (remaining 185645 not shown) Histogram of bond angle deviations from ideal: 91.53 - 102.72: 9772 102.72 - 113.91: 131706 113.91 - 125.10: 113974 125.10 - 136.28: 18883 136.28 - 147.47: 11 Bond angle restraints: 274346 Sorted by residual: angle pdb=" C1' MIAAX 37 " pdb=" N9 MIAAX 37 " pdb=" C8 MIAAX 37 " ideal model delta sigma weight residual 81.43 122.23 -40.80 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C1' 2MGAA 966 " pdb=" N9 2MGAA 966 " pdb=" C4 2MGAA 966 " ideal model delta sigma weight residual 109.53 147.47 -37.94 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C1' 2MGBA1835 " pdb=" N9 2MGBA1835 " pdb=" C4 2MGBA1835 " ideal model delta sigma weight residual 109.53 147.46 -37.93 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C1' 2MGBA2445 " pdb=" N9 2MGBA2445 " pdb=" C4 2MGBA2445 " ideal model delta sigma weight residual 109.53 145.77 -36.24 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C1' 2MGAA1516 " pdb=" N9 2MGAA1516 " pdb=" C4 2MGAA1516 " ideal model delta sigma weight residual 109.53 145.56 -36.03 3.00e+00 1.11e-01 1.44e+02 ... (remaining 274341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 96197 35.61 - 71.22: 4252 71.22 - 106.83: 352 106.83 - 142.44: 31 142.44 - 178.05: 18 Dihedral angle restraints: 100850 sinusoidal: 75481 harmonic: 25369 Sorted by residual: dihedral pdb=" CA HISB5 31 " pdb=" C HISB5 31 " pdb=" N ILEB5 32 " pdb=" CA ILEB5 32 " ideal model delta harmonic sigma weight residual -180.00 -120.44 -59.56 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA HISAE 89 " pdb=" C HISAE 89 " pdb=" N THRAE 90 " pdb=" CA THRAE 90 " ideal model delta harmonic sigma weight residual -180.00 -124.74 -55.26 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA VALAM 65 " pdb=" C VALAM 65 " pdb=" N GLUAM 66 " pdb=" CA GLUAM 66 " ideal model delta harmonic sigma weight residual -180.00 -131.14 -48.86 0 5.00e+00 4.00e-02 9.55e+01 ... (remaining 100847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 31140 0.104 - 0.208: 2909 0.208 - 0.312: 344 0.312 - 0.416: 57 0.416 - 0.520: 12 Chirality restraints: 34462 Sorted by residual: chirality pdb=" CA SERCC 712 " pdb=" N SERCC 712 " pdb=" C SERCC 712 " pdb=" CB SERCC 712 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" CA LEUCC 448 " pdb=" N LEUCC 448 " pdb=" C LEUCC 448 " pdb=" CB LEUCC 448 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CB ILECC1079 " pdb=" CA ILECC1079 " pdb=" CG1 ILECC1079 " pdb=" CG2 ILECC1079 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.50e+00 ... (remaining 34459 not shown) Planarity restraints: 17135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2UBA2449 " -0.913 2.00e-02 2.50e+03 6.11e-01 8.39e+03 pdb=" C4' H2UBA2449 " 0.203 2.00e-02 2.50e+03 pdb=" O4' H2UBA2449 " 0.717 2.00e-02 2.50e+03 pdb=" C3' H2UBA2449 " -0.196 2.00e-02 2.50e+03 pdb=" O3' H2UBA2449 " 0.960 2.00e-02 2.50e+03 pdb=" C2' H2UBA2449 " -0.613 2.00e-02 2.50e+03 pdb=" O2' H2UBA2449 " -0.649 2.00e-02 2.50e+03 pdb=" C1' H2UBA2449 " 0.455 2.00e-02 2.50e+03 pdb=" N1 H2UBA2449 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MCAA1407 " -0.068 2.00e-02 2.50e+03 6.05e-01 8.23e+03 pdb=" C4' 5MCAA1407 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 5MCAA1407 " -0.622 2.00e-02 2.50e+03 pdb=" C3' 5MCAA1407 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 5MCAA1407 " 0.656 2.00e-02 2.50e+03 pdb=" C2' 5MCAA1407 " 0.168 2.00e-02 2.50e+03 pdb=" O2' 5MCAA1407 " -0.990 2.00e-02 2.50e+03 pdb=" C1' 5MCAA1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MCAA1407 " 0.922 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGBA2445 " -0.064 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' 2MGBA2445 " -0.419 2.00e-02 2.50e+03 pdb=" O4' 2MGBA2445 " -0.583 2.00e-02 2.50e+03 pdb=" C3' 2MGBA2445 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MGBA2445 " 0.660 2.00e-02 2.50e+03 pdb=" C2' 2MGBA2445 " 0.147 2.00e-02 2.50e+03 pdb=" O2' 2MGBA2445 " -1.033 2.00e-02 2.50e+03 pdb=" C1' 2MGBA2445 " -0.219 2.00e-02 2.50e+03 pdb=" N9 2MGBA2445 " 0.918 2.00e-02 2.50e+03 ... (remaining 17132 not shown) Histogram of nonbonded interaction distances: 0.28 - 1.21: 21 1.21 - 2.13: 254 2.13 - 3.05: 106549 3.05 - 3.98: 545961 3.98 - 4.90: 938225 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1591010 Sorted by model distance: nonbonded pdb=" CG PROAC 98 " pdb=" CE LYSCD 74 " model vdw 0.284 3.840 nonbonded pdb=" NE ARGAC 88 " pdb=" ND1 HISCD 80 " model vdw 0.604 3.200 nonbonded pdb=" CZ ARGAC 88 " pdb=" CG HISCD 80 " model vdw 0.641 3.490 nonbonded pdb=" O GLUAC 85 " pdb=" CG LYSCD 79 " model vdw 0.682 3.440 nonbonded pdb=" N LYSAC 89 " pdb=" NZ LYSCD 79 " model vdw 0.779 3.200 ... (remaining 1591005 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 'CA' and (resid 6 through 157 or resid 169 through 233)) selection = (chain 'CB' and resid 6 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4793 5.49 5 Mg 487 5.21 5 S 258 5.16 5 C 89478 2.51 5 N 31858 2.21 5 O 45968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.100 Extract box with map and model: 34.310 Check model and map are aligned: 1.740 Convert atoms to be neutral: 0.990 Process input model: 569.020 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 622.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.013 0.336 185650 Z= 0.832 Angle : 1.115 40.804 274346 Z= 0.620 Chirality : 0.065 0.520 34462 Planarity : 0.021 0.611 17135 Dihedral : 16.314 178.051 84504 Min Nonbonded Distance : 0.284 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.80 % Favored : 93.54 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.08), residues: 8760 helix: -0.79 (0.07), residues: 3077 sheet: -1.67 (0.12), residues: 1512 loop : -1.72 (0.09), residues: 4171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2302 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1926 time to evaluate : 7.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 376 outliers final: 73 residues processed: 2166 average time/residue: 2.2684 time to fit residues: 7089.3710 Evaluate side-chains 1404 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1331 time to evaluate : 7.897 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 58 residues processed: 19 average time/residue: 1.1757 time to fit residues: 49.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1132 optimal weight: 4.9990 chunk 1016 optimal weight: 20.0000 chunk 563 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 685 optimal weight: 6.9990 chunk 543 optimal weight: 10.0000 chunk 1051 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 639 optimal weight: 7.9990 chunk 782 optimal weight: 6.9990 chunk 1217 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 24 ASN AB 51 ASN AB 94 HIS AC 123 GLN AC 140 ASN AD 126 ASN ** AD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 12 GLN ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 68 ASN AG 142 HIS AJ 15 HIS ** AK 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 28 GLN AO 37 ASN AO 40 GLN AR 52 GLN AS 69 HIS AT 48 GLN AT 82 GLN BC 70 ASN BC 163 GLN BD 136 ASN BE 41 GLN BE 90 GLN BF 127 ASN BG 45 HIS BH 66 ASN BK 67 ASN BK 128 ASN BN 45 GLN BO 18 GLN BQ 7 GLN BQ 15 GLN BQ 56 HIS BQ 66 ASN BR 20 GLN BR 59 GLN BR 71 GLN BS 86 GLN ** BU 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BV 46 GLN BV 69 ASN ** BV 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 12 GLN BZ 20 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 147 GLN CC 618 GLN CC 799 ASN CC1116 HIS CC1299 ASN CD 206 ASN CD 266 ASN CD 294 ASN CD 623 GLN CD 792 ASN CD 921 GLN CD 954 ASN CD1108 GLN CD1218 HIS CE 60 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 185650 Z= 0.437 Angle : 0.799 16.096 274346 Z= 0.422 Chirality : 0.044 0.423 34462 Planarity : 0.007 0.138 17135 Dihedral : 14.371 179.414 67050 Min Nonbonded Distance : 0.964 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.08 % Rotamer Outliers : 5.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: -0.72 (0.09), residues: 8760 helix: 0.90 (0.09), residues: 3101 sheet: -1.12 (0.12), residues: 1548 loop : -1.27 (0.09), residues: 4111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 1474 time to evaluate : 8.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 421 outliers final: 168 residues processed: 1737 average time/residue: 2.0619 time to fit residues: 5286.5127 Evaluate side-chains 1467 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1299 time to evaluate : 7.865 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 121 residues processed: 51 average time/residue: 1.3790 time to fit residues: 128.4879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 676 optimal weight: 10.0000 chunk 377 optimal weight: 0.8980 chunk 1013 optimal weight: 0.8980 chunk 829 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 1219 optimal weight: 0.8980 chunk 1317 optimal weight: 9.9990 chunk 1086 optimal weight: 0.0470 chunk 1209 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 978 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 140 ASN ** AD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN AE 135 ASN ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 142 HIS AI 5 GLN AI 110 GLN AJ 20 GLN AK 22 HIS ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN AT 82 GLN BC 153 GLN BC 163 GLN BD 36 GLN BE 24 ASN BE 41 GLN BE 97 ASN BE 115 GLN BE 165 HIS ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 73 ASN BK 67 ASN BK 128 ASN BO 107 ASN BQ 15 GLN BR 20 GLN BR 59 GLN BR 71 GLN BS 86 GLN BU 48 GLN BV 40 ASN BW 12 GLN BZ 20 ASN B1 20 HIS ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 147 GLN CB 128 HIS CC1299 ASN CD 720 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.115 185650 Z= 0.151 Angle : 0.628 16.743 274346 Z= 0.345 Chirality : 0.035 0.365 34462 Planarity : 0.006 0.125 17135 Dihedral : 13.993 177.253 67050 Min Nonbonded Distance : 1.106 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -0.08 (0.09), residues: 8760 helix: 1.49 (0.09), residues: 3104 sheet: -0.73 (0.12), residues: 1538 loop : -0.96 (0.09), residues: 4118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1853 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1501 time to evaluate : 7.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 352 outliers final: 144 residues processed: 1725 average time/residue: 2.0790 time to fit residues: 5321.6549 Evaluate side-chains 1442 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1298 time to evaluate : 7.790 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 109 residues processed: 36 average time/residue: 1.6030 time to fit residues: 101.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1205 optimal weight: 10.0000 chunk 917 optimal weight: 0.5980 chunk 633 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 582 optimal weight: 7.9990 chunk 819 optimal weight: 0.0020 chunk 1224 optimal weight: 9.9990 chunk 1296 optimal weight: 20.0000 chunk 639 optimal weight: 8.9990 chunk 1160 optimal weight: 7.9990 chunk 349 optimal weight: 0.5980 overall best weight: 3.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AE 73 ASN AE 146 ASN ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 GLN AT 82 GLN BC 60 GLN BC 163 GLN BE 24 ASN BF 27 GLN BG 73 ASN BK 67 ASN BK 128 ASN BK 136 GLN BO 18 GLN BO 107 ASN BQ 15 GLN BQ 66 ASN BR 20 GLN BR 52 GLN BR 71 GLN BS 86 GLN BU 91 GLN BV 40 ASN BW 12 GLN BX 40 GLN BY 16 ASN BZ 20 ASN B1 9 GLN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 20 ASN CB 84 ASN CC 133 ASN CC 327 GLN CC 628 HIS CC 658 GLN CC 856 ASN CC1257 GLN ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.042 185650 Z= 0.319 Angle : 0.695 106.100 274346 Z= 0.364 Chirality : 0.037 0.375 34462 Planarity : 0.006 0.130 17135 Dihedral : 13.879 176.715 67050 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.90 % 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: -0.09 (0.09), residues: 8760 helix: 1.34 (0.09), residues: 3102 sheet: -0.63 (0.12), residues: 1578 loop : -0.89 (0.09), residues: 4080 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1324 time to evaluate : 8.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 368 outliers final: 188 residues processed: 1548 average time/residue: 2.1147 time to fit residues: 4885.5289 Evaluate side-chains 1447 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1259 time to evaluate : 8.031 Switching outliers to nearest non-outliers outliers start: 188 outliers final: 139 residues processed: 49 average time/residue: 1.4081 time to fit residues: 128.6739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1079 optimal weight: 0.8980 chunk 735 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 965 optimal weight: 6.9990 chunk 534 optimal weight: 7.9990 chunk 1106 optimal weight: 4.9990 chunk 895 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 661 optimal weight: 6.9990 chunk 1163 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AD 54 GLN ** AE 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AJ 58 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 GLN AQ 9 GLN AT 82 GLN BC 163 GLN BE 24 ASN BE 90 GLN BE 115 GLN BE 136 GLN BF 27 GLN BG 73 ASN BK 67 ASN BK 128 ASN BK 136 GLN BO 18 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BS 86 GLN BV 40 ASN BW 12 GLN BW 78 GLN BY 16 ASN BZ 20 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CB 84 ASN CC 490 GLN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC1135 GLN ** CD 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CD 294 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.172 185650 Z= 0.418 Angle : 0.735 14.243 274346 Z= 0.391 Chirality : 0.042 0.418 34462 Planarity : 0.007 0.137 17135 Dihedral : 14.035 178.009 67050 Min Nonbonded Distance : 0.969 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer Outliers : 5.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: -0.27 (0.09), residues: 8760 helix: 1.06 (0.09), residues: 3097 sheet: -0.57 (0.13), residues: 1574 loop : -0.95 (0.09), residues: 4089 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 408 poor density : 1302 time to evaluate : 8.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 408 outliers final: 219 residues processed: 1557 average time/residue: 2.0403 time to fit residues: 4732.4182 Evaluate side-chains 1454 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1235 time to evaluate : 7.838 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 154 residues processed: 67 average time/residue: 1.4320 time to fit residues: 170.6832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 436 optimal weight: 10.0000 chunk 1167 optimal weight: 10.0000 chunk 256 optimal weight: 0.9980 chunk 761 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 1297 optimal weight: 10.0000 chunk 1077 optimal weight: 6.9990 chunk 600 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 429 optimal weight: 20.0000 chunk 681 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 18 HIS ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AD 40 GLN ** AE 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 GLN AT 82 GLN BC 163 GLN BE 24 ASN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 11 ASN BK 67 ASN BK 128 ASN BK 136 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 71 GLN BS 86 GLN BV 40 ASN BW 12 GLN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 37 GLN CA 84 ASN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 490 GLN CC 799 ASN CC 955 GLN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC1268 GLN ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.858 185650 Z= 0.328 Angle : 0.733 106.040 274346 Z= 0.384 Chirality : 0.039 0.410 34462 Planarity : 0.007 0.135 17135 Dihedral : 14.022 178.269 67050 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.90 % 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: -0.25 (0.09), residues: 8760 helix: 1.05 (0.09), residues: 3100 sheet: -0.53 (0.13), residues: 1558 loop : -0.92 (0.09), residues: 4102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1268 time to evaluate : 8.109 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 333 outliers final: 219 residues processed: 1494 average time/residue: 2.0584 time to fit residues: 4593.4085 Evaluate side-chains 1460 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1241 time to evaluate : 8.018 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 168 residues processed: 53 average time/residue: 1.4310 time to fit residues: 137.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1250 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 739 optimal weight: 5.9990 chunk 947 optimal weight: 6.9990 chunk 734 optimal weight: 8.9990 chunk 1092 optimal weight: 6.9990 chunk 724 optimal weight: 2.9990 chunk 1292 optimal weight: 2.9990 chunk 808 optimal weight: 9.9990 chunk 787 optimal weight: 5.9990 chunk 596 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN ** AE 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 49 GLN AT 48 GLN AT 82 GLN BC 163 GLN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN BK 136 GLN BO 18 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 71 GLN BS 86 GLN BV 40 ASN BW 12 GLN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CC 955 GLN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 45 ASN ** CD 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.038 185650 Z= 0.474 Angle : 0.767 106.099 274346 Z= 0.398 Chirality : 0.043 0.424 34462 Planarity : 0.007 0.137 17135 Dihedral : 14.013 177.873 67050 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.90 % 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: -0.31 (0.09), residues: 8760 helix: 0.98 (0.09), residues: 3092 sheet: -0.53 (0.13), residues: 1566 loop : -0.95 (0.09), residues: 4102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1248 time to evaluate : 8.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 332 outliers final: 232 residues processed: 1468 average time/residue: 2.1491 time to fit residues: 4726.2100 Evaluate side-chains 1465 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1233 time to evaluate : 8.810 Switching outliers to nearest non-outliers outliers start: 232 outliers final: 180 residues processed: 53 average time/residue: 1.5684 time to fit residues: 151.9049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 799 optimal weight: 8.9990 chunk 516 optimal weight: 7.9990 chunk 771 optimal weight: 0.9990 chunk 389 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 821 optimal weight: 1.9990 chunk 880 optimal weight: 0.0570 chunk 639 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 1015 optimal weight: 30.0000 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AG 130 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN AT 82 GLN BC 163 GLN BE 97 ASN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN BK 136 GLN BO 18 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 71 GLN BS 86 GLN BV 40 ASN BW 12 GLN BZ 20 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 41 ASN CC 799 ASN CC 808 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.332 185650 Z= 0.186 Angle : 0.630 15.621 274346 Z= 0.344 Chirality : 0.035 0.375 34462 Planarity : 0.006 0.126 17135 Dihedral : 13.832 177.176 67050 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: -0.05 (0.09), residues: 8760 helix: 1.23 (0.09), residues: 3102 sheet: -0.39 (0.13), residues: 1544 loop : -0.84 (0.09), residues: 4114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1602 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1323 time to evaluate : 8.793 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 279 outliers final: 187 residues processed: 1536 average time/residue: 2.0622 time to fit residues: 4728.0470 Evaluate side-chains 1438 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1251 time to evaluate : 7.751 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 161 residues processed: 26 average time/residue: 1.3924 time to fit residues: 70.4400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1175 optimal weight: 0.9990 chunk 1238 optimal weight: 1.9990 chunk 1129 optimal weight: 5.9990 chunk 1204 optimal weight: 0.6980 chunk 1237 optimal weight: 0.9990 chunk 724 optimal weight: 2.9990 chunk 524 optimal weight: 8.9990 chunk 945 optimal weight: 9.9990 chunk 369 optimal weight: 1.9990 chunk 1088 optimal weight: 8.9990 chunk 1139 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AD 40 GLN AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 82 GLN BC 163 GLN BE 24 ASN BE 97 ASN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN BK 136 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BS 86 GLN BV 40 ASN BW 12 GLN BX 40 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 294 ASN ** CD 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.507 185650 Z= 0.232 Angle : 0.648 73.900 274346 Z= 0.349 Chirality : 0.035 0.843 34462 Planarity : 0.006 0.126 17135 Dihedral : 13.831 177.180 67050 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.04 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: -0.05 (0.09), residues: 8760 helix: 1.24 (0.09), residues: 3102 sheet: -0.39 (0.13), residues: 1544 loop : -0.84 (0.09), residues: 4114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1255 time to evaluate : 8.019 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 183 residues processed: 1432 average time/residue: 2.1318 time to fit residues: 4571.9282 Evaluate side-chains 1432 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1249 time to evaluate : 7.912 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 162 residues processed: 21 average time/residue: 1.4844 time to fit residues: 61.6915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 1200 optimal weight: 0.9990 chunk 790 optimal weight: 0.8980 chunk 1273 optimal weight: 30.0000 chunk 777 optimal weight: 0.1980 chunk 604 optimal weight: 7.9990 chunk 885 optimal weight: 2.9990 chunk 1335 optimal weight: 1.9990 chunk 1229 optimal weight: 3.9990 chunk 1063 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 821 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AD 40 GLN AE 83 HIS AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 82 GLN BC 163 GLN BE 24 ASN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN BK 136 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BS 86 GLN BV 40 ASN BW 12 GLN BX 40 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 294 ASN ** CD 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.948 185650 Z= 0.246 Angle : 0.683 105.773 274346 Z= 0.359 Chirality : 0.035 0.872 34462 Planarity : 0.006 0.126 17135 Dihedral : 13.831 177.188 67050 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.02 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.90 % 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: -0.05 (0.09), residues: 8760 helix: 1.24 (0.09), residues: 3102 sheet: -0.40 (0.13), residues: 1549 loop : -0.84 (0.09), residues: 4109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1254 time to evaluate : 8.042 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 178 residues processed: 1422 average time/residue: 2.0499 time to fit residues: 4355.0381 Evaluate side-chains 1420 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1242 time to evaluate : 7.937 Switching outliers to nearest non-outliers outliers start: 178 outliers final: 165 residues processed: 14 average time/residue: 1.7655 time to fit residues: 47.4792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1341 random chunks: chunk 652 optimal weight: 8.9990 chunk 845 optimal weight: 10.0000 chunk 1133 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 chunk 980 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 1065 optimal weight: 8.9990 chunk 445 optimal weight: 10.0000 chunk 1094 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN AD 40 GLN AJ 20 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 82 GLN BE 24 ASN BE 136 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN BK 136 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BS 86 GLN BV 40 ASN BW 12 GLN BX 40 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 294 ASN ** CD 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.081112 restraints weight = 323020.624| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.07 r_work: 0.2931 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.2901 rms_B_bonded: 1.22 restraints_weight: 0.1250 r_work: 0.2883 rms_B_bonded: 1.43 restraints_weight: 0.0625 r_work: 0.2861 rms_B_bonded: 1.74 restraints_weight: 0.0312 r_work: 0.2834 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.2799 rms_B_bonded: 2.72 restraints_weight: 0.0078 r_work: 0.2755 rms_B_bonded: 3.51 restraints_weight: 0.0039 r_work: 0.2693 rms_B_bonded: 4.66 restraints_weight: 0.0020 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.947 185650 Z= 0.246 Angle : 0.683 105.744 274346 Z= 0.359 Chirality : 0.035 0.871 34462 Planarity : 0.006 0.126 17135 Dihedral : 13.831 177.188 67050 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.03 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.90 % 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: -0.05 (0.09), residues: 8760 helix: 1.24 (0.09), residues: 3102 sheet: -0.40 (0.13), residues: 1549 loop : -0.84 (0.09), residues: 4109 =============================================================================== Job complete usr+sys time: 60736.37 seconds wall clock time: 1046 minutes 51.12 seconds (62811.12 seconds total)