Starting phenix.real_space_refine (version: dev) on Tue Apr 12 09:29:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426_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/6zu1_11426/04_2022/6zu1_11426_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zu1_11426/04_2022/6zu1_11426_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: 0.15s 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: 11 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 53 106.431 120.288 57.063 1.00 31.76 S ATOM A0Z7G SG CYSB6 11 172.014 174.480 73.640 1.00 44.52 S ATOM A0Z85 SG CYSB6 14 172.655 170.941 73.667 1.00 40.41 S ATOM A0ZB0 SG CYSB6 27 175.089 173.216 74.707 1.00 40.40 S ATOM A0ZH2 SG CYSB7 16 61.001 175.683 65.737 1.00 66.47 S ATOM A1BST SG CYSCD 70 117.519 235.116 175.398 1.00111.48 S ATOM A1BT7 SG CYSCD 72 120.975 236.082 174.927 1.00114.84 S ATOM A1GAV SG CYSCD 814 82.463 230.395 232.413 1.00 70.39 S ATOM A1GQK SG CYSCD 888 83.067 232.580 230.192 1.00 52.47 S ATOM A1GRZ SG CYSCD 895 80.522 230.712 229.612 1.00 59.80 S ATOM A1GSK SG CYSCD 898 80.066 233.028 231.882 1.00 54.18 S Time building chain proxies: 64.32, per 1000 atoms: 0.37 Number of scatterers: 172846 At special positions: 0 Unit cell: (252.48, 331.38, 293.508, 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: 53.53 Conformation dependent library (CDL) restraints added in 10.6 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: 70.64 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: 4.248A 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: 5.679A 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: 4.523A 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: 4.772A 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: 3.676A 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: 3.535A 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: 4.215A 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: 5.162A 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: 3.772A pdb=" N ILECC 292 " --> pdb=" O PROCC 288 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYSCC 295 " --> pdb=" O TYRCC 291 " (cutoff:3.500A) removed outlier: 5.919A 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: 4.725A pdb=" N SERCC 383 " --> pdb=" O GLUCC 379 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.796A 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: 3.981A pdb=" N GLUCC 477 " --> pdb=" O ARGCC 473 " (cutoff:3.500A) Processing helix chain 'CC' and resid 483 through 488 removed outlier: 6.743A 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: 5.444A 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: 3.740A pdb=" N ARGCC 529 " --> pdb=" O THRCC 525 " (cutoff:3.500A) Processing helix chain 'CC' and resid 544 through 549 removed outlier: 3.693A 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: 4.252A 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: 4.216A pdb=" N TYRCC 614 " --> pdb=" O GLUCC 610 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VALCC 615 " --> pdb=" O GLUCC 611 " (cutoff:3.500A) Processing helix chain 'CC' and resid 662 through 668 removed outlier: 4.925A 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: 4.493A 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: 4.648A pdb=" N VALCC 978 " --> pdb=" O ARGCC 974 " (cutoff:3.500A) Processing helix chain 'CC' and resid 993 through 1000 removed outlier: 5.505A 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: 4.118A pdb=" N GLUCC1030 " --> pdb=" O GLUCC1026 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1081 through 1086 removed outlier: 3.758A 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: 3.707A pdb=" N LEUCC1113 " --> pdb=" O ILECC1109 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLYCC1125 " --> pdb=" O ALACC1121 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLNCC1135 " --> pdb=" O METCC1131 " (cutoff:3.500A) Processing helix chain 'CC' and resid 1137 through 1151 removed outlier: 3.564A 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: 3.867A 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: 4.357A 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: 4.439A 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: 4.615A 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: 5.157A 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: 3.616A pdb=" N ILECD 185 " --> pdb=" O GLYCD 181 " (cutoff:3.500A) removed outlier: 3.648A 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: 4.702A pdb=" N ASNCD 206 " --> pdb=" O ARGCD 202 " (cutoff:3.500A) removed outlier: 3.755A 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: 5.209A pdb=" N LYSCD 216 " --> pdb=" O THRCD 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLUCD 225 " --> pdb=" O ILECD 221 " (cutoff:3.500A) removed outlier: 5.343A 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: 4.592A 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: 3.881A pdb=" N ALACD 305 " --> pdb=" O GLUCD 301 " (cutoff:3.500A) Processing helix chain 'CD' and resid 326 through 333 removed outlier: 3.528A 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: 4.233A pdb=" N LEUCD 387 " --> pdb=" O GLYCD 383 " (cutoff:3.500A) Processing helix chain 'CD' and resid 393 through 404 removed outlier: 4.095A 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: 4.663A pdb=" N ASPCD 410 " --> pdb=" O ALACD 406 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLUCD 414 " --> pdb=" O ASPCD 410 " (cutoff:3.500A) removed outlier: 4.562A 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: 5.204A 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: 3.911A 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: 4.583A 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: 3.782A 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: 5.798A 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: 4.217A pdb=" N ALACD 659 " --> pdb=" O SERCD 655 " (cutoff:3.500A) Processing helix chain 'CD' and resid 674 through 704 removed outlier: 4.000A pdb=" N TYRCD 679 " --> pdb=" O ALACD 675 " (cutoff:3.500A) removed outlier: 3.927A 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: 3.812A 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: 3.833A pdb=" N GLYCD 778 " --> pdb=" O ILECD 774 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.522A pdb=" N ILECD 918 " --> pdb=" O ALACD 914 " (cutoff:3.500A) Proline residue: CD 926 - end of helix removed outlier: 5.423A 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: 5.955A 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: 3.976A 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: 4.693A pdb=" N VALCD1240 " --> pdb=" O GLUCD1236 " (cutoff:3.500A) removed outlier: 3.524A 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: 4.423A pdb=" N ILECD1256 " --> pdb=" O HISCD1252 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLNCD1259 " --> pdb=" O VALCD1255 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARGCD1262 " --> pdb=" O ARGCD1258 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1281 through 1296 removed outlier: 3.745A pdb=" N GLUCD1291 " --> pdb=" O ILECD1287 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1308 through 1316 removed outlier: 4.741A pdb=" N LEUCD1314 " --> pdb=" O THRCD1310 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THRCD1316 " --> pdb=" O ALACD1312 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1318 through 1326 removed outlier: 3.578A pdb=" N ALACD1322 " --> pdb=" O SERCD1318 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHECD1325 " --> pdb=" O SERCD1321 " (cutoff:3.500A) removed outlier: 3.619A 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: 4.122A pdb=" N ASNCD1350 " --> pdb=" O GLYCD1346 " (cutoff:3.500A) Processing helix chain 'CD' and resid 1360 through 1373 removed outlier: 4.650A pdb=" N ARGCD1373 " --> pdb=" O ARGCD1369 " (cutoff:3.500A) Processing helix chain 'CD' and resid 336 through 341 removed outlier: 4.312A 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: 3.797A 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: 5.652A pdb=" N LEUCE 19 " --> pdb=" O ASNCE 15 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALCE 20 " --> pdb=" O ARGCE 16 " (cutoff:3.500A) Processing helix chain 'CE' and resid 45 through 57 removed outlier: 3.644A pdb=" N LEUCE 51 " --> pdb=" O THRCE 47 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.926A 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: 3.608A pdb=" N ASPCA 15 " --> pdb=" O THRCA 27 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THRCA 22 " --> pdb=" O THRCA 207 " (cutoff:3.500A) removed outlier: 3.627A 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: 8.110A 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: 6.683A 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: 3.647A 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: 7.496A 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: 5.545A pdb=" N ALACB 138 " --> pdb=" O GLYCB 106 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLUCB 58 " --> pdb=" O LYSCB 145 " (cutoff:3.500A) removed outlier: 5.766A 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: 6.745A 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: 5.620A pdb=" N TYRCC 172 " --> pdb=" O PHECC 188 " (cutoff:3.500A) removed outlier: 3.816A 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: 5.264A pdb=" N LYSCC 236 " --> pdb=" O ARGCC 233 " (cutoff:3.500A) removed outlier: 6.131A 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: 4.953A 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: 8.146A 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: 4.807A 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: 3.781A pdb=" N VALCC 736 " --> pdb=" O GLYCC 747 " (cutoff:3.500A) removed outlier: 6.740A 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: 3.867A 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: 4.299A 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: 4.862A pdb=" N ASNCC1072 " --> pdb=" O GLYCC1068 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYSCC1065 " --> pdb=" O LEUCC1235 " (cutoff:3.500A) removed outlier: 4.694A 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: 5.521A 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: 6.531A 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: 4.495A 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: 5.342A 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: 5.790A pdb=" N ASNCD 954 " --> pdb=" O GLYCD1013 " (cutoff:3.500A) removed outlier: 4.363A 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: 3.528A 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: 3.651A 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: 7.166A pdb=" N THRCD1045 " --> pdb=" O LEUCD1062 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALCD1060 " --> pdb=" O THRCD1047 " (cutoff:3.500A) removed outlier: 4.240A 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: 5.001A 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: 3.733A 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: 4.402A 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: 263.63 Time building geometry restraints manager: 60.15 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: 67415 1.41 - 1.55: 91921 1.55 - 1.69: 9640 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: 91.50 - 102.69: 9658 102.69 - 113.89: 131643 113.89 - 125.08: 114100 125.08 - 136.28: 18934 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: 96194 35.61 - 71.22: 4250 71.22 - 106.83: 349 106.83 - 142.44: 31 142.44 - 178.05: 18 Dihedral angle restraints: 100842 sinusoidal: 75473 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 100839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 31144 0.104 - 0.208: 2906 0.208 - 0.312: 348 0.312 - 0.416: 55 0.416 - 0.520: 13 Chirality restraints: 34466 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 6.76e+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 1.99 0.52 2.00e-01 2.50e+01 6.66e+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 2.14 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 34463 not shown) Planarity restraints: 17134 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 17131 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 12 1.81 - 2.59: 3157 2.59 - 3.36: 202936 3.36 - 4.13: 565228 4.13 - 4.90: 819120 Nonbonded interactions: 1590453 Sorted by model distance: nonbonded pdb="MG MGBA3255 " pdb="MG MGBA3276 " model vdw 1.042 1.300 nonbonded pdb="MG MGBB 204 " pdb="MG MGBB 207 " model vdw 1.084 1.300 nonbonded pdb="MG MGBA3230 " pdb="MG MGBA3286 " model vdw 1.093 1.300 nonbonded pdb="MG MGBA3143 " pdb="MG MGBA3274 " model vdw 1.120 1.300 nonbonded pdb="MG MGBB 202 " pdb="MG MGBB 205 " model vdw 1.146 1.300 ... (remaining 1590448 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.130 Extract box with map and model: 34.710 Check model and map are aligned: 1.670 Convert atoms to be neutral: 0.970 Process input model: 588.200 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 648.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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= 0.833 Angle : 1.115 40.804 274346 Z= 0.620 Chirality : 0.065 0.520 34466 Planarity : 0.021 0.611 17134 Dihedral : 16.301 178.051 84496 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 6.42 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 2276 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1900 time to evaluate : 7.713 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 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: 376 outliers final: 76 residues processed: 2140 average time/residue: 2.2333 time to fit residues: 6904.8654 Evaluate side-chains 1434 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1358 time to evaluate : 8.494 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 59 residues processed: 19 average time/residue: 1.2508 time to fit residues: 52.4943 ------------------------------------------------------------------------------- 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: 6.9990 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: 6.9990 chunk 406 optimal weight: 8.9990 chunk 639 optimal weight: 7.9990 chunk 782 optimal weight: 7.9990 chunk 1217 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 51 ASN ** AB 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN AC 140 ASN AD 59 GLN AD 126 ASN ** AD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN AE 135 ASN ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 68 ASN ** AI 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 15 HIS AJ 20 GLN ** AK 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 49 GLN 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 37 ASN 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** ** BU 91 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 93 GLN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 824 GLN CC 834 GLN CC 922 ASN CC1116 HIS CC1299 ASN CD 266 ASN CD 489 ASN CD 651 HIS CD 865 HIS CD 954 ASN CD1108 GLN CD1218 HIS CE 62 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.070 185650 Z= 0.533 Angle : 0.840 16.255 274346 Z= 0.439 Chirality : 0.048 0.433 34466 Planarity : 0.008 0.143 17134 Dihedral : 14.443 178.524 67042 Min Nonbonded Distance : 0.931 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer Outliers : 5.68 % 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: -0.83 (0.09), residues: 8760 helix: 0.74 (0.09), residues: 3113 sheet: -1.18 (0.12), residues: 1580 loop : -1.28 (0.09), residues: 4067 *********************** 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 1863 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1444 time to evaluate : 7.720 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 419 outliers final: 163 residues processed: 1690 average time/residue: 2.0666 time to fit residues: 5175.6013 Evaluate side-chains 1448 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1285 time to evaluate : 7.442 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 113 residues processed: 51 average time/residue: 1.3973 time to fit residues: 130.4662 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1013 optimal weight: 1.9990 chunk 829 optimal weight: 0.6980 chunk 335 optimal weight: 1.9990 chunk 1219 optimal weight: 3.9990 chunk 1317 optimal weight: 0.9980 chunk 1086 optimal weight: 10.0000 chunk 1209 optimal weight: 30.0000 chunk 415 optimal weight: 9.9990 chunk 978 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 24 ASN AC 140 ASN AD 152 GLN AE 83 HIS ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 110 GLN AJ 20 GLN AK 22 HIS AK 81 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN AT 82 GLN BC 153 GLN BC 163 GLN BE 24 ASN BE 41 GLN BE 97 ASN BE 165 HIS ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 73 ASN BK 67 ASN BK 128 ASN BO 18 GLN BO 107 ASN BQ 15 GLN BR 20 GLN BR 59 GLN BR 71 GLN BS 86 GLN BU 48 GLN BU 91 GLN BV 40 ASN BW 12 GLN BZ 20 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN CB 84 ASN ** CB 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 238 GLN CC 922 ASN CC1299 ASN CD 458 ASN CD 720 ASN CD 865 HIS CD 954 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 185650 Z= 0.171 Angle : 0.632 15.575 274346 Z= 0.347 Chirality : 0.036 0.410 34466 Planarity : 0.006 0.125 17134 Dihedral : 14.024 177.935 67042 Min Nonbonded Distance : 1.046 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.19 (0.09), residues: 8760 helix: 1.36 (0.09), residues: 3109 sheet: -0.82 (0.12), residues: 1531 loop : -0.97 (0.09), residues: 4120 *********************** 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 1865 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1489 time to evaluate : 7.452 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 outliers start: 376 outliers final: 146 residues processed: 1727 average time/residue: 2.1092 time to fit residues: 5393.3369 Evaluate side-chains 1461 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1315 time to evaluate : 7.413 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 110 residues processed: 39 average time/residue: 1.4754 time to fit residues: 104.7691 ------------------------------------------------------------------------------- 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: 8.9990 chunk 917 optimal weight: 10.0000 chunk 633 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 582 optimal weight: 7.9990 chunk 819 optimal weight: 0.0270 chunk 1224 optimal weight: 8.9990 chunk 1296 optimal weight: 40.0000 chunk 639 optimal weight: 8.9990 chunk 1160 optimal weight: 5.9990 chunk 349 optimal weight: 0.6980 overall best weight: 4.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 140 ASN AE 73 ASN AE 83 HIS AI 110 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN 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 BO 107 ASN BQ 15 GLN BQ 66 ASN BR 20 GLN BR 52 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** CA 84 ASN CA 93 GLN CA 103 ASN CA 227 GLN ** CC 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 618 GLN CC 620 ASN CC 658 GLN CC 856 ASN CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 266 ASN CD 651 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 185650 Z= 0.378 Angle : 0.708 15.174 274346 Z= 0.378 Chirality : 0.041 0.434 34466 Planarity : 0.007 0.136 17134 Dihedral : 14.019 178.250 67042 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer Outliers : 5.44 % 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: -0.26 (0.09), residues: 8760 helix: 1.16 (0.09), residues: 3104 sheet: -0.70 (0.12), residues: 1573 loop : -0.96 (0.09), residues: 4083 *********************** 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 1739 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1338 time to evaluate : 7.619 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 outliers start: 401 outliers final: 212 residues processed: 1581 average time/residue: 2.0793 time to fit residues: 4908.6901 Evaluate side-chains 1480 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1268 time to evaluate : 7.399 Switching outliers to nearest non-outliers outliers start: 212 outliers final: 150 residues processed: 65 average time/residue: 1.4563 time to fit residues: 167.7290 ------------------------------------------------------------------------------- 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: 10.0000 chunk 735 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 965 optimal weight: 6.9990 chunk 534 optimal weight: 6.9990 chunk 1106 optimal weight: 5.9990 chunk 895 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 661 optimal weight: 6.9990 chunk 1163 optimal weight: 6.9990 chunk 327 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 100 GLN AC 140 ASN AE 73 ASN AE 83 HIS ** AI 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 58 ASN AJ 99 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 8 ASN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 GLN AP 79 ASN AT 82 GLN BC 163 GLN BE 115 GLN BE 136 GLN BG 73 ASN BH 11 ASN BK 67 ASN BK 128 ASN ** BL 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 107 ASN BQ 15 GLN BR 20 GLN BR 71 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN BZ 20 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN ** CC 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 15 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 185650 Z= 0.311 Angle : 0.671 14.663 274346 Z= 0.361 Chirality : 0.039 0.407 34466 Planarity : 0.006 0.132 17134 Dihedral : 13.949 177.590 67042 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer Outliers : 5.25 % 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: -0.20 (0.09), residues: 8760 helix: 1.18 (0.09), residues: 3108 sheet: -0.62 (0.13), residues: 1573 loop : -0.91 (0.09), residues: 4079 *********************** 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 1697 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1310 time to evaluate : 7.585 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 outliers start: 387 outliers final: 214 residues processed: 1565 average time/residue: 2.0427 time to fit residues: 4776.9286 Evaluate side-chains 1446 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1232 time to evaluate : 7.511 Switching outliers to nearest non-outliers outliers start: 214 outliers final: 158 residues processed: 58 average time/residue: 1.3968 time to fit residues: 147.8873 ------------------------------------------------------------------------------- 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: 0.7980 chunk 256 optimal weight: 3.9990 chunk 761 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 1297 optimal weight: 20.0000 chunk 1077 optimal weight: 0.7980 chunk 600 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 429 optimal weight: 20.0000 chunk 681 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 100 GLN AC 140 ASN ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN AE 83 HIS AJ 20 GLN AJ 99 GLN AM 8 ASN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN AT 82 GLN BC 163 GLN BE 115 GLN BE 136 GLN BG 73 ASN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN ** BK 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 107 ASN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 71 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN CB 84 ASN CB 128 HIS ** CC 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC1135 GLN CC1257 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 185650 Z= 0.206 Angle : 0.623 19.741 274346 Z= 0.340 Chirality : 0.036 0.383 34466 Planarity : 0.006 0.127 17134 Dihedral : 13.819 177.345 67042 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.86 % Rotamer Outliers : 4.46 % 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: -0.04 (0.09), residues: 8760 helix: 1.33 (0.09), residues: 3101 sheet: -0.53 (0.13), residues: 1556 loop : -0.85 (0.09), residues: 4103 *********************** 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 1664 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1335 time to evaluate : 8.002 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 outliers start: 329 outliers final: 198 residues processed: 1576 average time/residue: 2.0722 time to fit residues: 4873.8361 Evaluate side-chains 1433 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1235 time to evaluate : 7.447 Switching outliers to nearest non-outliers outliers start: 198 outliers final: 159 residues processed: 40 average time/residue: 1.4392 time to fit residues: 106.2952 ------------------------------------------------------------------------------- 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: 5.9990 chunk 146 optimal weight: 10.0000 chunk 739 optimal weight: 2.9990 chunk 947 optimal weight: 0.0770 chunk 734 optimal weight: 6.9990 chunk 1092 optimal weight: 5.9990 chunk 724 optimal weight: 0.9980 chunk 1292 optimal weight: 2.9990 chunk 808 optimal weight: 6.9990 chunk 787 optimal weight: 4.9990 chunk 596 optimal weight: 7.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 100 GLN AC 140 ASN AD 164 GLN AE 73 ASN AE 83 HIS AG 130 ASN AJ 20 GLN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN AT 48 GLN AT 82 GLN BC 163 GLN BE 24 ASN BG 73 ASN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 33 GLN BK 67 ASN BK 128 ASN ** BK 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 98 GLN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BR 71 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN BW 78 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN CB 84 ASN CC 193 ASN CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 910 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 185650 Z= 0.239 Angle : 0.632 14.091 274346 Z= 0.343 Chirality : 0.036 0.397 34466 Planarity : 0.006 0.129 17134 Dihedral : 13.757 177.498 67042 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer Outliers : 4.33 % 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: -0.01 (0.09), residues: 8760 helix: 1.31 (0.09), residues: 3105 sheet: -0.48 (0.13), residues: 1555 loop : -0.80 (0.09), residues: 4100 *********************** 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 1594 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1275 time to evaluate : 7.778 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 outliers start: 319 outliers final: 215 residues processed: 1502 average time/residue: 2.1166 time to fit residues: 4742.0049 Evaluate side-chains 1444 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1229 time to evaluate : 7.515 Switching outliers to nearest non-outliers outliers start: 215 outliers final: 170 residues processed: 47 average time/residue: 1.4153 time to fit residues: 123.2361 ------------------------------------------------------------------------------- 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: 0.0170 chunk 516 optimal weight: 8.9990 chunk 771 optimal weight: 1.9990 chunk 389 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 821 optimal weight: 4.9990 chunk 880 optimal weight: 6.9990 chunk 639 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 1015 optimal weight: 5.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 100 GLN AC 140 ASN AD 40 GLN AE 73 ASN AE 83 HIS ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 5 GLN AJ 20 GLN AN 49 GLN AP 79 ASN AT 82 GLN BC 163 GLN BE 136 GLN BG 73 ASN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN ** BK 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BR 71 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 CA 93 GLN CA 227 GLN CB 84 ASN CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 294 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 185650 Z= 0.199 Angle : 0.622 14.392 274346 Z= 0.338 Chirality : 0.035 0.386 34466 Planarity : 0.006 0.126 17134 Dihedral : 13.738 177.423 67042 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer Outliers : 3.72 % 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: 0.03 (0.09), residues: 8760 helix: 1.32 (0.09), residues: 3106 sheet: -0.41 (0.13), residues: 1537 loop : -0.78 (0.09), residues: 4117 *********************** 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 1529 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1255 time to evaluate : 8.459 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. outliers start: 274 outliers final: 211 residues processed: 1460 average time/residue: 2.1029 time to fit residues: 4576.0794 Evaluate side-chains 1414 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1203 time to evaluate : 7.583 Switching outliers to nearest non-outliers outliers start: 211 outliers final: 179 residues processed: 35 average time/residue: 1.3792 time to fit residues: 92.2275 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1238 optimal weight: 2.9990 chunk 1129 optimal weight: 0.6980 chunk 1204 optimal weight: 2.9990 chunk 1237 optimal weight: 0.9990 chunk 724 optimal weight: 3.9990 chunk 524 optimal weight: 8.9990 chunk 945 optimal weight: 9.9990 chunk 369 optimal weight: 0.7980 chunk 1088 optimal weight: 10.0000 chunk 1139 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 100 GLN AC 140 ASN AD 40 GLN ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN AE 83 HIS ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN AT 82 GLN BC 163 GLN BE 24 ASN BG 73 ASN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BR 52 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN CB 84 ASN CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 185650 Z= 0.163 Angle : 0.614 14.526 274346 Z= 0.336 Chirality : 0.034 0.419 34466 Planarity : 0.006 0.124 17134 Dihedral : 13.715 177.361 67042 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer Outliers : 3.62 % 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: 0.07 (0.09), residues: 8760 helix: 1.36 (0.09), residues: 3100 sheet: -0.38 (0.13), residues: 1536 loop : -0.76 (0.09), residues: 4124 *********************** 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 1519 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1252 time to evaluate : 8.352 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 outliers start: 267 outliers final: 211 residues processed: 1453 average time/residue: 2.1596 time to fit residues: 4702.0807 Evaluate side-chains 1420 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1209 time to evaluate : 7.448 Switching outliers to nearest non-outliers outliers start: 211 outliers final: 176 residues processed: 40 average time/residue: 1.6173 time to fit residues: 114.8712 ------------------------------------------------------------------------------- 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: 0.8980 chunk 790 optimal weight: 10.0000 chunk 1273 optimal weight: 6.9990 chunk 777 optimal weight: 9.9990 chunk 604 optimal weight: 7.9990 chunk 885 optimal weight: 0.3980 chunk 1335 optimal weight: 2.9990 chunk 1229 optimal weight: 8.9990 chunk 1063 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 821 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 140 ASN ** AD 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN AE 83 HIS ** AI 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 8 ASN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 GLN AP 79 ASN AT 82 GLN BC 163 GLN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN BW 78 GLN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 185650 Z= 0.335 Angle : 0.680 15.843 274346 Z= 0.364 Chirality : 0.039 0.415 34466 Planarity : 0.006 0.133 17134 Dihedral : 13.777 178.565 67042 Min Nonbonded Distance : 0.999 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer Outliers : 3.17 % 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: -0.06 (0.09), residues: 8760 helix: 1.18 (0.09), residues: 3107 sheet: -0.42 (0.13), residues: 1561 loop : -0.80 (0.10), residues: 4092 ********************** 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 1458 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1224 time to evaluate : 7.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METB4 1 " (corrupted residue). Skipping it. outliers start: 234 outliers final: 183 residues processed: 1418 average time/residue: 2.1351 time to fit residues: 4513.6627 Evaluate side-chains 1383 residues out of total 7373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1200 time to evaluate : 7.806 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 167 residues processed: 18 average time/residue: 1.3715 time to fit residues: 51.7044 ------------------------------------------------------------------------------- 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: 7.9990 chunk 845 optimal weight: 4.9990 chunk 1133 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 980 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 1065 optimal weight: 5.9990 chunk 445 optimal weight: 10.0000 chunk 1094 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 140 ASN AD 40 GLN AD 164 GLN AE 73 ASN AE 83 HIS ** AF 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AJ 35 GLN ** AN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN AT 82 GLN BC 163 GLN BE 24 ASN ** BG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 67 ASN BK 128 ASN ** BQ 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 15 GLN BR 20 GLN BS 86 GLN ** BU 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 40 ASN BW 12 GLN BY 16 ASN ** B4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 84 ASN CA 93 GLN CA 227 GLN ** CB 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 628 HIS CC 922 ASN ** CC1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.079391 restraints weight = 323472.624| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.06 r_work: 0.2898 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2871 rms_B_bonded: 1.16 restraints_weight: 0.1250 r_work: 0.2856 rms_B_bonded: 1.33 restraints_weight: 0.0625 r_work: 0.2838 rms_B_bonded: 1.56 restraints_weight: 0.0312 r_work: 0.2817 rms_B_bonded: 1.87 restraints_weight: 0.0156 r_work: 0.2792 rms_B_bonded: 2.26 restraints_weight: 0.0078 r_work: 0.2761 rms_B_bonded: 2.77 restraints_weight: 0.0039 r_work: 0.2723 rms_B_bonded: 3.44 restraints_weight: 0.0020 r_work: 0.2674 rms_B_bonded: 4.34 restraints_weight: 0.0010 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 185650 Z= 0.208 Angle : 0.641 15.123 274346 Z= 0.349 Chirality : 0.036 0.452 34466 Planarity : 0.006 0.127 17134 Dihedral : 13.754 179.529 67042 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer Outliers : 3.04 % 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: -0.04 (0.09), residues: 8760 helix: 1.19 (0.09), residues: 3102 sheet: -0.41 (0.13), residues: 1541 loop : -0.77 (0.10), residues: 4117 =============================================================================== Job complete usr+sys time: 60759.07 seconds wall clock time: 1046 minutes 56.49 seconds (62816.49 seconds total)