Starting phenix.real_space_refine (version: dev) on Thu Jun 16 18:59:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug7_26486/06_2022/7ug7_26486_updated.pdb" } resolution = 2.58 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= -0.000 sd= 0.003 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 "LS PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 154353 Number of models: 1 Model: "" Number of chains: 70 Chain: "16" Number of atoms: 32505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32505 Classifications: {'RNA': 1514} Modifications used: {'rna3p': 9, 'rna2p': 1, 'rna3p_pur': 745, 'rna3p_pyr': 561, 'rna2p_pur': 115, 'rna2p_pyr': 83} Link IDs: {'rna3p': 1314, 'rna2p': 199} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 6 Chain: "SB" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1770 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "SC" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "SD" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "SE" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "SF" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "SG" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1236 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "SH" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "SI" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "SJ" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "SK" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "SL" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115, 'PCIS': 1} 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: "SM" 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: "SN" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "SO" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "SP" 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: "SQ" 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: "SR" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 555 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "SS" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "ST" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "SU" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "23" Number of atoms: 62334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62334 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1385, 'rna3p_pyr': 1064, 'rna2p_pur': 281, 'rna2p_pyr': 149} Link IDs: {'rna3p': 2466, 'rna2p': 436} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "5" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 50, 'p5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "LA" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "LB" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "LC" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Chain: "LD" 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: "LE" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "LF" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "LI" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "LJ" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 974 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "LK" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "LM" Number of atoms: 1138 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Conformer: "B" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} bond proxies already assigned to first conformer: 1139 Chain: "LN" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "LO" Number of atoms: 1063 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1052 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Conformer: "B" Number of residues, atoms: 144, 1052 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} bond proxies already assigned to first conformer: 1049 Chain: "LP" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} 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: "LQ" 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: "LR" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "LS" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "LT" 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: "LU" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "LV" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "LW" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "LX" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 721 Classifications: {'peptide': 94} Link IDs: {'TRANS': 93} Chain breaks: 1 Chain: "LY" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "La" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 595 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Lb" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Lc" 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: "Ld" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Le" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 529 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Lf" 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: "Lg" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lh" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Li" Number of atoms: 512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Conformer: "B" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} bond proxies already assigned to first conformer: 502 Chain: "Lj" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "EF" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5179 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Dt" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'rna3p': 4, 'rna2p': 1, 'rna3p_pur': 32, 'rna3p_pyr': 28, 'rna2p_pur': 6, 'rna2p_pyr': 6} Link IDs: {'rna3p': 64, 'rna2p': 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Chain: "Pt" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1637 Classifications: {'RNA': 76} Modifications used: {'rna3p': 5, 'rna2p': 3, 'p5*END': 1, 'rna3p_pur': 31, 'rna3p_pyr': 27, 'rna2p_pur': 6, 'rna2p_pyr': 4} Link IDs: {'rna3p': 63, 'rna2p': 12} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen planarities: 1 Chain: "mR" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pyr': 3, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna2p_pyr': 1} Link IDs: {'rna3p': 7, 'rna2p': 2} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 60 Classifications: {'peptide': 8} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6, 'NMTRANS': 1} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Planarities with less than four sites: {'0UO:plan-2': 1, 'DHA:plan-1': 1, 'DBB:plan-1': 1, 'BB9:plan-1': 1, 'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "16" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 89 Unusual residues: {'PUT': 2, ' MG': 77} Classifications: {'undetermined': 79} Link IDs: {None: 78} Chain: "23" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 389 Unusual residues: {'PUT': 9, ' MG': 315, 'SPD': 2} Classifications: {'undetermined': 326} Link IDs: {None: 325} Chain: "5" 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: "LB" 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: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "La" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "EF" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'GDP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Pt" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'peptide': 2} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="PHEPt3002 " pdbres=" MGPt3003 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0WWB SG CYSLe 16 63.757 117.509 200.337 1.00108.82 S ATOM A0WWN SG CYSLe 18 60.435 117.916 201.512 1.00107.71 S ATOM A0X0L SG CYSLe 37 60.834 116.676 197.875 1.00109.16 S ATOM A0X16 SG CYSLe 40 61.978 120.304 198.819 1.00111.62 S ATOM A0YM5 SG CYSLj 11 63.243 150.030 93.443 1.00 54.87 S ATOM A0YMU SG CYSLj 14 65.536 147.200 91.950 1.00 52.96 S ATOM A0YPP SG CYSLj 27 65.253 150.766 90.518 1.00 53.24 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHISLM 80 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHISLM 80 " occ=0.50 residue: pdb=" N AARGLO 78 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGLO 78 " occ=0.50 residue: pdb=" N ALYSLi 23 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYSLi 23 " occ=0.50 Time building chain proxies: 67.29, per 1000 atoms: 0.44 Number of scatterers: 154353 At special positions: 0 Unit cell: (240.312, 269.824, 267.716, 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 2 29.99 S 189 16.00 P 4702 15.00 Mg 404 11.99 O 42152 8.00 N 28613 7.00 C 78291 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: 59.04 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNLe 301 " pdb="ZN ZNLe 301 " - pdb=" SG CYSLe 40 " pdb="ZN ZNLe 301 " - pdb=" SG CYSLe 37 " pdb="ZN ZNLe 301 " - pdb=" SG CYSLe 16 " pdb="ZN ZNLe 301 " - pdb=" SG CYSLe 18 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" ND1 HISLj 33 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 27 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 11 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 14 " Number of angles added : 9 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL B 1 " Input volumes are d-peptide like pdb=" CB DBB B 6 " Number of C-beta restraints generated: 12470 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: 206 helices and 89 sheets defined 39.4% alpha, 20.0% beta 1574 base pairs and 2715 stacking pairs defined. Time for finding SS restraints: 70.96 Creating SS restraints... Processing helix chain 'SB' and resid 5 through 13 removed outlier: 3.616A pdb=" N METSB 9 " --> pdb=" O SERSB 5 " (cutoff:3.500A) Processing helix chain 'SB' and resid 42 through 64 Proline residue: SB 48 - end of helix removed outlier: 4.182A pdb=" N GLUSB 52 " --> pdb=" O PROSB 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALASB 53 " --> pdb=" O METSB 49 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARGSB 63 " --> pdb=" O LYSSB 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYSSB 64 " --> pdb=" O ILESB 60 " (cutoff:3.500A) Processing helix chain 'SB' and resid 76 through 88 removed outlier: 3.521A pdb=" N CYSSB 87 " --> pdb=" O ALASB 83 " (cutoff:3.500A) Processing helix chain 'SB' and resid 103 through 123 removed outlier: 3.869A pdb=" N ASPSB 123 " --> pdb=" O THRSB 119 " (cutoff:3.500A) Processing helix chain 'SB' and resid 130 through 148 removed outlier: 6.528A pdb=" N ALASB 134 " --> pdb=" O THRSB 130 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEUSB 135 " --> pdb=" O LYSSB 131 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N METSB 136 " --> pdb=" O LYSSB 132 " (cutoff:3.500A) Processing helix chain 'SB' and resid 165 through 170 Processing helix chain 'SB' and resid 171 through 180 Processing helix chain 'SB' and resid 206 through 229 Processing helix chain 'SC' and resid 6 through 12 removed outlier: 3.686A pdb=" N ARGSC 11 " --> pdb=" O PROSC 7 " (cutoff:3.500A) Processing helix chain 'SC' and resid 28 through 48 removed outlier: 3.739A pdb=" N GLUSC 46 " --> pdb=" O TYRSC 42 " (cutoff:3.500A) Processing helix chain 'SC' and resid 72 through 78 removed outlier: 3.808A pdb=" N VALSC 76 " --> pdb=" O ARGSC 72 " (cutoff:3.500A) Processing helix chain 'SC' and resid 81 through 96 removed outlier: 3.540A pdb=" N ALASC 95 " --> pdb=" O VALSC 91 " (cutoff:3.500A) Processing helix chain 'SC' and resid 108 through 113 removed outlier: 3.990A pdb=" N ASPSC 112 " --> pdb=" O LYSSC 108 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALASC 113 " --> pdb=" O PROSC 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 108 through 113' Processing helix chain 'SC' and resid 114 through 127 Processing helix chain 'SC' and resid 129 through 145 removed outlier: 3.633A pdb=" N LYSSC 135 " --> pdb=" O ARGSC 131 " (cutoff:3.500A) Processing helix chain 'SD' and resid 7 through 16 removed outlier: 4.395A pdb=" N LEUSD 11 " --> pdb=" O PROSD 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SERSD 12 " --> pdb=" O LYSSD 8 " (cutoff:3.500A) Processing helix chain 'SD' and resid 27 through 32 Processing helix chain 'SD' and resid 49 through 66 removed outlier: 3.577A pdb=" N TYRSD 65 " --> pdb=" O VALSD 61 " (cutoff:3.500A) Processing helix chain 'SD' and resid 68 through 83 removed outlier: 5.098A pdb=" N LYSSD 83 " --> pdb=" O ALASD 79 " (cutoff:3.500A) Processing helix chain 'SD' and resid 85 through 97 removed outlier: 3.550A pdb=" N ASNSD 89 " --> pdb=" O ASNSD 85 " (cutoff:3.500A) Processing helix chain 'SD' and resid 98 through 106 Processing helix chain 'SD' and resid 110 through 120 Processing helix chain 'SD' and resid 146 through 152 removed outlier: 4.367A pdb=" N GLNSD 152 " --> pdb=" O LYSSD 148 " (cutoff:3.500A) Processing helix chain 'SD' and resid 153 through 166 removed outlier: 3.585A pdb=" N GLNSD 164 " --> pdb=" O GLUSD 160 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLUSD 166 " --> pdb=" O ALASD 162 " (cutoff:3.500A) Processing helix chain 'SD' and resid 196 through 206 removed outlier: 4.049A pdb=" N ILESD 200 " --> pdb=" O ASNSD 196 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYSSD 206 " --> pdb=" O GLUSD 202 " (cutoff:3.500A) Processing helix chain 'SD' and resid 39 through 44 removed outlier: 4.881A pdb=" N ALASD 43 " --> pdb=" O GLNSD 40 " (cutoff:3.500A) Processing helix chain 'SE' and resid 55 through 71 Processing helix chain 'SE' and resid 108 through 119 Processing helix chain 'SE' and resid 132 through 148 removed outlier: 5.747A pdb=" N ASNSE 148 " --> pdb=" O LEUSE 144 " (cutoff:3.500A) Processing helix chain 'SE' and resid 149 through 158 Processing helix chain 'SF' and resid 11 through 19 removed outlier: 3.769A pdb=" N SERSF 15 " --> pdb=" O HISSF 11 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLUSF 16 " --> pdb=" O PROSF 12 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLNSF 17 " --> pdb=" O ASPSF 13 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VALSF 18 " --> pdb=" O GLNSF 14 " (cutoff:3.500A) Proline residue: SF 19 - end of helix No H-bonds generated for 'chain 'SF' and resid 11 through 19' Processing helix chain 'SF' and resid 20 through 33 removed outlier: 3.749A pdb=" N ALASF 32 " --> pdb=" O ALASF 28 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLUSF 33 " --> pdb=" O ILESF 29 " (cutoff:3.500A) Processing helix chain 'SF' and resid 67 through 81 Processing helix chain 'SF' and resid 100 through 106 Processing helix chain 'SG' and resid 20 through 31 removed outlier: 3.792A pdb=" N ALASG 24 " --> pdb=" O SERSG 20 " (cutoff:3.500A) Processing helix chain 'SG' and resid 35 through 54 removed outlier: 3.859A pdb=" N ALASG 39 " --> pdb=" O LYSSG 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SERSG 41 " --> pdb=" O SERSG 37 " (cutoff:3.500A) Processing helix chain 'SG' and resid 57 through 70 removed outlier: 4.208A pdb=" N ALASG 61 " --> pdb=" O SERSG 57 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALSG 69 " --> pdb=" O ALASG 65 " (cutoff:3.500A) Processing helix chain 'SG' and resid 92 through 112 removed outlier: 3.604A pdb=" N ASNSG 97 " --> pdb=" O PROSG 93 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALASG 98 " --> pdb=" O VALSG 94 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLUSG 106 " --> pdb=" O ARGSG 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARGSG 109 " --> pdb=" O VALSG 105 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLYSG 112 " --> pdb=" O ALASG 108 " (cutoff:3.500A) Processing helix chain 'SG' and resid 115 through 130 Processing helix chain 'SG' and resid 132 through 155 removed outlier: 5.036A pdb=" N ALASG 150 " --> pdb=" O GLUSG 146 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHESG 151 " --> pdb=" O ALASG 147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HISSG 153 " --> pdb=" O LYSSG 149 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYRSG 154 " --> pdb=" O ALASG 150 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARGSG 155 " --> pdb=" O PHESG 151 " (cutoff:3.500A) Processing helix chain 'SH' and resid 5 through 21 Processing helix chain 'SH' and resid 30 through 44 Processing helix chain 'SH' and resid 112 through 120 Processing helix chain 'SI' and resid 34 through 39 Processing helix chain 'SI' and resid 41 through 56 removed outlier: 3.950A pdb=" N VALSI 48 " --> pdb=" O ALASI 44 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARGSI 49 " --> pdb=" O ARGSI 45 " (cutoff:3.500A) Proline residue: SI 51 - end of helix removed outlier: 4.848A pdb=" N LEUSI 54 " --> pdb=" O GLNSI 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALSI 55 " --> pdb=" O PROSI 51 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASPSI 56 " --> pdb=" O LEUSI 52 " (cutoff:3.500A) Processing helix chain 'SI' and resid 71 through 91 removed outlier: 3.730A pdb=" N TYRSI 90 " --> pdb=" O ALASI 86 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASPSI 91 " --> pdb=" O LEUSI 87 " (cutoff:3.500A) Processing helix chain 'SI' and resid 92 through 102 removed outlier: 3.954A pdb=" N SERSI 96 " --> pdb=" O GLUSI 92 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLUSI 97 " --> pdb=" O SERSI 93 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 14 through 33 Processing helix chain 'SJ' and resid 80 through 90 Processing helix chain 'SK' and resid 46 through 51 removed outlier: 3.640A pdb=" N GLYSK 51 " --> pdb=" O ALASK 47 " (cutoff:3.500A) Processing helix chain 'SK' and resid 54 through 60 removed outlier: 4.376A pdb=" N SERSK 58 " --> pdb=" O GLYSK 54 " (cutoff:3.500A) Proline residue: SK 60 - end of helix Processing helix chain 'SK' and resid 61 through 76 removed outlier: 3.618A pdb=" N ALASK 73 " --> pdb=" O ARGSK 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALSK 74 " --> pdb=" O CYSSK 70 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLUSK 76 " --> pdb=" O ASPSK 72 " (cutoff:3.500A) Processing helix chain 'SK' and resid 92 through 104 removed outlier: 3.759A pdb=" N ILESK 97 " --> pdb=" O ARGSK 93 " (cutoff:3.500A) Processing helix chain 'SL' and resid 3 through 11 Proline residue: SL 11 - end of helix Processing helix chain 'SL' and resid 113 through 118 Processing helix chain 'SM' and resid 14 through 23 removed outlier: 5.278A pdb=" N TYRSM 23 " --> pdb=" O LEUSM 19 " (cutoff:3.500A) Processing helix chain 'SM' and resid 26 through 38 Processing helix chain 'SM' and resid 49 through 64 removed outlier: 4.250A pdb=" N ILESM 53 " --> pdb=" O SERSM 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASPSM 54 " --> pdb=" O GLUSM 50 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THRSM 55 " --> pdb=" O GLYSM 51 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEUSM 56 " --> pdb=" O GLNSM 52 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASPSM 58 " --> pdb=" O ASPSM 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALASM 61 " --> pdb=" O ARGSM 57 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSSM 62 " --> pdb=" O ASPSM 58 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHESM 63 " --> pdb=" O GLUSM 59 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VALSM 64 " --> pdb=" O VALSM 60 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 84 removed outlier: 3.684A pdb=" N GLYSM 84 " --> pdb=" O LEUSM 80 " (cutoff:3.500A) Processing helix chain 'SM' and resid 85 through 94 removed outlier: 3.505A pdb=" N HISSM 91 " --> pdb=" O ARGSM 87 " (cutoff:3.500A) Processing helix chain 'SM' and resid 106 through 111 Processing helix chain 'SN' and resid 2 through 21 removed outlier: 3.509A pdb=" N METSN 6 " --> pdb=" O ALASN 2 " (cutoff:3.500A) Processing helix chain 'SN' and resid 24 through 34 Processing helix chain 'SN' and resid 38 through 51 removed outlier: 6.052A pdb=" N TRPSN 42 " --> pdb=" O ASPSN 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEUSN 51 " --> pdb=" O LYSSN 47 " (cutoff:3.500A) Processing helix chain 'SN' and resid 56 through 61 removed outlier: 3.979A pdb=" N GLNSN 60 " --> pdb=" O SERSN 56 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARGSN 61 " --> pdb=" O PROSN 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'SN' and resid 56 through 61' Processing helix chain 'SN' and resid 80 through 91 Processing helix chain 'SO' and resid 4 through 16 removed outlier: 3.858A pdb=" N SERSO 13 " --> pdb=" O ALASO 9 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLUSO 14 " --> pdb=" O LYSSO 10 " (cutoff:3.500A) Processing helix chain 'SO' and resid 24 through 43 removed outlier: 4.230A pdb=" N GLYSO 41 " --> pdb=" O ASNSO 37 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HISSO 42 " --> pdb=" O HISSO 38 " (cutoff:3.500A) Processing helix chain 'SO' and resid 49 through 74 removed outlier: 3.509A pdb=" N GLYSO 55 " --> pdb=" O HISSO 51 " (cutoff:3.500A) Processing helix chain 'SO' and resid 75 through 86 Processing helix chain 'SP' and resid 53 through 64 Processing helix chain 'SP' and resid 68 through 82 Processing helix chain 'SR' and resid 11 through 17 removed outlier: 3.633A pdb=" N ALASR 15 " --> pdb=" O CYSSR 11 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLYSR 17 " --> pdb=" O PHESR 13 " (cutoff:3.500A) Processing helix chain 'SR' and resid 25 through 34 removed outlier: 4.170A pdb=" N LEUSR 29 " --> pdb=" O ASPSR 25 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASNSR 31 " --> pdb=" O ALASR 27 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYRSR 32 " --> pdb=" O THRSR 28 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THRSR 34 " --> pdb=" O LYSSR 30 " (cutoff:3.500A) Processing helix chain 'SR' and resid 41 through 46 Processing helix chain 'SR' and resid 48 through 66 Processing helix chain 'SS' and resid 12 through 26 removed outlier: 3.603A pdb=" N SERSS 25 " --> pdb=" O LYSSS 21 " (cutoff:3.500A) Processing helix chain 'SS' and resid 70 through 76 removed outlier: 3.942A pdb=" N PHESS 74 " --> pdb=" O LYSSS 70 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALASS 75 " --> pdb=" O LEUSS 71 " (cutoff:3.500A) Proline residue: SS 76 - end of helix No H-bonds generated for 'chain 'SS' and resid 70 through 76' Processing helix chain 'ST' and resid 4 through 41 Processing helix chain 'ST' and resid 43 through 65 Proline residue: ST 56 - end of helix Processing helix chain 'ST' and resid 68 through 87 Processing helix chain 'SU' and resid 11 through 27 Processing helix chain 'SU' and resid 28 through 37 removed outlier: 4.543A pdb=" N PHESU 37 " --> pdb=" O ARGSU 33 " (cutoff:3.500A) Processing helix chain 'SU' and resid 40 through 69 removed outlier: 3.600A pdb=" N GLUSU 63 " --> pdb=" O LYSSU 59 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARGSU 69 " --> pdb=" O ALASU 65 " (cutoff:3.500A) Processing helix chain 'LA' and resid 5 through 16 removed outlier: 4.522A pdb=" N ASPLA 16 " --> pdb=" O ARGLA 12 " (cutoff:3.500A) Processing helix chain 'LA' and resid 22 through 34 Processing helix chain 'LA' and resid 181 through 200 Processing helix chain 'LB' and resid 10 through 17 removed outlier: 3.542A pdb=" N ARGLB 14 " --> pdb=" O SERLB 10 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HISLB 15 " --> pdb=" O PROLB 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALLB 16 " --> pdb=" O GLYLB 12 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VALLB 17 " --> pdb=" O ARGLB 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 10 through 17' Processing helix chain 'LB' and resid 30 through 35 removed outlier: 3.637A pdb=" N LEULB 34 " --> pdb=" O PHELB 30 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLULB 35 " --> pdb=" O ALALB 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 30 through 35' Processing helix chain 'LB' and resid 131 through 136 Proline residue: LB 136 - end of helix Processing helix chain 'LB' and resid 207 through 215 removed outlier: 3.995A pdb=" N ALALB 211 " --> pdb=" O LYSLB 207 " (cutoff:3.500A) Processing helix chain 'LB' and resid 221 through 226 removed outlier: 3.595A pdb=" N METLB 225 " --> pdb=" O ARGLB 221 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASNLB 226 " --> pdb=" O GLYLB 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 221 through 226' Processing helix chain 'LB' and resid 260 through 268 removed outlier: 3.508A pdb=" N ASPLB 264 " --> pdb=" O ASNLB 260 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYSLB 265 " --> pdb=" O LYSLB 261 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHELB 266 " --> pdb=" O ARGLB 262 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILELB 267 " --> pdb=" O THRLB 263 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VALLB 268 " --> pdb=" O ASPLB 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 260 through 268' Processing helix chain 'LC' and resid 56 through 61 removed outlier: 5.503A pdb=" N THRLC 61 " --> pdb=" O ALALC 57 " (cutoff:3.500A) Processing helix chain 'LC' and resid 62 through 72 removed outlier: 3.603A pdb=" N HISLC 67 " --> pdb=" O PROLC 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALALC 71 " --> pdb=" O HISLC 67 " (cutoff:3.500A) Processing helix chain 'LC' and resid 98 through 103 removed outlier: 4.112A pdb=" N ALALC 102 " --> pdb=" O VALLC 98 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASPLC 103 " --> pdb=" O GLULC 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 98 through 103' Processing helix chain 'LC' and resid 120 through 125 Processing helix chain 'LC' and resid 39 through 44 Processing helix chain 'LD' and resid 15 through 20 Processing helix chain 'LD' and resid 24 through 40 removed outlier: 3.873A pdb=" N ARGLD 40 " --> pdb=" O ALALD 36 " (cutoff:3.500A) Processing helix chain 'LD' and resid 97 through 116 Processing helix chain 'LD' and resid 130 through 142 Processing helix chain 'LD' and resid 154 through 163 removed outlier: 4.471A pdb=" N ASNLD 163 " --> pdb=" O LEULD 159 " (cutoff:3.500A) Processing helix chain 'LD' and resid 176 through 184 removed outlier: 5.870A pdb=" N ASPLD 184 " --> pdb=" O LEULD 180 " (cutoff:3.500A) Processing helix chain 'LD' and resid 189 through 201 Processing helix chain 'LE' and resid 2 through 21 removed outlier: 3.577A pdb=" N TYRLE 7 " --> pdb=" O LYSLE 3 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VALLE 13 " --> pdb=" O LYSLE 9 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYSLE 14 " --> pdb=" O ASPLE 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLULE 19 " --> pdb=" O LYSLE 15 " (cutoff:3.500A) Processing helix chain 'LE' and resid 24 through 29 removed outlier: 3.728A pdb=" N VALLE 28 " --> pdb=" O SERLE 24 " (cutoff:3.500A) Proline residue: LE 29 - end of helix No H-bonds generated for 'chain 'LE' and resid 24 through 29' Processing helix chain 'LE' and resid 46 through 62 removed outlier: 3.805A pdb=" N LEULE 50 " --> pdb=" O ASPLE 46 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYLE 62 " --> pdb=" O ALALE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 93 through 111 removed outlier: 3.597A pdb=" N TRPLE 97 " --> pdb=" O GLYLE 93 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VALLE 108 " --> pdb=" O ILELE 104 " (cutoff:3.500A) Proline residue: LE 109 - end of helix Processing helix chain 'LE' and resid 162 through 174 Processing helix chain 'LE' and resid 134 through 139 removed outlier: 3.565A pdb=" N ILELE 137 " --> pdb=" O GLULE 134 " (cutoff:3.500A) Proline residue: LE 139 - end of helix Processing helix chain 'LF' and resid 2 through 8 Proline residue: LF 8 - end of helix Processing helix chain 'LF' and resid 60 through 81 Processing helix chain 'LF' and resid 137 through 153 removed outlier: 3.753A pdb=" N TYRLF 151 " --> pdb=" O ASPLF 147 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARGLF 152 " --> pdb=" O LEULF 148 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARGLF 153 " --> pdb=" O ARGLF 149 " (cutoff:3.500A) Processing helix chain 'LI' and resid 22 through 29 removed outlier: 3.563A pdb=" N ALALI 26 " --> pdb=" O LYSLI 22 " (cutoff:3.500A) Processing helix chain 'LI' and resid 40 through 51 Processing helix chain 'LI' and resid 52 through 76 removed outlier: 3.538A pdb=" N LEULI 75 " --> pdb=" O LYSLI 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLULI 76 " --> pdb=" O ILELI 72 " (cutoff:3.500A) Processing helix chain 'LI' and resid 95 through 107 Processing helix chain 'LI' and resid 111 through 116 removed outlier: 4.794A pdb=" N VALLI 115 " --> pdb=" O ALALI 111 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARGLI 116 " --> pdb=" O LYSLI 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 111 through 116' Processing helix chain 'LJ' and resid 4 through 22 Processing helix chain 'LJ' and resid 34 through 49 Processing helix chain 'LJ' and resid 56 through 65 Processing helix chain 'LJ' and resid 71 through 77 removed outlier: 4.147A pdb=" N ALALJ 75 " --> pdb=" O CYSLJ 71 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VALLJ 77 " --> pdb=" O LYSLJ 73 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 88 through 104 removed outlier: 3.977A pdb=" N ALALJ 92 " --> pdb=" O HISLJ 88 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALALJ 93 " --> pdb=" O PROLJ 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALALJ 104 " --> pdb=" O ALALJ 100 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 119 through 129 removed outlier: 3.800A pdb=" N ASPLJ 124 " --> pdb=" O ALALJ 120 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARGLJ 125 " --> pdb=" O SERLJ 121 " (cutoff:3.500A) Processing helix chain 'LK' and resid 24 through 32 removed outlier: 3.521A pdb=" N GLNLK 31 " --> pdb=" O ALALK 27 " (cutoff:3.500A) Processing helix chain 'LK' and resid 36 through 47 removed outlier: 3.588A pdb=" N LYSLK 45 " --> pdb=" O ALALK 41 " (cutoff:3.500A) Processing helix chain 'LK' and resid 75 through 85 Processing helix chain 'LK' and resid 102 through 114 removed outlier: 3.785A pdb=" N GLNLK 107 " --> pdb=" O ARGLK 103 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLULK 108 " --> pdb=" O ALALK 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILELK 109 " --> pdb=" O GLNLK 105 " (cutoff:3.500A) Processing helix chain 'LK' and resid 121 through 137 Processing helix chain 'LK' and resid 15 through 20 removed outlier: 5.782A pdb=" N ALALK 18 " --> pdb=" O ALALK 15 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASNLK 19 " --> pdb=" O GLYLK 16 " (cutoff:3.500A) Proline residue: LK 20 - end of helix No H-bonds generated for 'chain 'LK' and resid 15 through 20' Processing helix chain 'LM' and resid 24 through 38 removed outlier: 3.974A pdb=" N GLULM 31 " --> pdb=" O ARGLM 27 " (cutoff:3.500A) Processing helix chain 'LM' and resid 88 through 96 Processing helix chain 'LM' and resid 97 through 110 removed outlier: 4.306A pdb=" N ILELM 101 " --> pdb=" O PROLM 97 " (cutoff:3.500A) Proline residue: LM 110 - end of helix Processing helix chain 'LM' and resid 112 through 123 removed outlier: 3.742A pdb=" N LYSLM 121 " --> pdb=" O ALALM 117 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEULM 122 " --> pdb=" O METLM 118 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYSLM 123 " --> pdb=" O PHELM 119 " (cutoff:3.500A) Processing helix chain 'LN' and resid 104 through 109 removed outlier: 4.662A pdb=" N ARGLN 108 " --> pdb=" O THRLN 104 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SERLN 109 " --> pdb=" O ARGLN 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 104 through 109' Processing helix chain 'LN' and resid 112 through 119 Processing helix chain 'LO' and resid 37 through 42 removed outlier: 5.348A pdb=" N SERLO 42 " --> pdb=" O GLNLO 38 " (cutoff:3.500A) Processing helix chain 'LO' and resid 56 through 62 Proline residue: LO 62 - end of helix Processing helix chain 'LO' and resid 68 through 75 removed outlier: 3.794A pdb=" N ALALO 72 " --> pdb=" O SERLO 68 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILELO 73 " --> pdb=" O ARGLO 69 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALALO 75 " --> pdb=" O ALALO 71 " (cutoff:3.500A) Processing helix chain 'LO' and resid 78 through 86 removed outlier: 3.671A pdb=" N LEULO 82 " --> pdb=" O AARGLO 78 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALALO 83 " --> pdb=" O LEULO 79 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYSLO 84 " --> pdb=" O SERLO 80 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLULO 86 " --> pdb=" O LEULO 82 " (cutoff:3.500A) Processing helix chain 'LO' and resid 91 through 99 Processing helix chain 'LO' and resid 128 through 139 removed outlier: 3.539A pdb=" N ALALO 133 " --> pdb=" O LYSLO 129 " (cutoff:3.500A) Processing helix chain 'LP' and resid 42 through 58 removed outlier: 3.526A pdb=" N VALLP 57 " --> pdb=" O METLP 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSLP 58 " --> pdb=" O THRLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 109 through 125 removed outlier: 3.702A pdb=" N GLULP 115 " --> pdb=" O GLULP 111 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYSLP 123 " --> pdb=" O LEULP 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEULP 124 " --> pdb=" O ALALP 120 " (cutoff:3.500A) Proline residue: LP 125 - end of helix Processing helix chain 'LQ' and resid 13 through 32 Processing helix chain 'LQ' and resid 37 through 58 removed outlier: 4.265A pdb=" N ARGLQ 46 " --> pdb=" O LYSLQ 42 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VALLQ 47 " --> pdb=" O GLULQ 43 " (cutoff:3.500A) Proline residue: LQ 50 - end of helix removed outlier: 4.423A pdb=" N THRLQ 57 " --> pdb=" O THRLQ 53 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASPLQ 58 " --> pdb=" O LEULQ 54 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 59 through 71 Processing helix chain 'LQ' and resid 72 through 88 removed outlier: 3.604A pdb=" N LEULQ 83 " --> pdb=" O LEULQ 79 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLYLQ 84 " --> pdb=" O PHELQ 80 " (cutoff:3.500A) Proline residue: LQ 85 - end of helix Processing helix chain 'LR' and resid 2 through 22 removed outlier: 4.103A pdb=" N ALALR 6 " --> pdb=" O ASPLR 2 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARGLR 13 " --> pdb=" O ARGLR 9 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALALR 14 " --> pdb=" O ARGLR 10 " (cutoff:3.500A) Processing helix chain 'LR' and resid 55 through 63 removed outlier: 3.866A pdb=" N GLULR 60 " --> pdb=" O LYSLR 56 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLNLR 61 " --> pdb=" O ALALR 57 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYSLR 63 " --> pdb=" O ALALR 59 " (cutoff:3.500A) Processing helix chain 'LR' and resid 67 through 86 Processing helix chain 'LR' and resid 101 through 114 removed outlier: 3.511A pdb=" N GLYLR 114 " --> pdb=" O ALALR 110 " (cutoff:3.500A) Processing helix chain 'LS' and resid 2 through 13 Processing helix chain 'LS' and resid 97 through 104 removed outlier: 4.752A pdb=" N ARGLS 101 " --> pdb=" O LEULS 97 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLULS 102 " --> pdb=" O TYRLS 98 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARGLS 103 " --> pdb=" O TYRLS 99 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THRLS 104 " --> pdb=" O LEULS 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 97 through 104' Processing helix chain 'LT' and resid 6 through 22 removed outlier: 3.767A pdb=" N LYSLT 22 " --> pdb=" O LEULT 18 " (cutoff:3.500A) Processing helix chain 'LT' and resid 26 through 31 removed outlier: 3.538A pdb=" N ARGLT 30 " --> pdb=" O GLYLT 26 " (cutoff:3.500A) Processing helix chain 'LT' and resid 32 through 37 removed outlier: 3.593A pdb=" N GLNLT 37 " --> pdb=" O ARGLT 33 " (cutoff:3.500A) Processing helix chain 'LT' and resid 39 through 73 removed outlier: 3.720A pdb=" N ARGLT 51 " --> pdb=" O TYRLT 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYSLT 54 " --> pdb=" O ARGLT 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGLT 55 " --> pdb=" O ARGLT 51 " (cutoff:3.500A) Processing helix chain 'LT' and resid 75 through 87 Processing helix chain 'LT' and resid 91 through 102 Processing helix chain 'LT' and resid 103 through 118 Processing helix chain 'LV' and resid 13 through 25 removed outlier: 3.547A pdb=" N LEULV 19 " --> pdb=" O GLNLV 15 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VALLV 20 " --> pdb=" O LYSLV 16 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEULV 23 " --> pdb=" O LEULV 19 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILELV 24 " --> pdb=" O VALLV 20 " (cutoff:3.500A) Processing helix chain 'LV' and resid 28 through 39 removed outlier: 3.537A pdb=" N ASPLV 34 " --> pdb=" O SERLV 30 " (cutoff:3.500A) Processing helix chain 'LV' and resid 41 through 61 removed outlier: 3.704A pdb=" N VALLV 45 " --> pdb=" O LYSLV 41 " (cutoff:3.500A) Processing helix chain 'LV' and resid 65 through 70 removed outlier: 5.594A pdb=" N LYSLV 70 " --> pdb=" O ILELV 66 " (cutoff:3.500A) Processing helix chain 'LW' and resid 3 through 11 removed outlier: 4.439A pdb=" N LEULW 11 " --> pdb=" O LEULW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 17 through 27 Processing helix chain 'LW' and resid 39 through 50 Processing helix chain 'LX' and resid 66 through 71 removed outlier: 3.679A pdb=" N VALLX 70 " --> pdb=" O GLNLX 66 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALALX 71 " --> pdb=" O VALLX 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'LX' and resid 66 through 71' Processing helix chain 'LY' and resid 13 through 24 Processing helix chain 'LY' and resid 43 through 53 removed outlier: 3.569A pdb=" N ALALY 52 " --> pdb=" O METLY 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYSLY 53 " --> pdb=" O ASNLY 49 " (cutoff:3.500A) Processing helix chain 'LY' and resid 54 through 59 removed outlier: 4.124A pdb=" N SERLY 58 " --> pdb=" O ALALY 54 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 52 through 63 Processing helix chain 'Lb' and resid 64 through 75 Processing helix chain 'Lc' and resid 2 through 10 removed outlier: 4.525A pdb=" N LEULc 6 " --> pdb=" O LYSLc 2 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGLc 7 " --> pdb=" O ALALc 3 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLULc 8 " --> pdb=" O LYSLc 4 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYSLc 9 " --> pdb=" O GLULc 5 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SERLc 10 " --> pdb=" O LEULc 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lc' and resid 2 through 10' Processing helix chain 'Lc' and resid 11 through 35 Processing helix chain 'Lc' and resid 40 through 62 removed outlier: 4.295A pdb=" N LYSLc 44 " --> pdb=" O SERLc 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALALc 61 " --> pdb=" O LEULc 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLYLc 62 " --> pdb=" O ASNLc 58 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 17 through 28 Processing helix chain 'Ld' and resid 41 through 52 Processing helix chain 'Le' and resid 55 through 65 removed outlier: 3.962A pdb=" N ASNLe 65 " --> pdb=" O ASNLe 61 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 9 through 19 removed outlier: 4.689A pdb=" N HISLf 19 " --> pdb=" O METLf 15 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 26 through 31 Proline residue: Lg 31 - end of helix Processing helix chain 'Lh' and resid 8 through 16 Processing helix chain 'Lh' and resid 17 through 25 removed outlier: 4.163A pdb=" N THRLh 24 " --> pdb=" O ALALh 20 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYSLh 25 " --> pdb=" O ARGLh 21 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 26 through 38 Processing helix chain 'Li' and resid 7 through 14 Processing helix chain 'Li' and resid 32 through 37 removed outlier: 4.283A pdb=" N LYSLi 36 " --> pdb=" O ILELi 32 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALALi 37 " --> pdb=" O LEULi 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 32 through 37' Processing helix chain 'Li' and resid 38 through 46 Proline residue: Li 46 - end of helix Processing helix chain 'Li' and resid 51 through 63 removed outlier: 4.327A pdb=" N GLYLi 56 " --> pdb=" O LYSLi 52 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEULi 57 " --> pdb=" O GLYLi 53 " (cutoff:3.500A) Proline residue: Li 63 - end of helix Processing helix chain 'EF' and resid 22 through 39 removed outlier: 4.886A pdb=" N LYSEF 39 " --> pdb=" O GLYEF 35 " (cutoff:3.500A) Processing helix chain 'EF' and resid 95 through 106 removed outlier: 3.887A pdb=" N VALEF 99 " --> pdb=" O PHEEF 95 " (cutoff:3.500A) Processing helix chain 'EF' and resid 120 through 134 removed outlier: 3.537A pdb=" N ARGEF 128 " --> pdb=" O GLUEF 124 " (cutoff:3.500A) Processing helix chain 'EF' and resid 150 through 161 Processing helix chain 'EF' and resid 210 through 231 removed outlier: 4.566A pdb=" N LEUEF 214 " --> pdb=" O ASPEF 210 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLUEF 217 " --> pdb=" O GLUEF 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAEF 229 " --> pdb=" O SEREF 225 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SEREF 230 " --> pdb=" O ALAEF 226 " (cutoff:3.500A) Processing helix chain 'EF' and resid 232 through 240 Processing helix chain 'EF' and resid 244 through 259 Processing helix chain 'EF' and resid 274 through 285 removed outlier: 3.543A pdb=" N ASPEF 280 " --> pdb=" O GLNEF 276 " (cutoff:3.500A) Processing helix chain 'EF' and resid 426 through 443 removed outlier: 4.293A pdb=" N LYSEF 430 " --> pdb=" O ALAEF 426 " (cutoff:3.500A) Proline residue: EF 443 - end of helix Processing helix chain 'EF' and resid 462 through 476 Processing helix chain 'EF' and resid 546 through 564 removed outlier: 3.650A pdb=" N ILEEF 550 " --> pdb=" O PROEF 546 " (cutoff:3.500A) Proline residue: EF 551 - end of helix removed outlier: 3.884A pdb=" N ALAEF 563 " --> pdb=" O GLUEF 559 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLYEF 564 " --> pdb=" O GLNEF 560 " (cutoff:3.500A) Processing helix chain 'EF' and resid 589 through 609 removed outlier: 4.938A pdb=" N LYSEF 609 " --> pdb=" O PHEEF 605 " (cutoff:3.500A) Processing helix chain 'EF' and resid 624 through 639 removed outlier: 3.550A pdb=" N THREF 628 " --> pdb=" O PROEF 624 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLYEF 629 " --> pdb=" O GLUEF 625 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASPEF 630 " --> pdb=" O GLUEF 626 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARGEF 639 " --> pdb=" O LEUEF 635 " (cutoff:3.500A) Processing helix chain 'EF' and resid 659 through 664 removed outlier: 4.139A pdb=" N PHEEF 664 " --> pdb=" O LEUEF 660 " (cutoff:3.500A) Processing helix chain 'EF' and resid 665 through 675 removed outlier: 3.612A pdb=" N GLNEF 669 " --> pdb=" O GLYEF 665 " (cutoff:3.500A) Processing helix chain 'EF' and resid 691 through 700 Processing sheet with id= 1, first strand: chain 'SB' and resid 15 through 18 removed outlier: 5.741A pdb=" N HISSB 15 " --> pdb=" O ILESB 41 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HISSB 39 " --> pdb=" O GLYSB 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'SB' and resid 90 through 93 removed outlier: 3.571A pdb=" N PHESB 90 " --> pdb=" O ILESB 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALASB 185 " --> pdb=" O PHESB 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'SC' and resid 53 through 59 removed outlier: 4.009A pdb=" N ARGSC 54 " --> pdb=" O HISSC 69 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THRSC 70 " --> pdb=" O ALASC 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'SC' and resid 164 through 169 removed outlier: 3.512A pdb=" N THRSC 191 " --> pdb=" O GLYSC 194 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'SD' and resid 141 through 144 removed outlier: 4.408A pdb=" N ASPSD 141 " --> pdb=" O PHESD 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'SE' and resid 12 through 16 removed outlier: 6.692A pdb=" N LEUSE 36 " --> pdb=" O ILESE 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'SE' and resid 84 through 88 removed outlier: 3.738A pdb=" N ALASE 99 " --> pdb=" O ASNSE 122 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASNSE 122 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'SE' and resid 32 through 40 Processing sheet with id= 9, first strand: chain 'SF' and resid 38 through 42 removed outlier: 3.504A pdb=" N ARGSF 38 " --> pdb=" O ASNSF 63 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYRSF 59 " --> pdb=" O TRPSF 42 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HISSF 3 " --> pdb=" O THRSF 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'SF' and resid 43 through 47 removed outlier: 6.430A pdb=" N HISSF 55 " --> pdb=" O LEUSF 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'SG' and resid 72 through 79 removed outlier: 6.374A pdb=" N THRSG 72 " --> pdb=" O VALSG 91 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VALSG 89 " --> pdb=" O GLUSG 74 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'SH' and resid 23 through 29 removed outlier: 6.381A pdb=" N ALASH 23 " --> pdb=" O LEUSH 63 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLUSH 58 " --> pdb=" O GLUSH 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASPSH 48 " --> pdb=" O THRSH 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'SH' and resid 74 through 77 removed outlier: 6.706A pdb=" N VALSH 103 " --> pdb=" O ILESH 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'SI' and resid 5 through 11 removed outlier: 3.590A pdb=" N TYRSI 6 " --> pdb=" O ILESI 21 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'SI' and resid 26 through 30 removed outlier: 3.986A pdb=" N LYSSI 27 " --> pdb=" O LEUSI 61 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'SJ' and resid 44 through 52 removed outlier: 3.882A pdb=" N ILESJ 6 " --> pdb=" O ILESJ 76 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'SK' and resid 19 through 26 Processing sheet with id= 18, first strand: chain 'SL' and resid 29 through 32 removed outlier: 5.028A pdb=" N LEUSL 81 " --> pdb=" O VALSL 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'SL' and resid 36 through 41 removed outlier: 4.936A pdb=" N LYSSL 51 " --> pdb=" O ILESL 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'SP' and resid 4 through 10 removed outlier: 4.318A pdb=" N PHESP 16 " --> pdb=" O HISSP 9 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLYSP 49 " --> pdb=" O ASNSP 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'SQ' and resid 7 through 11 removed outlier: 6.825A pdb=" N GLUSQ 60 " --> pdb=" O VALSQ 76 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SERSQ 72 " --> pdb=" O CYSSQ 64 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'SQ' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'SS' and resid 30 through 34 removed outlier: 3.507A pdb=" N LEUSS 31 " --> pdb=" O THRSS 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THRSS 33 " --> pdb=" O ALASS 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEUSS 47 " --> pdb=" O VALSS 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LA' and resid 60 through 65 removed outlier: 3.646A pdb=" N GLYLA 61 " --> pdb=" O TYRLA 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYRLA 163 " --> pdb=" O GLYLA 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLYLA 159 " --> pdb=" O LEULA 65 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LA' and resid 169 through 174 removed outlier: 5.883A pdb=" N GLYLA 169 " --> pdb=" O LEULA 48 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THRLA 173 " --> pdb=" O VALLA 44 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VALLA 212 " --> pdb=" O VALLA 224 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LB' and resid 75 through 79 removed outlier: 4.419A pdb=" N ASPLB 114 " --> pdb=" O VALLB 78 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LB' and resid 80 through 83 removed outlier: 3.724A pdb=" N ARGLB 80 " --> pdb=" O LEULB 93 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASNLB 90 " --> pdb=" O ALALB 106 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LB' and resid 139 through 142 removed outlier: 4.266A pdb=" N SERLB 139 " --> pdb=" O ILELB 164 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THRLB 173 " --> pdb=" O VALLB 165 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLULB 180 " --> pdb=" O LEULB 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LC' and resid 3 through 7 removed outlier: 7.436A pdb=" N ASPLC 200 " --> pdb=" O THRLC 112 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THRLC 112 " --> pdb=" O ASPLC 200 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LC' and resid 10 through 16 removed outlier: 3.586A pdb=" N GLYLC 10 " --> pdb=" O VALLC 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VALLC 20 " --> pdb=" O THRLC 16 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LC' and resid 79 through 84 removed outlier: 5.957A pdb=" N ARGLC 46 " --> pdb=" O LEULC 84 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLNLC 49 " --> pdb=" O THRLC 35 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLNLC 94 " --> pdb=" O VALLC 34 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LC' and resid 105 through 108 removed outlier: 6.521A pdb=" N LYSLC 105 " --> pdb=" O VALLC 177 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LD' and resid 1 through 5 removed outlier: 5.686A pdb=" N SERLD 10 " --> pdb=" O LEULD 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LD' and resid 117 through 120 Processing sheet with id= 35, first strand: chain 'LE' and resid 72 through 75 removed outlier: 6.795A pdb=" N LYSLE 72 " --> pdb=" O GLNLE 81 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLNLE 81 " --> pdb=" O LYSLE 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LE' and resid 85 through 92 removed outlier: 5.760A pdb=" N ILELE 85 " --> pdb=" O VALLE 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSLE 33 " --> pdb=" O THRLE 157 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLYLE 39 " --> pdb=" O GLYLE 151 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLYLE 151 " --> pdb=" O GLYLE 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LF' and resid 16 through 19 Processing sheet with id= 38, first strand: chain 'LF' and resid 41 through 45 Processing sheet with id= 39, first strand: chain 'LF' and resid 94 through 99 removed outlier: 6.767A pdb=" N ASNLF 101 " --> pdb=" O LEULF 117 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LF' and resid 121 through 125 removed outlier: 5.616A pdb=" N THRLF 129 " --> pdb=" O LEULF 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LI' and resid 2 through 5 removed outlier: 6.958A pdb=" N GLNLI 2 " --> pdb=" O ALALI 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LI' and resid 78 through 82 removed outlier: 4.130A pdb=" N VALLI 78 " --> pdb=" O ILELI 143 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LJ' and resid 24 through 28 removed outlier: 3.796A pdb=" N SERLJ 24 " --> pdb=" O SERLJ 85 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LK' and resid 8 through 14 Processing sheet with id= 45, first strand: chain 'LM' and resid 52 through 57 removed outlier: 4.907A pdb=" N ASPLM 19 " --> pdb=" O LEULM 140 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LM' and resid 74 through 78 removed outlier: 7.571A pdb=" N GLYLM 83 " --> pdb=" O THRLM 78 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LN' and resid 18 through 21 removed outlier: 4.379A pdb=" N THRLN 6 " --> pdb=" O CYSLN 21 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASNLN 82 " --> pdb=" O METLN 7 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LN' and resid 68 through 71 removed outlier: 3.893A pdb=" N SERLN 75 " --> pdb=" O ARGLN 71 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LP' and resid 37 through 40 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'LP' and resid 62 through 65 removed outlier: 3.667A pdb=" N TYRLP 103 " --> pdb=" O LEULP 33 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEULP 33 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYSLP 100 " --> pdb=" O ALALP 35 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LP' and resid 30 through 36 removed outlier: 7.859A pdb=" N SERLP 30 " --> pdb=" O LYSLP 133 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYSLP 127 " --> pdb=" O VALLP 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LQ' and resid 33 through 36 removed outlier: 4.402A pdb=" N METLQ 110 " --> pdb=" O CYSLQ 100 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TYRLQ 94 " --> pdb=" O VALLQ 116 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LR' and resid 49 through 52 Processing sheet with id= 54, first strand: chain 'LS' and resid 38 through 45 removed outlier: 6.001A pdb=" N THRLS 25 " --> pdb=" O LYSLS 87 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LS' and resid 49 through 52 removed outlier: 3.667A pdb=" N ALALS 49 " --> pdb=" O THRLS 60 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N SERLS 57 " --> pdb=" O THRLS 76 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LU' and resid 11 through 15 removed outlier: 6.105A pdb=" N LEULU 39 " --> pdb=" O GLYLU 50 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LU' and resid 18 through 23 removed outlier: 4.330A pdb=" N GLNLU 18 " --> pdb=" O ILELU 98 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASPLU 95 " --> pdb=" O VALLU 64 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYSLU 60 " --> pdb=" O THRLU 99 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLULU 31 " --> pdb=" O VALLU 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LU' and resid 57 through 60 Processing sheet with id= 59, first strand: chain 'LU' and resid 65 through 68 Processing sheet with id= 60, first strand: chain 'LU' and resid 71 through 78 removed outlier: 4.199A pdb=" N TYRLU 83 " --> pdb=" O ARGLU 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LV' and resid 2 through 8 Processing sheet with id= 62, first strand: chain 'LW' and resid 12 through 15 removed outlier: 5.431A pdb=" N VALLW 31 " --> pdb=" O HISLW 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASNLW 28 " --> pdb=" O LEULW 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYSLW 81 " --> pdb=" O VALLW 34 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYSLW 66 " --> pdb=" O ARGLW 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASPLW 79 " --> pdb=" O LYSLW 64 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYSLW 64 " --> pdb=" O ASPLW 79 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYSLW 81 " --> pdb=" O VALLW 62 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VALLW 62 " --> pdb=" O LYSLW 81 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALALW 83 " --> pdb=" O THRLW 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THRLW 60 " --> pdb=" O ALALW 83 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VALLW 85 " --> pdb=" O VALLW 58 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VALLW 58 " --> pdb=" O VALLW 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LX' and resid 40 through 46 removed outlier: 5.191A pdb=" N ASNLX 40 " --> pdb=" O ALALX 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LX' and resid 83 through 87 Processing sheet with id= 65, first strand: chain 'LY' and resid 2 through 5 Processing sheet with id= 66, first strand: chain 'LY' and resid 37 through 42 removed outlier: 3.581A pdb=" N ILELY 89 " --> pdb=" O PROLY 27 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'La' and resid 51 through 54 removed outlier: 4.070A pdb=" N THRLa 58 " --> pdb=" O GLYLa 54 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'La' and resid 65 through 71 Processing sheet with id= 69, first strand: chain 'Lb' and resid 12 through 19 removed outlier: 4.337A pdb=" N ASNLb 23 " --> pdb=" O SERLb 19 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Lb' and resid 34 through 41 Processing sheet with id= 71, first strand: chain 'Ld' and resid 33 through 39 removed outlier: 4.302A pdb=" N HISLd 34 " --> pdb=" O GLNLd 9 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N METLd 54 " --> pdb=" O THRLd 10 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Le' and resid 20 through 25 removed outlier: 4.281A pdb=" N ASNLe 20 " --> pdb=" O CYSLe 16 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEULe 32 " --> pdb=" O THRLe 13 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SERLe 15 " --> pdb=" O LEULe 32 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Lf' and resid 28 through 31 removed outlier: 6.492A pdb=" N SERLf 29 " --> pdb=" O LYSLf 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYSLf 37 " --> pdb=" O SERLf 29 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASPLf 31 " --> pdb=" O GLYLf 35 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Lg' and resid 8 through 12 Processing sheet with id= 75, first strand: chain 'Lg' and resid 34 through 39 removed outlier: 6.687A pdb=" N LEULg 34 " --> pdb=" O GLULg 51 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Li' and resid 22 through 25 removed outlier: 5.871A pdb=" N PHELi 22 " --> pdb=" O VALLi 50 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Lj' and resid 1 through 5 removed outlier: 6.648A pdb=" N HISLj 33 " --> pdb=" O CYSLj 27 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYSLj 27 " --> pdb=" O HISLj 33 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILELj 23 " --> pdb=" O GLNLj 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SERLj 28 " --> pdb=" O ASNLj 13 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASNLj 13 " --> pdb=" O SERLj 28 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'EF' and resid 67 through 73 removed outlier: 5.089A pdb=" N ALAEF 17 " --> pdb=" O THREF 89 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARGEF 137 " --> pdb=" O ILEEF 261 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEUEF 263 " --> pdb=" O ARGEF 137 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYSEF 266 " --> pdb=" O LEUEF 169 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'EF' and resid 181 through 185 removed outlier: 3.638A pdb=" N VALEF 182 " --> pdb=" O ILEEF 191 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THREF 201 " --> pdb=" O ASNEF 194 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'EF' and resid 294 through 298 removed outlier: 3.772A pdb=" N ILEEF 295 " --> pdb=" O ARGEF 309 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARGEF 309 " --> pdb=" O ILEEF 295 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLYEF 297 " --> pdb=" O ALAEF 307 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'EF' and resid 323 through 326 removed outlier: 4.930A pdb=" N LYSEF 323 " --> pdb=" O PHEEF 335 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHEEF 335 " --> pdb=" O LYSEF 323 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHEEF 335 " --> pdb=" O PHEEF 322 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHEEF 317 " --> pdb=" O ASPEF 399 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASPEF 395 " --> pdb=" O ALAEF 321 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THREF 396 " --> pdb=" O SEREF 352 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASPEF 347 " --> pdb=" O PHEEF 360 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'EF' and resid 341 through 344 removed outlier: 6.962A pdb=" N GLYEF 341 " --> pdb=" O ALAEF 379 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'EF' and resid 371 through 374 removed outlier: 4.176A pdb=" N ILEEF 363 " --> pdb=" O ILEEF 374 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARGEF 362 " --> pdb=" O ILEEF 386 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'EF' and resid 445 through 451 removed outlier: 3.850A pdb=" N GLNEF 455 " --> pdb=" O ASPEF 450 " (cutoff:3.500A) removed outlier: 14.163A pdb=" N ASNEF 454 " --> pdb=" O PROEF 422 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THREF 456 " --> pdb=" O VALEF 420 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N SEREF 417 " --> pdb=" O PROEF 486 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'EF' and resid 500 through 508 removed outlier: 3.730A pdb=" N GLNEF 514 " --> pdb=" O LYSEF 507 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLUEF 535 " --> pdb=" O METEF 574 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'EF' and resid 644 through 648 removed outlier: 4.120A pdb=" N GLYEF 651 " --> pdb=" O GLUEF 648 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'EF' and resid 333 through 337 Processing sheet with id= 88, first strand: chain 'EF' and resid 490 through 494 Processing sheet with id= 89, first strand: chain 'EF' and resid 516 through 519 removed outlier: 3.593A pdb=" N HISEF 517 " --> pdb=" O SEREF 582 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHEEF 580 " --> pdb=" O VALEF 519 " (cutoff:3.500A) 2331 hydrogen bonds defined for protein. 6874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3959 hydrogen bonds 6236 hydrogen bond angles 0 basepair planarities 1574 basepair parallelities 2715 stacking parallelities Total time for adding SS restraints: 355.61 Time building geometry restraints manager: 65.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 13189 1.30 - 1.43: 69784 1.43 - 1.56: 74064 1.56 - 1.69: 9401 1.69 - 1.81: 335 Bond restraints: 166773 Sorted by residual: bond pdb=" C4 5MU231939 " pdb=" C5 5MU231939 " ideal model delta sigma weight residual 1.805 1.478 0.327 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C4 5MU23 747 " pdb=" C5 5MU23 747 " ideal model delta sigma weight residual 1.805 1.478 0.327 2.00e-02 2.50e+03 2.68e+02 bond pdb=" N1 5MU231939 " pdb=" C6 5MU231939 " ideal model delta sigma weight residual 1.638 1.334 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" N1 5MU23 747 " pdb=" C6 5MU23 747 " ideal model delta sigma weight residual 1.638 1.336 0.302 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C DHA B 7 " pdb=" N SAR B 8 " ideal model delta sigma weight residual 1.329 1.509 -0.180 1.40e-02 5.10e+03 1.65e+02 ... (remaining 166768 not shown) Histogram of bond angle deviations from ideal: 95.42 - 103.96: 17877 103.96 - 112.51: 98001 112.51 - 121.05: 86740 121.05 - 129.59: 42822 129.59 - 138.13: 2954 Bond angle restraints: 248394 Sorted by residual: angle pdb=" C1' MIAPt 37 " pdb=" N9 MIAPt 37 " pdb=" C8 MIAPt 37 " ideal model delta sigma weight residual 81.43 127.25 -45.82 3.00e+00 1.11e-01 2.33e+02 angle pdb=" N3 MIAPt 37 " pdb=" C2 MIAPt 37 " pdb=" S10 MIAPt 37 " ideal model delta sigma weight residual 164.14 118.32 45.82 3.00e+00 1.11e-01 2.33e+02 angle pdb=" N1 MIAPt 37 " pdb=" C2 MIAPt 37 " pdb=" S10 MIAPt 37 " ideal model delta sigma weight residual 75.64 119.46 -43.82 3.00e+00 1.11e-01 2.13e+02 angle pdb=" C1' MIAPt 37 " pdb=" N9 MIAPt 37 " pdb=" C4 MIAPt 37 " ideal model delta sigma weight residual 159.69 124.06 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C BB9 B 2 " pdb=" CA BB9 B 2 " pdb=" CB BB9 B 2 " ideal model delta sigma weight residual 110.10 128.54 -18.44 1.90e+00 2.77e-01 9.42e+01 ... (remaining 248389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 85942 35.92 - 71.84: 3324 71.84 - 107.76: 170 107.76 - 143.68: 13 143.68 - 179.60: 10 Dihedral angle restraints: 89459 sinusoidal: 70118 harmonic: 19341 Sorted by residual: dihedral pdb=" CA VALLU 51 " pdb=" C VALLU 51 " pdb=" N PROLU 52 " pdb=" CA PROLU 52 " ideal model delta harmonic sigma weight residual -180.00 -53.74 -126.26 0 5.00e+00 4.00e-02 6.38e+02 dihedral pdb=" C DHA B 7 " pdb=" N DHA B 7 " pdb=" CA DHA B 7 " pdb=" CB DHA B 7 " ideal model delta harmonic sigma weight residual -122.60 -179.59 56.99 0 2.50e+00 1.60e-01 5.20e+02 dihedral pdb=" N DHA B 7 " pdb=" C DHA B 7 " pdb=" CA DHA B 7 " pdb=" CB DHA B 7 " ideal model delta harmonic sigma weight residual 122.80 179.57 -56.77 0 2.50e+00 1.60e-01 5.16e+02 ... (remaining 89456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 20722 0.084 - 0.169: 8763 0.169 - 0.253: 1897 0.253 - 0.338: 106 0.338 - 0.422: 4 Chirality restraints: 31492 Sorted by residual: chirality pdb=" C3' GDt 20 " pdb=" C4' GDt 20 " pdb=" O3' GDt 20 " pdb=" C2' GDt 20 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA TYRSH 128 " pdb=" N TYRSH 128 " pdb=" C TYRSH 128 " pdb=" CB TYRSH 128 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C3' G23 784 " pdb=" C4' G23 784 " pdb=" O3' G23 784 " pdb=" C2' G23 784 " both_signs ideal model delta sigma weight residual False -2.48 -2.82 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 31489 not shown) Planarity restraints: 14024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC161407 " -0.024 2.00e-02 2.50e+03 5.98e-01 8.06e+03 pdb=" C4' 5MC161407 " -0.455 2.00e-02 2.50e+03 pdb=" O4' 5MC161407 " -0.576 2.00e-02 2.50e+03 pdb=" C3' 5MC161407 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 5MC161407 " 0.667 2.00e-02 2.50e+03 pdb=" C2' 5MC161407 " 0.149 2.00e-02 2.50e+03 pdb=" O2' 5MC161407 " -1.004 2.00e-02 2.50e+03 pdb=" C1' 5MC161407 " -0.246 2.00e-02 2.50e+03 pdb=" N1 5MC161407 " 0.888 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC232498 " -0.002 2.00e-02 2.50e+03 5.89e-01 7.82e+03 pdb=" C4' OMC232498 " -0.482 2.00e-02 2.50e+03 pdb=" O4' OMC232498 " -0.671 2.00e-02 2.50e+03 pdb=" C3' OMC232498 " 0.578 2.00e-02 2.50e+03 pdb=" O3' OMC232498 " 0.605 2.00e-02 2.50e+03 pdb=" C2' OMC232498 " 0.203 2.00e-02 2.50e+03 pdb=" O2' OMC232498 " -0.921 2.00e-02 2.50e+03 pdb=" C1' OMC232498 " -0.211 2.00e-02 2.50e+03 pdb=" N1 OMC232498 " 0.900 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG232251 " 0.062 2.00e-02 2.50e+03 5.74e-01 7.42e+03 pdb=" C4' OMG232251 " -0.459 2.00e-02 2.50e+03 pdb=" O4' OMG232251 " -0.735 2.00e-02 2.50e+03 pdb=" C3' OMG232251 " 0.585 2.00e-02 2.50e+03 pdb=" O3' OMG232251 " 0.508 2.00e-02 2.50e+03 pdb=" C2' OMG232251 " 0.237 2.00e-02 2.50e+03 pdb=" O2' OMG232251 " -0.833 2.00e-02 2.50e+03 pdb=" C1' OMG232251 " -0.258 2.00e-02 2.50e+03 pdb=" N9 OMG232251 " 0.892 2.00e-02 2.50e+03 ... (remaining 14021 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 95 2.14 - 2.83: 44637 2.83 - 3.52: 202701 3.52 - 4.21: 536120 4.21 - 4.90: 669083 Nonbonded interactions: 1452636 Sorted by model distance: nonbonded pdb=" O3' APt 76 " pdb=" C PHEPt3002 " model vdw 1.456 3.270 nonbonded pdb=" C DAL B 1 " pdb=" SG BB9 B 2 " model vdw 1.687 3.630 nonbonded pdb=" OP1 A161500 " pdb="MG MG161617 " model vdw 1.728 2.170 nonbonded pdb=" OP1 A232268 " pdb="MG MG233101 " model vdw 1.750 2.170 nonbonded pdb=" OP2 G231271 " pdb="MG MG233077 " model vdw 1.762 2.170 ... (remaining 1452631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 2 6.06 5 P 4702 5.49 5 Mg 404 5.21 5 S 189 5.16 5 C 78291 2.51 5 N 28613 2.21 5 O 42152 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=0.50 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 23.120 Check model and map are aligned: 1.820 Convert atoms to be neutral: 1.050 Process input model: 696.020 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.470 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: 0.030 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 740.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.327 166773 Z= 0.587 Angle : 1.123 45.822 248394 Z= 0.789 Chirality : 0.091 0.422 31492 Planarity : 0.018 0.598 14024 Dihedral : 15.035 179.599 76989 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.10), residues: 6667 helix: 0.84 (0.11), residues: 2221 sheet: 0.02 (0.14), residues: 1274 loop : -0.45 (0.10), residues: 3172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2102 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1983 time to evaluate : 7.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 24 residues processed: 2052 average time/residue: 2.2243 time to fit residues: 6665.9665 Evaluate side-chains 1467 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1443 time to evaluate : 7.215 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 10 average time/residue: 1.2081 time to fit residues: 30.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 945 optimal weight: 0.9990 chunk 848 optimal weight: 5.9990 chunk 471 optimal weight: 40.0000 chunk 289 optimal weight: 10.0000 chunk 572 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 877 optimal weight: 8.9990 chunk 339 optimal weight: 6.9990 chunk 533 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 1017 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 146 ASN SB 170 HIS SB 177 ASN SC 19 ASN SC 32 ASN SC 123 GLN ** SC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 71 GLN SD 74 ASN SD 89 ASN SD 136 GLN SD 140 ASN ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 19 ASN SE 43 ASN SE 70 ASN SE 89 HIS SE 132 ASN SF 37 HIS SF 46 GLN SF 52 ASN SF 94 HIS SG 68 ASN SG 148 ASN SI 5 GLN SI 50 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 15 HIS SJ 64 GLN SJ 99 GLN SK 29 ASN SK 119 ASN SL 5 ASN SL 73 ASN SM 52 GLN SN 60 GLN SN 62 ASN ** SO 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 40 GLN SO 80 GLN SP 26 ASN SP 40 ASN SP 63 GLN ** SQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 52 GLN ST 78 ASN ST 82 GLN LA 47 ASN LB 90 ASN LB 143 ASN LC 42 ASN LD 41 GLN LE 27 GLN LE 37 ASN LF 139 GLN LF 143 GLN LI 18 GLN LI 20 ASN LI 66 ASN LK 30 GLN LK 94 ASN LN 29 HIS LN 93 GLN LO 104 GLN LQ 11 ASN ** LQ 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 10 GLN LS 75 GLN LU 6 GLN LU 11 GLN LU 18 GLN LU 43 ASN LW 28 ASN LX 27 ASN LY 75 GLN Lb 23 ASN Lc 15 ASN Lc 25 GLN Lf 5 GLN Lg 45 GLN Lh 26 ASN EF 12 ASN EF 150 ASN EF 157 GLN EF 170 GLN ** EF 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EF 221 ASN EF 259 ASN EF 514 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.107 166773 Z= 0.384 Angle : 0.708 17.420 248394 Z= 0.380 Chirality : 0.043 0.449 31492 Planarity : 0.007 0.146 14024 Dihedral : 13.682 178.882 63764 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.78 % Rotamer Outliers : 5.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 6667 helix: 1.19 (0.10), residues: 2296 sheet: -0.00 (0.13), residues: 1396 loop : -0.34 (0.11), residues: 2975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1420 time to evaluate : 7.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 301 outliers final: 107 residues processed: 1550 average time/residue: 2.1431 time to fit residues: 4916.4276 Evaluate side-chains 1435 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1328 time to evaluate : 7.438 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 60 residues processed: 53 average time/residue: 1.4112 time to fit residues: 138.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 565 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 846 optimal weight: 5.9990 chunk 692 optimal weight: 10.0000 chunk 280 optimal weight: 40.0000 chunk 1018 optimal weight: 9.9990 chunk 1100 optimal weight: 5.9990 chunk 907 optimal weight: 5.9990 chunk 1010 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 817 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 18 HIS SB 122 GLN SB 170 HIS SB 177 ASN SC 19 ASN SC 32 ASN SC 123 GLN ** SC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 140 ASN ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 19 ASN SE 70 ASN SE 132 ASN SE 135 ASN SF 94 HIS SH 4 GLN SH 118 GLN SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 58 ASN SL 73 ASN SM 105 ASN SN 60 GLN SO 37 ASN SO 40 GLN SO 80 GLN SQ 45 HIS SS 14 HIS LA 168 ASN LB 134 ASN LD 41 GLN LE 37 ASN LF 139 GLN LF 143 GLN LI 2 GLN LI 133 GLN LK 111 GLN ** LQ 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 10 GLN LU 6 GLN LU 18 GLN LU 43 ASN LU 87 GLN LX 27 ASN Lg 45 GLN EF 194 ASN EF 514 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.146 166773 Z= 0.377 Angle : 0.665 16.338 248394 Z= 0.360 Chirality : 0.040 0.375 31492 Planarity : 0.007 0.145 14024 Dihedral : 13.433 179.954 63764 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: 0.24 (0.10), residues: 6667 helix: 1.06 (0.11), residues: 2314 sheet: -0.08 (0.14), residues: 1392 loop : -0.34 (0.11), residues: 2961 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1363 time to evaluate : 7.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 313 outliers final: 134 residues processed: 1522 average time/residue: 2.1512 time to fit residues: 4869.2036 Evaluate side-chains 1419 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1285 time to evaluate : 7.411 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 80 residues processed: 59 average time/residue: 1.5378 time to fit residues: 160.5933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1006 optimal weight: 0.8980 chunk 766 optimal weight: 3.9990 chunk 528 optimal weight: 10.0000 chunk 112 optimal weight: 40.0000 chunk 486 optimal weight: 10.0000 chunk 684 optimal weight: 10.0000 chunk 1022 optimal weight: 20.0000 chunk 1082 optimal weight: 5.9990 chunk 534 optimal weight: 10.0000 chunk 969 optimal weight: 6.9990 chunk 291 optimal weight: 30.0000 overall best weight: 5.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SC 32 ASN SC 123 GLN ** SC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 140 ASN ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 19 ASN SE 70 ASN SE 132 ASN SF 14 GLN SF 58 HIS ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 58 ASN ** SK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 60 GLN SO 37 ASN SO 40 GLN SO 80 GLN SP 9 HIS SP 40 ASN LD 41 GLN LE 37 ASN ** LE 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 139 GLN LF 143 GLN LI 2 GLN LK 105 GLN LP 45 GLN LP 60 GLN ** LQ 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN LU 87 GLN LX 27 ASN Lg 45 GLN EF 344 ASN EF 482 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 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 : 0.005 0.082 166773 Z= 0.325 Angle : 0.640 15.805 248394 Z= 0.347 Chirality : 0.038 0.351 31492 Planarity : 0.007 0.140 14024 Dihedral : 13.332 179.933 63764 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.51 % Rotamer Outliers : 5.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: 0.30 (0.10), residues: 6667 helix: 1.16 (0.11), residues: 2311 sheet: -0.06 (0.14), residues: 1405 loop : -0.33 (0.11), residues: 2951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1326 time to evaluate : 7.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 298 outliers final: 161 residues processed: 1494 average time/residue: 2.1440 time to fit residues: 4773.8069 Evaluate side-chains 1436 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1275 time to evaluate : 7.459 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 106 residues processed: 61 average time/residue: 1.3840 time to fit residues: 156.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 901 optimal weight: 5.9990 chunk 614 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 806 optimal weight: 6.9990 chunk 446 optimal weight: 10.0000 chunk 923 optimal weight: 6.9990 chunk 748 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 552 optimal weight: 10.0000 chunk 971 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SC 32 ASN SC 123 GLN ** SC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 71 GLN SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 61 GLN SE 70 ASN SE 132 ASN ** SF 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 56 HIS SJ 58 ASN ** SJ 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 60 GLN SN 62 ASN SO 37 ASN SO 40 GLN SO 80 GLN SP 9 HIS ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 13 GLN ** ST 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 153 GLN LD 41 GLN LE 37 ASN ** LE 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 104 ASN LF 139 GLN LF 143 GLN LI 2 GLN LI 128 HIS LI 145 ASN LN 93 GLN LQ 62 ASN LR 98 GLN LS 12 GLN LT 71 GLN LU 18 GLN LU 43 ASN Le 30 HIS Lg 45 GLN EF 482 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.111 166773 Z= 0.411 Angle : 0.683 15.781 248394 Z= 0.366 Chirality : 0.041 0.407 31492 Planarity : 0.007 0.145 14024 Dihedral : 13.338 179.860 63764 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.97 % Rotamer Outliers : 5.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: 0.18 (0.10), residues: 6667 helix: 1.03 (0.11), residues: 2314 sheet: -0.13 (0.14), residues: 1401 loop : -0.37 (0.11), residues: 2952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1304 time to evaluate : 7.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 301 outliers final: 174 residues processed: 1470 average time/residue: 2.1476 time to fit residues: 4699.4732 Evaluate side-chains 1432 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1258 time to evaluate : 7.438 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 106 residues processed: 72 average time/residue: 1.5384 time to fit residues: 193.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 364 optimal weight: 7.9990 chunk 974 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 635 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 1083 optimal weight: 20.0000 chunk 899 optimal weight: 7.9990 chunk 501 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 568 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SC 32 ASN SC 123 GLN ** SC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 71 GLN SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 164 GLN SE 19 ASN SE 70 ASN SE 132 ASN ** SF 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 62 ASN SO 37 ASN SO 40 GLN SP 9 HIS ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 40 ASN ** ST 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 41 GLN LE 37 ASN ** LE 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 104 ASN LF 115 HIS LF 139 GLN LF 143 GLN LI 18 GLN LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN Le 30 HIS Lg 45 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 166773 Z= 0.355 Angle : 0.653 15.785 248394 Z= 0.353 Chirality : 0.039 0.368 31492 Planarity : 0.007 0.141 14024 Dihedral : 13.281 179.370 63764 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.30 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 6667 helix: 1.07 (0.11), residues: 2308 sheet: -0.17 (0.14), residues: 1407 loop : -0.37 (0.11), residues: 2952 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1281 time to evaluate : 7.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 273 outliers final: 172 residues processed: 1442 average time/residue: 2.1927 time to fit residues: 4727.2929 Evaluate side-chains 1421 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1249 time to evaluate : 7.367 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 117 residues processed: 63 average time/residue: 1.5404 time to fit residues: 173.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1044 optimal weight: 8.9990 chunk 122 optimal weight: 30.0000 chunk 617 optimal weight: 10.0000 chunk 791 optimal weight: 20.0000 chunk 613 optimal weight: 20.0000 chunk 912 optimal weight: 9.9990 chunk 605 optimal weight: 10.0000 chunk 1079 optimal weight: 8.9990 chunk 675 optimal weight: 20.0000 chunk 658 optimal weight: 10.0000 chunk 498 optimal weight: 8.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SC 123 GLN SD 71 GLN SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 164 GLN SE 61 GLN SE 70 ASN SE 132 ASN ** SF 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 148 ASN ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 62 ASN SO 37 ASN SO 40 GLN SO 80 GLN SP 9 HIS SP 18 GLN LD 41 GLN LE 37 ASN ** LE 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 101 ASN LF 104 ASN LF 139 GLN LF 143 GLN LI 18 GLN LQ 81 ASN LS 7 GLN LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN LW 48 GLN Lb 16 ASN Lc 45 GLN Le 30 HIS Lg 45 GLN EF 482 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.105 166773 Z= 0.520 Angle : 0.741 16.054 248394 Z= 0.391 Chirality : 0.044 0.416 31492 Planarity : 0.007 0.149 14024 Dihedral : 13.401 179.394 63764 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.58 % Rotamer Outliers : 5.23 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 6667 helix: 0.86 (0.11), residues: 2309 sheet: -0.28 (0.14), residues: 1401 loop : -0.49 (0.11), residues: 2957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1265 time to evaluate : 7.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 289 outliers final: 189 residues processed: 1432 average time/residue: 2.1751 time to fit residues: 4634.1869 Evaluate side-chains 1430 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1241 time to evaluate : 7.484 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 126 residues processed: 68 average time/residue: 1.6188 time to fit residues: 191.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 667 optimal weight: 6.9990 chunk 431 optimal weight: 8.9990 chunk 644 optimal weight: 0.8980 chunk 325 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 686 optimal weight: 5.9990 chunk 735 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 848 optimal weight: 4.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SD 71 GLN SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 164 GLN SE 61 GLN SE 70 ASN SF 14 GLN ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 52 GLN ** SN 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 62 ASN SO 37 ASN SO 40 GLN SO 80 GLN SP 9 HIS SP 18 GLN LD 41 GLN LE 37 ASN LF 101 ASN LF 104 ASN LF 139 GLN LI 18 GLN ** LK 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN Le 30 HIS Lg 45 GLN EF 85 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.138 166773 Z= 0.328 Angle : 0.656 16.017 248394 Z= 0.354 Chirality : 0.038 0.372 31492 Planarity : 0.007 0.140 14024 Dihedral : 13.302 179.292 63764 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.10), residues: 6667 helix: 1.00 (0.11), residues: 2313 sheet: -0.26 (0.14), residues: 1399 loop : -0.46 (0.11), residues: 2955 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1506 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1279 time to evaluate : 7.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 227 outliers final: 163 residues processed: 1420 average time/residue: 2.1876 time to fit residues: 4635.3258 Evaluate side-chains 1404 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1241 time to evaluate : 7.449 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 122 residues processed: 46 average time/residue: 1.5893 time to fit residues: 130.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 981 optimal weight: 6.9990 chunk 1034 optimal weight: 5.9990 chunk 943 optimal weight: 5.9990 chunk 1005 optimal weight: 0.3980 chunk 1033 optimal weight: 0.9990 chunk 605 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 789 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 909 optimal weight: 10.0000 chunk 951 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SD 71 GLN SD 74 ASN ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 61 GLN SE 132 ASN SE 135 ASN SF 14 GLN SF 68 GLN ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN SI 75 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 62 ASN SO 37 ASN SO 40 GLN SO 80 GLN ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 51 ASN LC 148 GLN LD 115 GLN LE 37 ASN LF 104 ASN LF 139 GLN LI 18 GLN LS 7 GLN LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN ** LW 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 45 GLN Le 30 HIS Lg 45 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 166773 Z= 0.166 Angle : 0.600 15.832 248394 Z= 0.328 Chirality : 0.033 0.361 31492 Planarity : 0.006 0.137 14024 Dihedral : 13.143 179.797 63764 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.30 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.10), residues: 6667 helix: 1.22 (0.11), residues: 2319 sheet: -0.19 (0.14), residues: 1372 loop : -0.33 (0.11), residues: 2976 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1321 time to evaluate : 6.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 126 residues processed: 1451 average time/residue: 2.1341 time to fit residues: 4644.7903 Evaluate side-chains 1387 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1261 time to evaluate : 6.696 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 101 residues processed: 28 average time/residue: 1.4684 time to fit residues: 75.6925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1002 optimal weight: 10.0000 chunk 660 optimal weight: 10.0000 chunk 1063 optimal weight: 6.9990 chunk 649 optimal weight: 10.0000 chunk 504 optimal weight: 10.0000 chunk 739 optimal weight: 8.9990 chunk 1115 optimal weight: 20.0000 chunk 1026 optimal weight: 5.9990 chunk 888 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 686 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 24 ASN SB 170 HIS SC 19 ASN SC 190 HIS SD 71 GLN SD 74 ASN SD 100 ASN ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 61 GLN SE 132 ASN SE 135 ASN SF 14 GLN SF 55 HIS ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 60 GLN SN 62 ASN SO 37 ASN SO 80 GLN SP 9 HIS ** SP 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 51 ASN LE 37 ASN LF 22 GLN LF 101 ASN LF 139 GLN LF 143 GLN LI 2 GLN LP 45 GLN LQ 11 ASN LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN LW 48 GLN Le 30 HIS Lg 45 GLN ** EF 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.450 166773 Z= 0.466 Angle : 0.713 25.526 248394 Z= 0.379 Chirality : 0.042 0.394 31492 Planarity : 0.007 0.149 14024 Dihedral : 13.211 179.806 63764 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.64 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 6667 helix: 1.01 (0.11), residues: 2314 sheet: -0.28 (0.14), residues: 1385 loop : -0.43 (0.11), residues: 2968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13334 Ramachandran restraints generated. 6667 Oldfield, 0 Emsley, 6667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1243 time to evaluate : 7.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 149 outliers final: 119 residues processed: 1357 average time/residue: 2.1761 time to fit residues: 4430.0228 Evaluate side-chains 1339 residues out of total 5531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1220 time to evaluate : 7.046 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 101 residues processed: 22 average time/residue: 1.6506 time to fit residues: 68.9692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 544 optimal weight: 6.9990 chunk 705 optimal weight: 1.9990 chunk 946 optimal weight: 4.9990 chunk 272 optimal weight: 40.0000 chunk 819 optimal weight: 0.4980 chunk 131 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 889 optimal weight: 1.9990 chunk 372 optimal weight: 30.0000 chunk 913 optimal weight: 1.9990 chunk 112 optimal weight: 40.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 170 HIS SC 19 ASN SD 71 GLN SD 74 ASN ** SD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 132 ASN SE 135 ASN ** SH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 5 GLN ** SI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 62 ASN SO 37 ASN SO 40 GLN SP 9 HIS ** SP 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 51 ASN LB 153 GLN LD 41 GLN LE 37 ASN LF 48 ASN LF 139 GLN LI 2 GLN LK 12 GLN LR 104 GLN LS 7 GLN LS 10 GLN LT 71 GLN LU 18 GLN LU 43 ASN LW 48 GLN Lc 45 GLN Le 30 HIS Lg 45 GLN ** EF 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068619 restraints weight = 361943.039| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.00 r_work: 0.2974 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 0.96 restraints_weight: 0.2500 r_work: 0.2957 rms_B_bonded: 1.01 restraints_weight: 0.1250 r_work: 0.2948 rms_B_bonded: 1.10 restraints_weight: 0.0625 r_work: 0.2938 rms_B_bonded: 1.20 restraints_weight: 0.0312 r_work: 0.2928 rms_B_bonded: 1.33 restraints_weight: 0.0156 r_work: 0.2918 rms_B_bonded: 1.49 restraints_weight: 0.0078 r_work: 0.2906 rms_B_bonded: 1.66 restraints_weight: 0.0039 r_work: 0.2894 rms_B_bonded: 1.86 restraints_weight: 0.0020 r_work: 0.2881 rms_B_bonded: 2.09 restraints_weight: 0.0010 r_work: 0.2867 rms_B_bonded: 2.35 restraints_weight: 0.0005 r_work: 0.2851 rms_B_bonded: 2.65 restraints_weight: 0.0002 r_work: 0.2835 rms_B_bonded: 2.98 restraints_weight: 0.0001 r_work: 0.2817 rms_B_bonded: 3.36 restraints_weight: 0.0001 r_work: 0.2797 rms_B_bonded: 3.79 restraints_weight: 0.0000 r_work: 0.2775 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work: 0.2752 rms_B_bonded: 4.84 restraints_weight: 0.0000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.445 166773 Z= 0.207 Angle : 0.614 18.145 248394 Z= 0.336 Chirality : 0.034 0.354 31492 Planarity : 0.006 0.147 14024 Dihedral : 13.099 179.193 63764 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.10), residues: 6667 helix: 1.18 (0.11), residues: 2324 sheet: -0.23 (0.14), residues: 1393 loop : -0.33 (0.11), residues: 2950 =============================================================================== Job complete usr+sys time: 62715.66 seconds wall clock time: 1069 minutes 42.90 seconds (64182.90 seconds total)