Starting phenix.real_space_refine (version: dev) on Mon May 16 18:21:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl4_12217/05_2022/7bl4_12217_updated.pdb" } resolution = 2.4 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= -0.044 sd= 0.814 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 "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 93560 Number of models: 1 Model: "" Number of chains: 47 Chain: "g" 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: "C" 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: "D" 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': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1483 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 1 Chain: "F" 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" 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: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" 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: "1" 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: "2" 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: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 144} Chain: "d" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna3p_pyr': 1081, 'rna2p_pur': 273, 'rna3p_pur': 1399, 'rna2p_pyr': 144} Link IDs: {'rna3p': 2479, 'rna2p': 417} Chain breaks: 1 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 105, 'rna2p': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "9" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GNP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85 SG CYS g 11 126.948 187.327 160.647 1.00111.00 S ATOM 110 SG CYS g 14 123.736 186.714 158.792 1.00109.54 S ATOM 213 SG CYS g 27 125.988 189.654 157.779 1.00109.91 S ATOM 24642 SG CYS d 16 153.723 88.741 206.750 1.00233.54 S ATOM 24796 SG CYS d 37 152.658 92.221 208.043 1.00231.77 S Time building chain proxies: 42.40, per 1000 atoms: 0.45 Number of scatterers: 93560 At special positions: 0 Unit cell: (197.96, 236.34, 234.32, 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 99 16.00 P 3018 15.00 Mg 6 11.99 O 26141 8.00 N 17384 7.00 C 46910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.28 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN d 100 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 37 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 16 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" ND1 HIS g 33 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 11 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 27 " Number of angles added : 3 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 49 sheets defined 24.8% alpha, 17.8% beta 978 base pairs and 1538 stacking pairs defined. Time for finding SS restraints: 40.70 Creating SS restraints... Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'E' and resid 155 through 161 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.918A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 18 Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 92 through 104 removed outlier: 4.398A pdb=" N GLU F 97 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR F 104 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.575A pdb=" N GLN G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU G 71 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 78 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.828A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 3.970A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.276A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.750A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 79 through 82 No H-bonds generated for 'chain 'L' and resid 79 through 82' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.281A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 12 through 21 Processing helix chain 'O' and resid 56 through 61 removed outlier: 3.592A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 56 through 61' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.554A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 113 Processing helix chain 'Q' and resid 6 through 19 removed outlier: 3.802A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.327A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 102 through 116 Processing helix chain 'S' and resid 14 through 23 removed outlier: 4.015A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 4.086A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 removed outlier: 3.526A pdb=" N GLU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 8 Processing helix chain 'T' and resid 18 through 25 Processing helix chain 'T' and resid 40 through 50 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.695A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 removed outlier: 3.651A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS X 60 " --> pdb=" O ARG X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'Y' and resid 5 through 7 No H-bonds generated for 'chain 'Y' and resid 5 through 7' Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.770A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 33 removed outlier: 3.602A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 55 removed outlier: 3.686A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR Y 55 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain '0' and resid 9 through 18 removed outlier: 4.748A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 22 Processing helix chain '2' and resid 25 through 37 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 3 through 9 removed outlier: 3.847A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 97 through 100 Processing helix chain 'M' and resid 43 through 57 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.626A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 43 through 50 removed outlier: 4.087A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 74 removed outlier: 3.650A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain '6' and resid 6 through 17 removed outlier: 3.542A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 62 Processing helix chain '6' and resid 94 through 97 No H-bonds generated for 'chain '6' and resid 94 through 97' Processing helix chain '9' and resid 57 through 59 No H-bonds generated for 'chain '9' and resid 57 through 59' Processing helix chain '9' and resid 127 through 130 Processing helix chain '9' and resid 172 through 179 removed outlier: 3.633A pdb=" N ILE 9 176 " --> pdb=" O LYS 9 172 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG 9 177 " --> pdb=" O SER 9 173 " (cutoff:3.500A) Processing helix chain '9' and resid 219 through 221 No H-bonds generated for 'chain '9' and resid 219 through 221' Processing helix chain '9' and resid 230 through 232 No H-bonds generated for 'chain '9' and resid 230 through 232' Processing helix chain '9' and resid 255 through 259 Processing helix chain '9' and resid 261 through 268 removed outlier: 3.964A pdb=" N GLU 9 265 " --> pdb=" O ILE 9 261 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS 9 268 " --> pdb=" O SER 9 264 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 292 through 304 removed outlier: 3.627A pdb=" N ALA 9 299 " --> pdb=" O GLU 9 295 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA 9 303 " --> pdb=" O ALA 9 299 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU 9 304 " --> pdb=" O ILE 9 300 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 removed outlier: 4.382A pdb=" N TRP 9 326 " --> pdb=" O LYS 9 322 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU 9 334 " --> pdb=" O THR 9 330 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 removed outlier: 3.769A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 34 No H-bonds generated for 'chain '3' and resid 32 through 34' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.518A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 60 removed outlier: 4.105A pdb=" N GLY 3 55 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE 3 58 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'g' and resid 14 through 19 Processing sheet with id= B, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= C, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.287A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.813A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.670A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.296A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.729A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.712A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 127 through 130 removed outlier: 3.629A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= L, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.842A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= N, first strand: chain 'G' and resid 93 through 98 Processing sheet with id= O, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.881A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.723A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.653A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= T, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= U, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.555A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.542A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 32 through 35 removed outlier: 3.628A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.039A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.388A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'S' and resid 81 through 87 Processing sheet with id= AA, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.809A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 67 through 69 Processing sheet with id= AC, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AD, first strand: chain 'U' and resid 63 through 65 removed outlier: 3.859A pdb=" N ASN U 26 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'U' and resid 40 through 44 Processing sheet with id= AF, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AG, first strand: chain 'V' and resid 3 through 6 removed outlier: 6.278A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA V 6 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL V 64 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AI, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AJ, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AK, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.527A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.524A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '1' and resid 19 through 25 removed outlier: 3.616A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 6 through 8 removed outlier: 6.862A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.627A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 128 through 132 removed outlier: 6.309A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.837A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 77 through 83 removed outlier: 9.218A pdb=" N VAL H 78 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE H 143 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE H 80 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN H 145 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER H 82 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL H 147 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 11 through 15 Processing sheet with id= AT, first strand: chain '6' and resid 23 through 25 removed outlier: 3.761A pdb=" N ILE 6 86 " --> pdb=" O CYS 6 36 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '9' and resid 64 through 66 removed outlier: 8.843A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '9' and resid 86 through 90 removed outlier: 3.680A pdb=" N VAL 9 45 " --> pdb=" O ALA 9 118 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA 9 118 " --> pdb=" O VAL 9 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET 9 47 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU 9 116 " --> pdb=" O MET 9 47 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA 9 49 " --> pdb=" O ARG 9 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG 9 114 " --> pdb=" O ALA 9 49 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '9' and resid 162 through 166 removed outlier: 6.855A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL 9 281 " --> pdb=" O ILE 9 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW 794 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2489 hydrogen bonds 3928 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 1538 stacking parallelities Total time for adding SS restraints: 165.17 Time building geometry restraints manager: 42.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16150 1.33 - 1.46: 41916 1.46 - 1.58: 37401 1.58 - 1.70: 6031 1.70 - 1.82: 176 Bond restraints: 101674 Sorted by residual: bond pdb=" N3B GNP 9 402 " pdb=" PG GNP 9 402 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' GNP 9 402 " pdb=" PA GNP 9 402 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C VAL H 31 " pdb=" N PRO H 32 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.86e+00 bond pdb=" O3A GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.687 1.641 0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" N3B GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.681 1.636 0.045 2.00e-02 2.50e+03 5.03e+00 ... (remaining 101669 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.15: 13884 105.15 - 112.37: 58440 112.37 - 119.59: 32729 119.59 - 126.81: 38925 126.81 - 134.03: 8260 Bond angle restraints: 152238 Sorted by residual: angle pdb=" C PRO F 175 " pdb=" N PHE F 176 " pdb=" CA PHE F 176 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" CA MET F 95 " pdb=" CB MET F 95 " pdb=" CG MET F 95 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" N ILE E 181 " pdb=" CA ILE E 181 " pdb=" C ILE E 181 " ideal model delta sigma weight residual 112.96 108.36 4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" C3' G A2505 " pdb=" O3' G A2505 " pdb=" P U A2506 " ideal model delta sigma weight residual 120.20 125.65 -5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C HIS 3 30 " pdb=" N ILE 3 31 " pdb=" CA ILE 3 31 " ideal model delta sigma weight residual 121.97 128.37 -6.40 1.80e+00 3.09e-01 1.27e+01 ... (remaining 152233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 52542 35.41 - 70.82: 1483 70.82 - 106.23: 131 106.23 - 141.64: 7 141.64 - 177.05: 10 Dihedral angle restraints: 54173 sinusoidal: 43702 harmonic: 10471 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 55.63 144.37 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 49.05 -177.05 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1061 " pdb=" C1' U A1061 " pdb=" N1 U A1061 " pdb=" C2 U A1061 " ideal model delta sinusoidal sigma weight residual -128.00 48.90 -176.90 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 54170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 17843 0.046 - 0.093: 1268 0.093 - 0.139: 346 0.139 - 0.185: 18 0.185 - 0.231: 4 Chirality restraints: 19479 Sorted by residual: chirality pdb=" C3' G A2505 " pdb=" C4' G A2505 " pdb=" O3' G A2505 " pdb=" C2' G A2505 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' U A1736 " pdb=" O4' U A1736 " pdb=" C2' U A1736 " pdb=" N1 U A1736 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 19476 not shown) Planarity restraints: 8060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.036 2.00e-02 2.50e+03 1.90e-02 8.10e+00 pdb=" N1 U A1736 " 0.041 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 175 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C PRO F 175 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO F 175 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE F 176 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2564 " 0.028 2.00e-02 2.50e+03 1.36e-02 5.05e+00 pdb=" N9 A A2564 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A A2564 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A2564 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A2564 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A2564 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A2564 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A A2564 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A2564 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A2564 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A2564 " 0.000 2.00e-02 2.50e+03 ... (remaining 8057 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1037 2.59 - 3.17: 71952 3.17 - 3.75: 186414 3.75 - 4.32: 252549 4.32 - 4.90: 336923 Nonbonded interactions: 848875 Sorted by model distance: nonbonded pdb="MG MG 9 401 " pdb=" O2G GNP 9 402 " model vdw 2.015 2.170 nonbonded pdb="MG MG 9 401 " pdb=" O1B GNP 9 402 " model vdw 2.037 2.170 nonbonded pdb=" OG SER 9 173 " pdb="MG MG 9 401 " model vdw 2.063 2.170 nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR J 3 " pdb=" O2 C A 995 " model vdw 2.137 2.440 ... (remaining 848870 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 3018 5.49 5 Mg 6 5.21 5 S 99 5.16 5 C 46910 2.51 5 N 17384 2.21 5 O 26141 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 17.670 Check model and map are aligned: 1.060 Convert atoms to be neutral: 0.610 Process input model: 364.570 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 404.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 : 0.002 0.096 101674 Z= 0.123 Angle : 0.453 11.173 152238 Z= 0.244 Chirality : 0.027 0.231 19479 Planarity : 0.003 0.046 8060 Dihedral : 13.361 177.047 47437 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3638 helix: 0.13 (0.18), residues: 883 sheet: 0.72 (0.20), residues: 719 loop : -0.95 (0.13), residues: 2036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1095 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 1095 average time/residue: 1.4841 time to fit residues: 2295.7662 Evaluate side-chains 930 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 928 time to evaluate : 4.066 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.6868 time to fit residues: 5.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 553 optimal weight: 10.0000 chunk 497 optimal weight: 30.0000 chunk 275 optimal weight: 0.0770 chunk 169 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 265 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 595 optimal weight: 10.0000 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN E 41 GLN E 90 GLN E 115 GLN E 195 GLN F 126 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN L 99 ASN L 104 GLN N 11 ASN O 38 GLN O 61 GLN Q 19 GLN Q 51 GLN Q 55 GLN R 11 GLN S 15 GLN T 28 ASN T 70 HIS U 44 HIS ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN X 15 ASN 1 25 ASN K 82 ASN K 88 ASN P 11 GLN H 33 GLN 6 91 GLN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 101674 Z= 0.428 Angle : 0.641 10.225 152238 Z= 0.327 Chirality : 0.038 0.311 19479 Planarity : 0.005 0.086 8060 Dihedral : 12.983 179.798 40262 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer Outliers : 5.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3638 helix: -0.06 (0.17), residues: 936 sheet: 0.19 (0.19), residues: 773 loop : -0.99 (0.13), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1046 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 94 residues processed: 1096 average time/residue: 1.5348 time to fit residues: 2361.8650 Evaluate side-chains 1084 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 990 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 31 residues processed: 68 average time/residue: 0.9154 time to fit residues: 108.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 495 optimal weight: 10.0000 chunk 405 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 596 optimal weight: 20.0000 chunk 644 optimal weight: 0.0770 chunk 531 optimal weight: 8.9990 chunk 591 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 478 optimal weight: 20.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN D 58 ASN D 130 GLN E 90 GLN E 195 GLN F 36 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN L 99 ASN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN R 11 GLN T 28 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Z 19 HIS 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN K 82 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 33 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 GLN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 101674 Z= 0.340 Angle : 0.572 10.521 152238 Z= 0.295 Chirality : 0.036 0.280 19479 Planarity : 0.005 0.082 8060 Dihedral : 13.046 178.128 40262 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer Outliers : 7.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3638 helix: 0.08 (0.17), residues: 928 sheet: -0.02 (0.19), residues: 774 loop : -1.00 (0.13), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1044 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 113 residues processed: 1122 average time/residue: 1.5312 time to fit residues: 2419.1790 Evaluate side-chains 1092 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 979 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 43 residues processed: 72 average time/residue: 0.8668 time to fit residues: 110.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 284 optimal weight: 0.0270 chunk 400 optimal weight: 6.9990 chunk 598 optimal weight: 20.0000 chunk 634 optimal weight: 2.9990 chunk 312 optimal weight: 8.9990 chunk 567 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 130 GLN E 24 ASN E 90 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS L 99 ASN L 104 GLN O 38 GLN Q 19 GLN Q 43 GLN Q 51 GLN R 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN 0 3 GLN 2 26 ASN K 82 ASN P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 GLN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 101674 Z= 0.347 Angle : 0.588 10.742 152238 Z= 0.303 Chirality : 0.036 0.289 19479 Planarity : 0.005 0.056 8060 Dihedral : 13.116 179.125 40262 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.73 % Rotamer Outliers : 7.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.86 (0.13), residues: 3638 helix: 0.06 (0.17), residues: 925 sheet: -0.07 (0.19), residues: 772 loop : -1.07 (0.13), residues: 1941 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1034 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 228 outliers final: 129 residues processed: 1120 average time/residue: 1.4989 time to fit residues: 2369.4897 Evaluate side-chains 1127 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 998 time to evaluate : 3.995 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 50 residues processed: 81 average time/residue: 0.8789 time to fit residues: 124.8147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 472 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 541 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 569 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 130 GLN E 24 ASN E 90 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 19 GLN Q 51 GLN Q 55 GLN R 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN K 82 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 101674 Z= 0.397 Angle : 0.618 10.416 152238 Z= 0.318 Chirality : 0.038 0.302 19479 Planarity : 0.005 0.079 8060 Dihedral : 13.231 179.634 40262 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer Outliers : 7.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.13), residues: 3638 helix: 0.02 (0.17), residues: 922 sheet: -0.18 (0.18), residues: 786 loop : -1.11 (0.13), residues: 1930 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1036 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 224 outliers final: 130 residues processed: 1128 average time/residue: 1.5414 time to fit residues: 2438.2545 Evaluate side-chains 1141 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1011 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 57 residues processed: 77 average time/residue: 0.8323 time to fit residues: 115.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 213 optimal weight: 0.9990 chunk 571 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 634 optimal weight: 0.9990 chunk 526 optimal weight: 10.0000 chunk 293 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN D 36 GLN D 130 GLN E 24 ASN E 90 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS L 99 ASN O 38 GLN Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN R 11 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 15 ASN K 82 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.096 101674 Z= 0.149 Angle : 0.532 13.360 152238 Z= 0.273 Chirality : 0.032 0.247 19479 Planarity : 0.004 0.076 8060 Dihedral : 13.134 176.217 40262 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.14), residues: 3638 helix: 0.31 (0.18), residues: 899 sheet: -0.01 (0.19), residues: 756 loop : -1.01 (0.13), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1039 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 98 residues processed: 1116 average time/residue: 1.5388 time to fit residues: 2414.8223 Evaluate side-chains 1099 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1001 time to evaluate : 3.981 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 57 residues processed: 47 average time/residue: 0.8337 time to fit residues: 72.2085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 632 optimal weight: 0.9980 chunk 395 optimal weight: 40.0000 chunk 385 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 23 ASN N 81 ASN O 100 HIS Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN R 86 GLN U 68 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 1 25 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 101674 Z= 0.442 Angle : 0.647 11.192 152238 Z= 0.330 Chirality : 0.039 0.305 19479 Planarity : 0.005 0.082 8060 Dihedral : 13.237 179.935 40262 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.51 % Rotamer Outliers : 6.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3638 helix: 0.03 (0.17), residues: 919 sheet: -0.15 (0.19), residues: 762 loop : -1.13 (0.13), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1034 time to evaluate : 7.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 129 residues processed: 1118 average time/residue: 1.5303 time to fit residues: 2403.6154 Evaluate side-chains 1112 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 983 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 65 residues processed: 68 average time/residue: 0.8182 time to fit residues: 101.3653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 391 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 122 optimal weight: 0.0770 chunk 401 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 496 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 24 ASN E 90 GLN E 195 GLN F 51 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN O 38 GLN Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN W 72 ASN X 15 ASN K 82 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 43 ASN ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 101674 Z= 0.325 Angle : 0.607 10.816 152238 Z= 0.311 Chirality : 0.036 0.281 19479 Planarity : 0.005 0.081 8060 Dihedral : 13.249 178.084 40262 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer Outliers : 5.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3638 helix: -0.01 (0.17), residues: 912 sheet: -0.27 (0.18), residues: 754 loop : -1.13 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1006 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 121 residues processed: 1094 average time/residue: 1.5538 time to fit residues: 2392.5272 Evaluate side-chains 1117 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 996 time to evaluate : 4.006 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 72 residues processed: 55 average time/residue: 0.9093 time to fit residues: 87.8967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 575 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 552 optimal weight: 10.0000 chunk 589 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 462 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 532 optimal weight: 8.9990 chunk 557 optimal weight: 8.9990 chunk 587 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 24 ASN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 81 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS X 15 ASN K 82 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 99 GLN ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.094 101674 Z= 0.501 Angle : 0.705 11.764 152238 Z= 0.359 Chirality : 0.041 0.331 19479 Planarity : 0.005 0.090 8060 Dihedral : 13.461 178.517 40262 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.55 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3638 helix: -0.20 (0.17), residues: 906 sheet: -0.37 (0.18), residues: 769 loop : -1.25 (0.13), residues: 1963 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1007 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 109 residues processed: 1096 average time/residue: 1.5475 time to fit residues: 2381.8627 Evaluate side-chains 1098 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 989 time to evaluate : 4.078 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 69 residues processed: 47 average time/residue: 0.7986 time to fit residues: 70.4462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 386 optimal weight: 0.6980 chunk 623 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 433 optimal weight: 5.9990 chunk 653 optimal weight: 1.9990 chunk 601 optimal weight: 20.0000 chunk 520 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 24 ASN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 43 GLN Q 51 GLN Q 55 GLN R 86 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN W 72 ASN X 15 ASN K 82 ASN K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 43 ASN ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 101674 Z= 0.223 Angle : 0.591 12.828 152238 Z= 0.303 Chirality : 0.034 0.263 19479 Planarity : 0.005 0.105 8060 Dihedral : 13.336 177.004 40262 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.09 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3638 helix: 0.02 (0.17), residues: 902 sheet: -0.35 (0.19), residues: 738 loop : -1.12 (0.13), residues: 1998 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1001 time to evaluate : 4.048 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 outliers start: 110 outliers final: 87 residues processed: 1072 average time/residue: 1.5147 time to fit residues: 2296.8212 Evaluate side-chains 1080 residues out of total 3007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 993 time to evaluate : 4.020 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 64 residues processed: 28 average time/residue: 0.8630 time to fit residues: 45.9241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 413 optimal weight: 20.0000 chunk 554 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 479 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 521 optimal weight: 50.0000 chunk 218 optimal weight: 6.9990 chunk 535 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 90 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 43 GLN Q 51 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN H 33 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079575 restraints weight = 176448.097| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.33 r_work: 0.3084 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work: 0.3067 rms_B_bonded: 1.28 restraints_weight: 0.1250 r_work: 0.3059 rms_B_bonded: 1.34 restraints_weight: 0.0625 r_work: 0.3051 rms_B_bonded: 1.40 restraints_weight: 0.0312 r_work: 0.3042 rms_B_bonded: 1.49 restraints_weight: 0.0156 r_work: 0.3034 rms_B_bonded: 1.58 restraints_weight: 0.0078 r_work: 0.3025 rms_B_bonded: 1.69 restraints_weight: 0.0039 r_work: 0.3016 rms_B_bonded: 1.81 restraints_weight: 0.0020 r_work: 0.3007 rms_B_bonded: 1.95 restraints_weight: 0.0010 r_work: 0.2997 rms_B_bonded: 2.09 restraints_weight: 0.0005 r_work: 0.2987 rms_B_bonded: 2.25 restraints_weight: 0.0002 r_work: 0.2976 rms_B_bonded: 2.42 restraints_weight: 0.0001 r_work: 0.2966 rms_B_bonded: 2.60 restraints_weight: 0.0001 r_work: 0.2954 rms_B_bonded: 2.79 restraints_weight: 0.0000 r_work: 0.2943 rms_B_bonded: 3.00 restraints_weight: 0.0000 r_work: 0.2930 rms_B_bonded: 3.23 restraints_weight: 0.0000 r_work: 0.2918 rms_B_bonded: 3.47 restraints_weight: 0.0000 r_work: 0.2904 rms_B_bonded: 3.73 restraints_weight: 0.0000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 101674 Z= 0.386 Angle : 0.648 12.425 152238 Z= 0.331 Chirality : 0.038 0.291 19479 Planarity : 0.005 0.077 8060 Dihedral : 13.363 178.861 40262 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3638 helix: -0.18 (0.17), residues: 919 sheet: -0.41 (0.18), residues: 776 loop : -1.17 (0.14), residues: 1943 =============================================================================== Job complete usr+sys time: 32147.44 seconds wall clock time: 558 minutes 37.26 seconds (33517.26 seconds total)