Starting phenix.real_space_refine (version: dev) on Thu Apr 7 22:37:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/04_2022/6yhs_10809.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 83514 Number of models: 1 Model: "" Number of chains: 34 Chain: "1" Number of atoms: 57324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2672, 57324 Classifications: {'RNA': 2672} Modifications used: {'rna3p_pyr': 988, 'rna2p_pur': 258, 'rna3p_pur': 1278, 'rna2p_pyr': 148} Link IDs: {'rna3p': 2265, 'rna2p': 406} Chain breaks: 5 Chain: "5" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna3p_pyr': 50, 'rna2p_pur': 8, 'rna3p_pur': 52, 'rna2p_pyr': 5} Link IDs: {'rna3p': 101, 'rna2p': 13} Chain: "6" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Classifications: {'RNA': 5} Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 1, 'rna3p_pur': 3} Link IDs: {'rna3p': 3, 'rna2p': 1} Chain: "8" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'RNA': 8} Modifications used: {'rna3p_pyr': 2, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna2p_pyr': 2} Link IDs: {'rna3p': 5, 'rna2p': 2} Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2109 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1571 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 4, 'TRANS': 205, 'PCIS': 1} Chain: "C" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1485 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 192} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 865 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 542 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 279 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1327 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1122 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "I" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1086 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "J" Number of atoms: 950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Conformer: "B" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} bond proxies already assigned to first conformer: 946 Chain: "K" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 864 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "L" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "M" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "P" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "Q" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 761 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "R" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "S" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "T" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "V" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 453 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "X" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "Y" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "a" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "b" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 294 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "1" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Unusual residues: {' MG': 157} Classifications: {'undetermined': 157} Link IDs: {None: 156} Chain: "5" 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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 83142 SG CYS b 11 112.936 51.846 184.643 1.00 24.03 S ATOM 83158 SG CYS b 14 114.363 54.777 182.653 1.00 25.61 S ATOM 83263 SG CYS b 27 116.654 50.952 183.339 1.00 23.72 S Time building chain proxies: 35.59, per 1000 atoms: 0.43 Number of scatterers: 83514 At special positions: 0 Unit cell: (207.58, 192.6, 224.7, 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 1 29.99 S 68 16.00 P 2800 15.00 Mg 160 11.99 O 23604 8.00 N 15545 7.00 C 41336 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: 28.73 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 11 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 14 " pdb="ZN ZN b 101 " - pdb=" ND1 HIS b 33 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 27 " Number of angles added : 3 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5582 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 47 sheets defined 28.8% alpha, 21.8% beta 901 base pairs and 1533 stacking pairs defined. Time for finding SS restraints: 31.07 Creating SS restraints... Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.873A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.701A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.959A pdb=" N ALA B 72 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 37 Processing helix chain 'C' and resid 96 through 114 removed outlier: 3.516A pdb=" N CYS C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.777A pdb=" N ALA C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 141 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.534A pdb=" N LEU C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.753A pdb=" N VAL C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 11 through 20 removed outlier: 4.375A pdb=" N GLN D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.880A pdb=" N ALA D 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.552A pdb=" N ASP D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.880A pdb=" N ILE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.821A pdb=" N ARG D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 111 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.664A pdb=" N GLY D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 81 removed outlier: 3.647A pdb=" N MET E 63 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 67 " --> pdb=" O MET E 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER E 80 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'F' and resid 24 through 38 removed outlier: 4.255A pdb=" N GLU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.918A pdb=" N VAL F 62 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 88 through 94 removed outlier: 3.643A pdb=" N LEU F 92 " --> pdb=" O ASN F 88 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 94 " --> pdb=" O GLU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.982A pdb=" N ILE F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 132 through 136 removed outlier: 3.654A pdb=" N GLN F 136 " --> pdb=" O ALA F 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 111 through 118 removed outlier: 3.607A pdb=" N ILE G 115 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 3.634A pdb=" N LEU H 63 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 93 through 100 Processing helix chain 'H' and resid 130 through 140 removed outlier: 3.575A pdb=" N LYS H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 58 Processing helix chain 'I' and resid 110 through 122 Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'J' and resid 13 through 32 Processing helix chain 'J' and resid 38 through 55 removed outlier: 3.652A pdb=" N GLU J 43 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Proline residue: J 50 - end of helix Processing helix chain 'J' and resid 59 through 71 Processing helix chain 'J' and resid 72 through 82 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'K' and resid 4 through 12 removed outlier: 3.737A pdb=" N ARG K 10 " --> pdb=" O GLN K 6 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG K 11 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 23 Processing helix chain 'K' and resid 66 through 82 removed outlier: 3.843A pdb=" N LYS K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 112 Processing helix chain 'L' and resid 5 through 14 removed outlier: 3.895A pdb=" N SER L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 59 Processing helix chain 'L' and resid 100 through 106 removed outlier: 3.557A pdb=" N LEU L 103 " --> pdb=" O LEU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 112 removed outlier: 3.659A pdb=" N ALA L 110 " --> pdb=" O SER L 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG L 112 " --> pdb=" O LYS L 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.538A pdb=" N ARG M 20 " --> pdb=" O LYS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 Processing helix chain 'M' and resid 31 through 72 removed outlier: 3.764A pdb=" N GLN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG M 51 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN M 72 " --> pdb=" O GLY M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 91 through 102 Processing helix chain 'M' and resid 102 through 118 Processing helix chain 'O' and resid 14 through 26 removed outlier: 3.975A pdb=" N LEU O 20 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 39 Processing helix chain 'O' and resid 43 through 62 removed outlier: 4.017A pdb=" N LEU O 47 " --> pdb=" O LYS O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 92 No H-bonds generated for 'chain 'O' and resid 90 through 92' Processing helix chain 'P' and resid 2 through 9 removed outlier: 4.043A pdb=" N ILE P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN P 8 " --> pdb=" O GLU P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 38 through 51 Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 48 through 55 Processing helix chain 'R' and resid 56 through 62 removed outlier: 6.526A pdb=" N ALA R 59 " --> pdb=" O GLU R 56 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE R 61 " --> pdb=" O ASN R 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 44 Processing helix chain 'T' and resid 53 through 63 Processing helix chain 'T' and resid 63 through 74 Processing helix chain 'U' and resid 12 through 34 removed outlier: 4.210A pdb=" N ALA U 16 " --> pdb=" O GLU U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR U 34 " --> pdb=" O MET U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.862A pdb=" N VAL U 45 " --> pdb=" O HIS U 41 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 25 Processing helix chain 'V' and resid 40 through 50 removed outlier: 3.792A pdb=" N MET V 46 " --> pdb=" O SER V 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL V 50 " --> pdb=" O MET V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 17 removed outlier: 3.534A pdb=" N ARG X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 20 No H-bonds generated for 'chain 'X' and resid 18 through 20' Processing helix chain 'Z' and resid 8 through 17 Processing helix chain 'Z' and resid 17 through 23 Processing helix chain 'Z' and resid 24 through 38 Processing helix chain 'a' and resid 7 through 12 Processing helix chain 'a' and resid 36 through 43 Processing helix chain 'a' and resid 53 through 61 Processing helix chain 'b' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.802A pdb=" N LYS A 37 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 60 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 6.544A pdb=" N ILE A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 81 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 93 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 116 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 131 removed outlier: 5.994A pdb=" N LEU A 164 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG A 175 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET A 181 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.315A pdb=" N VAL A 144 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 16 removed outlier: 5.599A pdb=" N LYS B 9 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 29 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 11 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 189 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 183 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 191 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU B 179 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 174 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B 114 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLN B 176 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 112 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B 115 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASP B 203 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 3.751A pdb=" N LEU B 79 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 53 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 48 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 38 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 50 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.606A pdb=" N GLY B 120 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.789A pdb=" N LEU C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 11 " --> pdb=" O LEU C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 117 through 120 removed outlier: 6.355A pdb=" N LEU C 146 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N SER C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 148 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA C 145 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL C 169 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 147 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.793A pdb=" N LYS D 33 " --> pdb=" O THR D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.604A pdb=" N VAL E 9 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.521A pdb=" N THR E 18 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AB6, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 99 Processing sheet with id=AB8, first strand: chain 'F' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.521A pdb=" N ARG G 17 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU G 45 " --> pdb=" O ARG G 17 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL G 19 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL G 43 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS G 21 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 41 " --> pdb=" O CYS G 21 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS G 23 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE G 39 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA G 83 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA G 84 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP G 9 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE G 86 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 69 through 70 removed outlier: 4.027A pdb=" N VAL G 76 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA L 52 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG L 65 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL L 50 " --> pdb=" O ARG L 65 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE L 67 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY L 48 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR L 28 " --> pdb=" O VAL L 89 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL L 89 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL L 30 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE L 87 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN L 32 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 103 removed outlier: 6.655A pdb=" N VAL G 102 " --> pdb=" O LEU G 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 80 Processing sheet with id=AC5, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=AC6, first strand: chain 'I' and resid 63 through 66 removed outlier: 6.693A pdb=" N ILE I 34 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU I 105 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE I 32 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 40 through 43 removed outlier: 6.947A pdb=" N ILE I 74 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP I 93 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS I 72 " --> pdb=" O TRP I 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.050A pdb=" N MET J 110 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 48 through 53 removed outlier: 6.760A pdb=" N VAL K 40 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN K 51 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA K 38 " --> pdb=" O GLN K 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER K 53 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE K 36 " --> pdb=" O SER K 53 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 29 " --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.556A pdb=" N VAL N 4 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU N 39 " --> pdb=" O GLY N 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.655A pdb=" N GLY N 65 " --> pdb=" O GLU N 95 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS N 97 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL N 63 " --> pdb=" O LYS N 97 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR N 99 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA N 61 " --> pdb=" O THR N 99 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE N 101 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL N 59 " --> pdb=" O ILE N 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 72 through 78 removed outlier: 4.193A pdb=" N TYR N 83 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 11 removed outlier: 5.523A pdb=" N CYS O 102 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY O 109 " --> pdb=" O VAL O 72 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL O 72 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 83 through 88 Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.582A pdb=" N GLY P 12 " --> pdb=" O LYS P 32 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS P 80 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL P 79 " --> pdb=" O ILE P 61 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE P 61 " --> pdb=" O VAL P 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS P 81 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR P 59 " --> pdb=" O LYS P 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR P 83 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL P 57 " --> pdb=" O TYR P 83 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR P 85 " --> pdb=" O VAL P 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 66 through 68 Processing sheet with id=AD8, first strand: chain 'Q' and resid 63 through 64 removed outlier: 6.929A pdb=" N ARG Q 31 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL Q 27 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN Q 9 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE Q 70 " --> pdb=" O ASP Q 79 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP Q 79 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 39 through 44 Processing sheet with id=AE1, first strand: chain 'Q' and resid 81 through 86 Processing sheet with id=AE2, first strand: chain 'R' and resid 5 through 7 removed outlier: 6.243A pdb=" N VAL R 76 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG R 97 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE R 78 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE R 95 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA R 80 " --> pdb=" O ALA R 93 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA R 93 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN R 82 " --> pdb=" O MET R 91 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LEU R 29 " --> pdb=" O MET R 91 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ALA R 93 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N PHE R 95 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE R 33 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ARG R 97 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR R 35 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 22 through 23 removed outlier: 6.804A pdb=" N LEU S 59 " --> pdb=" O ILE S 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'T' and resid 13 through 18 Processing sheet with id=AE6, first strand: chain 'T' and resid 33 through 40 Processing sheet with id=AE7, first strand: chain 'V' and resid 34 through 38 Processing sheet with id=AE8, first strand: chain 'X' and resid 27 through 29 Processing sheet with id=AE9, first strand: chain 'Y' and resid 16 through 22 Processing sheet with id=AF1, first strand: chain 'a' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'b' and resid 2 through 4 removed outlier: 5.962A pdb=" N LYS b 2 " --> pdb=" O ARG b 36 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE b 23 " --> pdb=" O GLN b 37 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2258 hydrogen bonds 3482 hydrogen bond angles 0 basepair planarities 901 basepair parallelities 1533 stacking parallelities Total time for adding SS restraints: 162.66 Time building geometry restraints manager: 31.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9376 1.32 - 1.44: 39563 1.44 - 1.57: 36190 1.57 - 1.69: 5591 1.69 - 1.81: 120 Bond restraints: 90840 Sorted by residual: bond pdb=" CA ARG X 17 " pdb=" C ARG X 17 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.80e-02 3.09e+03 7.51e+00 bond pdb=" C GLU I 76 " pdb=" N LYS I 77 " ideal model delta sigma weight residual 1.331 1.285 0.046 2.07e-02 2.33e+03 5.01e+00 bond pdb=" O3' U 1 567 " pdb=" P G 1 568 " ideal model delta sigma weight residual 1.607 1.581 0.026 1.50e-02 4.44e+03 2.89e+00 bond pdb=" P G 12434 " pdb=" OP1 G 12434 " ideal model delta sigma weight residual 1.485 1.451 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" P G 11981 " pdb=" OP2 G 11981 " ideal model delta sigma weight residual 1.485 1.452 0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 90835 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.20: 16473 106.20 - 113.47: 54292 113.47 - 120.74: 36307 120.74 - 128.02: 24733 128.02 - 135.29: 4732 Bond angle restraints: 136537 Sorted by residual: angle pdb=" C LYS H 38 " pdb=" N GLY H 39 " pdb=" CA GLY H 39 " ideal model delta sigma weight residual 122.43 116.38 6.05 8.90e-01 1.26e+00 4.62e+01 angle pdb=" O3' A 11746 " pdb=" C3' A 11746 " pdb=" C2' A 11746 " ideal model delta sigma weight residual 109.50 117.13 -7.63 1.50e+00 4.44e-01 2.58e+01 angle pdb=" O4' G 1 504 " pdb=" C1' G 1 504 " pdb=" N9 G 1 504 " ideal model delta sigma weight residual 108.20 115.09 -6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" O3' U 1 567 " pdb=" C3' U 1 567 " pdb=" C2' U 1 567 " ideal model delta sigma weight residual 113.70 120.33 -6.63 1.50e+00 4.44e-01 1.95e+01 angle pdb=" C3' A 11746 " pdb=" O3' A 11746 " pdb=" P A 11747 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 136532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 45992 35.67 - 71.34: 1945 71.34 - 107.01: 141 107.01 - 142.68: 11 142.68 - 178.35: 20 Dihedral angle restraints: 48109 sinusoidal: 39427 harmonic: 8682 Sorted by residual: dihedral pdb=" CA HIS a 30 " pdb=" C HIS a 30 " pdb=" N ILE a 31 " pdb=" CA ILE a 31 " ideal model delta harmonic sigma weight residual -180.00 -131.20 -48.80 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 29.82 170.18 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C 11130 " pdb=" C1' C 11130 " pdb=" N1 C 11130 " pdb=" C2 C 11130 " ideal model delta sinusoidal sigma weight residual -160.00 10.04 -170.04 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 48106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16057 0.080 - 0.161: 1423 0.161 - 0.241: 104 0.241 - 0.321: 14 0.321 - 0.402: 2 Chirality restraints: 17600 Sorted by residual: chirality pdb=" C3' U 1 567 " pdb=" C4' U 1 567 " pdb=" O3' U 1 567 " pdb=" C2' U 1 567 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3' A 11746 " pdb=" C4' A 11746 " pdb=" O3' A 11746 " pdb=" C2' A 11746 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C3' C 11171 " pdb=" C4' C 11171 " pdb=" O3' C 11171 " pdb=" C2' C 11171 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 17597 not shown) Planarity restraints: 6899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 504 " -0.067 2.00e-02 2.50e+03 2.73e-02 2.24e+01 pdb=" N9 G 1 504 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G 1 504 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 1 504 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 504 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 1 504 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 1 504 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G 1 504 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G 1 504 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 504 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 1 504 " 0.015 2.00e-02 2.50e+03 pdb=" C4 G 1 504 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12696 " -0.050 2.00e-02 2.50e+03 2.65e-02 1.58e+01 pdb=" N1 U 12696 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U 12696 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U 12696 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 12696 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U 12696 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U 12696 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U 12696 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 12696 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 970 " 0.053 2.00e-02 2.50e+03 2.37e-02 1.55e+01 pdb=" N9 A 1 970 " -0.054 2.00e-02 2.50e+03 pdb=" C8 A 1 970 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 1 970 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 1 970 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 970 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A 1 970 " 0.015 2.00e-02 2.50e+03 pdb=" N1 A 1 970 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 970 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A 1 970 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 1 970 " -0.011 2.00e-02 2.50e+03 ... (remaining 6896 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 339 2.49 - 3.09: 50222 3.09 - 3.70: 148377 3.70 - 4.30: 241427 4.30 - 4.90: 313211 Nonbonded interactions: 753576 Sorted by model distance: nonbonded pdb=" OP1 A 12578 " pdb="MG MG 13015 " model vdw 1.890 2.170 nonbonded pdb=" O2 U 1 536 " pdb=" O6 G 1 539 " model vdw 1.892 2.432 nonbonded pdb=" OP1 A 11769 " pdb="MG MG 13078 " model vdw 1.910 2.170 nonbonded pdb=" OP2 G 12811 " pdb="MG MG 13157 " model vdw 1.932 2.170 nonbonded pdb=" O4 U 11662 " pdb="MG MG 13117 " model vdw 1.956 2.170 ... (remaining 753571 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 1 6.06 5 P 2800 5.49 5 Mg 160 5.21 5 S 68 5.16 5 C 41336 2.51 5 N 15545 2.21 5 O 23604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 17.390 Check model and map are aligned: 0.930 Convert atoms to be neutral: 0.550 Process input model: 334.190 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.260 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 370.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.007 0.056 90840 Z= 0.439 Angle : 0.787 9.618 136537 Z= 0.416 Chirality : 0.047 0.402 17600 Planarity : 0.006 0.062 6899 Dihedral : 15.675 178.353 42527 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer Outliers : 7.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.13), residues: 3016 helix: -1.90 (0.16), residues: 728 sheet: -1.19 (0.19), residues: 642 loop : -2.22 (0.12), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 520 time to evaluate : 3.466 Fit side-chains outliers start: 165 outliers final: 97 residues processed: 647 average time/residue: 1.6293 time to fit residues: 1411.5391 Evaluate side-chains 576 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 479 time to evaluate : 3.351 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 80 residues processed: 17 average time/residue: 0.6658 time to fit residues: 23.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 0.9990 chunk 433 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 519 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 142 HIS E 19 GLN E 45 GLN E 106 ASN E 139 GLN F 136 GLN G 88 ASN L 5 HIS L 15 GLN O 63 ASN P 90 GLN Q 43 HIS S 17 ASN T 6 GLN T 23 ASN U 44 GLN X 37 HIS a 30 HIS b 35 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 90840 Z= 0.224 Angle : 0.598 9.209 136537 Z= 0.319 Chirality : 0.039 0.300 17600 Planarity : 0.005 0.059 6899 Dihedral : 14.158 179.304 36948 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.80 (0.14), residues: 3016 helix: -0.49 (0.18), residues: 748 sheet: -0.66 (0.19), residues: 659 loop : -1.78 (0.13), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 493 time to evaluate : 3.518 Fit side-chains revert: symmetry clash outliers start: 168 outliers final: 102 residues processed: 612 average time/residue: 1.6604 time to fit residues: 1368.3491 Evaluate side-chains 577 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 475 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 81 residues processed: 21 average time/residue: 0.7654 time to fit residues: 30.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 353 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 520 optimal weight: 7.9990 chunk 562 optimal weight: 0.4980 chunk 463 optimal weight: 9.9990 chunk 516 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 417 optimal weight: 2.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN J 62 ASN L 15 GLN S 17 ASN X 6 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 90840 Z= 0.444 Angle : 0.783 9.597 136537 Z= 0.401 Chirality : 0.047 0.407 17600 Planarity : 0.006 0.065 6899 Dihedral : 14.425 178.500 36948 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer Outliers : 7.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.59 (0.14), residues: 3016 helix: -0.34 (0.18), residues: 754 sheet: -0.47 (0.20), residues: 644 loop : -1.66 (0.14), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 479 time to evaluate : 3.455 Fit side-chains revert: symmetry clash outliers start: 184 outliers final: 133 residues processed: 615 average time/residue: 1.6074 time to fit residues: 1336.4254 Evaluate side-chains 605 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 472 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 104 residues processed: 29 average time/residue: 0.9296 time to fit residues: 46.4229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 0.0870 chunk 391 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 522 optimal weight: 0.7980 chunk 552 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN S 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 90840 Z= 0.209 Angle : 0.583 9.228 136537 Z= 0.311 Chirality : 0.038 0.295 17600 Planarity : 0.005 0.059 6899 Dihedral : 14.037 178.926 36948 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.85 % Rotamer Outliers : 6.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.11 (0.14), residues: 3016 helix: 0.31 (0.19), residues: 743 sheet: -0.28 (0.20), residues: 646 loop : -1.45 (0.14), residues: 1627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 475 time to evaluate : 3.687 Fit side-chains outliers start: 156 outliers final: 116 residues processed: 597 average time/residue: 1.5708 time to fit residues: 1269.0483 Evaluate side-chains 587 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 471 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 98 residues processed: 19 average time/residue: 0.7263 time to fit residues: 27.7693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 0.9990 chunk 313 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 471 optimal weight: 8.9990 chunk 382 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 496 optimal weight: 0.3980 chunk 139 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 46 ASN S 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 90840 Z= 0.294 Angle : 0.648 9.372 136537 Z= 0.341 Chirality : 0.041 0.334 17600 Planarity : 0.005 0.061 6899 Dihedral : 14.091 179.210 36948 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer Outliers : 7.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.01 (0.14), residues: 3016 helix: 0.34 (0.19), residues: 749 sheet: -0.18 (0.20), residues: 669 loop : -1.40 (0.14), residues: 1598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 467 time to evaluate : 3.559 Fit side-chains revert: symmetry clash outliers start: 164 outliers final: 126 residues processed: 593 average time/residue: 1.6439 time to fit residues: 1312.3919 Evaluate side-chains 591 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 465 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 103 residues processed: 23 average time/residue: 0.9168 time to fit residues: 37.0558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 5.9990 chunk 497 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 553 optimal weight: 0.3980 chunk 459 optimal weight: 0.9990 chunk 256 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 46 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 90840 Z= 0.358 Angle : 0.703 9.465 136537 Z= 0.366 Chirality : 0.043 0.370 17600 Planarity : 0.006 0.062 6899 Dihedral : 14.170 179.892 36948 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.05 (0.14), residues: 3016 helix: 0.26 (0.19), residues: 749 sheet: -0.19 (0.20), residues: 680 loop : -1.40 (0.14), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 468 time to evaluate : 3.476 Fit side-chains revert: symmetry clash outliers start: 168 outliers final: 133 residues processed: 599 average time/residue: 1.5835 time to fit residues: 1278.9576 Evaluate side-chains 598 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 465 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 109 residues processed: 24 average time/residue: 0.7954 time to fit residues: 35.9831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 315 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 465 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 551 optimal weight: 10.0000 chunk 345 optimal weight: 0.3980 chunk 336 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 63 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN I 110 ASN L 15 GLN N 46 ASN O 62 ASN S 17 ASN T 35 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 90840 Z= 0.153 Angle : 0.527 9.120 136537 Z= 0.283 Chirality : 0.035 0.258 17600 Planarity : 0.004 0.056 6899 Dihedral : 13.833 179.261 36948 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer Outliers : 5.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -0.68 (0.15), residues: 3016 helix: 0.81 (0.19), residues: 746 sheet: -0.11 (0.20), residues: 649 loop : -1.21 (0.14), residues: 1621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 482 time to evaluate : 3.496 Fit side-chains revert: symmetry clash outliers start: 137 outliers final: 108 residues processed: 598 average time/residue: 1.6036 time to fit residues: 1298.0776 Evaluate side-chains 582 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 474 time to evaluate : 3.407 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 98 residues processed: 10 average time/residue: 0.8117 time to fit residues: 17.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 350 optimal weight: 20.0000 chunk 375 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 433 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 46 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 90840 Z= 0.450 Angle : 0.783 9.645 136537 Z= 0.400 Chirality : 0.047 0.414 17600 Planarity : 0.006 0.073 6899 Dihedral : 14.276 179.672 36948 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.79 % Rotamer Outliers : 6.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -1.03 (0.14), residues: 3016 helix: 0.15 (0.18), residues: 769 sheet: -0.12 (0.20), residues: 668 loop : -1.35 (0.14), residues: 1579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 469 time to evaluate : 3.564 Fit side-chains revert: symmetry clash outliers start: 148 outliers final: 118 residues processed: 587 average time/residue: 1.6610 time to fit residues: 1322.1532 Evaluate side-chains 582 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 464 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 100 residues processed: 18 average time/residue: 0.8281 time to fit residues: 28.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 6.9990 chunk 528 optimal weight: 2.9990 chunk 481 optimal weight: 0.5980 chunk 513 optimal weight: 0.0000 chunk 309 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 403 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 464 optimal weight: 3.9990 chunk 485 optimal weight: 2.9990 chunk 511 optimal weight: 4.9990 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 46 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 90840 Z= 0.190 Angle : 0.584 9.360 136537 Z= 0.310 Chirality : 0.037 0.272 17600 Planarity : 0.004 0.058 6899 Dihedral : 14.026 179.131 36948 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -0.77 (0.15), residues: 3016 helix: 0.62 (0.19), residues: 751 sheet: -0.09 (0.21), residues: 638 loop : -1.24 (0.14), residues: 1627 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 464 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 103 residues processed: 574 average time/residue: 1.6618 time to fit residues: 1280.8325 Evaluate side-chains 570 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 467 time to evaluate : 3.445 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 98 residues processed: 5 average time/residue: 0.8566 time to fit residues: 10.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 5.9990 chunk 543 optimal weight: 9.9990 chunk 331 optimal weight: 0.2980 chunk 257 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 chunk 569 optimal weight: 0.4980 chunk 524 optimal weight: 0.0670 chunk 453 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 chunk 278 optimal weight: 0.5980 overall best weight: 1.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 63 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS H 6 ASN L 15 GLN N 46 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 90840 Z= 0.141 Angle : 0.536 9.245 136537 Z= 0.288 Chirality : 0.035 0.261 17600 Planarity : 0.004 0.056 6899 Dihedral : 13.902 178.860 36948 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -0.56 (0.15), residues: 3016 helix: 0.85 (0.19), residues: 760 sheet: -0.01 (0.21), residues: 636 loop : -1.12 (0.14), residues: 1620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 471 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 97 residues processed: 574 average time/residue: 1.7052 time to fit residues: 1315.5271 Evaluate side-chains 563 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 466 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 96 residues processed: 2 average time/residue: 1.3356 time to fit residues: 7.3525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 1.9990 chunk 483 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 454 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 466 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS L 15 GLN N 46 ASN S 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116388 restraints weight = 85868.277| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.56 r_work: 0.3078 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work: 0.2870 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 90840 Z= 0.268 Angle : 0.619 9.262 136537 Z= 0.326 Chirality : 0.039 0.315 17600 Planarity : 0.005 0.059 6899 Dihedral : 13.947 178.344 36948 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer Outliers : 4.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: -0.63 (0.15), residues: 3016 helix: 0.70 (0.19), residues: 759 sheet: 0.01 (0.20), residues: 670 loop : -1.16 (0.14), residues: 1587 =============================================================================== Job complete usr+sys time: 17814.64 seconds wall clock time: 313 minutes 52.51 seconds (18832.51 seconds total)