Starting phenix.real_space_refine (version: dev) on Mon May 16 16:40:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/05_2022/7bl6_12219_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 0.170 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 "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 92769 Number of models: 1 Model: "" Number of chains: 42 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85 SG CYS g 11 67.792 178.993 66.710 1.00277.97 S ATOM 110 SG CYS g 14 70.774 177.662 68.668 1.00281.13 S ATOM 213 SG CYS g 27 69.296 181.145 69.478 1.00293.05 S ATOM 24643 SG CYS d 16 21.903 84.234 28.463 1.00436.92 S ATOM 24797 SG CYS d 37 23.738 87.221 26.891 1.00411.36 S Time building chain proxies: 37.71, per 1000 atoms: 0.41 Number of scatterers: 92769 At special positions: 0 Unit cell: (180.96, 233.16, 234.9, 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 94 16.00 P 3018 15.00 Mg 2 11.99 O 25977 8.00 N 17251 7.00 C 46425 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: 36.17 Conformation dependent library (CDL) restraints added in 3.5 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 27 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " Number of angles added : 3 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 48 sheets defined 24.2% alpha, 17.6% beta 979 base pairs and 1519 stacking pairs defined. Time for finding SS restraints: 41.22 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 207 through 211 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 71 removed outlier: 3.603A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' 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 162 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: 3.980A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' 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 93 through 104 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 162 through 171 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.960A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.877A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 3.837A 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 99 through 108 removed outlier: 3.688A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.799A 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 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: 3.925A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.777A 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 88 Processing helix chain 'O' and resid 4 through 20 removed outlier: 4.494A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 85 Processing helix chain 'O' and resid 102 through 113 Processing helix chain 'Q' and resid 8 through 19 Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.440A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.623A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.761A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 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 10 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 14 through 22 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 54 through 57 removed outlier: 3.963A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 57' Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 25 through 33 Processing helix chain 'Y' and resid 40 through 55 removed outlier: 3.525A pdb=" N LYS Y 44 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.558A 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 19 removed outlier: 3.713A pdb=" N SER 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (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 11 removed outlier: 4.352A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (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 removed outlier: 3.539A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 100' Processing helix chain 'M' and resid 43 through 56 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.896A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.086A 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 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.588A pdb=" N ARG H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 54 through 74 removed outlier: 4.096A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.737A 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 '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: 3.691A pdb=" N ILE 9 176 " --> pdb=" O LYS 9 172 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG 9 177 " --> pdb=" O SER 9 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 9 178 " --> pdb=" O THR 9 174 " (cutoff:3.500A) Processing helix chain '9' and resid 230 through 233 Processing helix chain '9' and resid 255 through 268 removed outlier: 3.989A pdb=" N ARG 9 260 " --> pdb=" O VAL 9 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE 9 262 " --> pdb=" O ASN 9 258 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER 9 264 " --> pdb=" O ARG 9 260 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 9 265 " --> pdb=" O ILE 9 261 " (cutoff:3.500A) removed outlier: 3.758A 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 285 through 287 No H-bonds generated for 'chain '9' and resid 285 through 287' Processing helix chain '9' and resid 291 through 304 removed outlier: 3.503A pdb=" N GLU 9 294 " --> pdb=" O VAL 9 291 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU 9 295 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 9 296 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE 9 300 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 removed outlier: 3.859A pdb=" N TRP 9 326 " --> pdb=" O LYS 9 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 9 334 " --> pdb=" O THR 9 330 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 removed outlier: 3.612A 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: 3.635A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 60 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: 4.340A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.079A 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: 3.966A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.889A 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: 4.582A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.000A 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: 4.072A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= I, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.939A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.812A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.273A 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: 3.792A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.619A 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 removed outlier: 3.510A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.957A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.128A 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: 6.667A 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: 6.855A 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 removed outlier: 3.649A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR N 112 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS N 99 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU N 114 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE N 97 " --> pdb=" O GLU N 114 " (cutoff:3.500A) 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 40 through 42 removed outlier: 3.733A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'R' and resid 20 through 23 removed outlier: 4.157A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.929A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 102 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS R 60 " --> pdb=" O GLY R 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.050A 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: 4.143A 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: 6.271A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.984A 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: 6.673A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.929A 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 69 through 71 removed outlier: 4.176A pdb=" N ASP U 8 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL U 24 " --> pdb=" O ASP U 8 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 40 through 44 Processing sheet with id= AE, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AF, first strand: chain 'V' and resid 3 through 6 removed outlier: 6.879A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA V 6 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL V 64 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AH, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AI, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AJ, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.559A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.516A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '1' and resid 19 through 24 removed outlier: 3.634A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.964A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.601A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 128 through 132 removed outlier: 6.316A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP M 64 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 39 through 42 removed outlier: 4.183A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 72 through 74 removed outlier: 3.874A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 78 through 83 Processing sheet with id= AS, first strand: chain 'd' and resid 11 through 15 removed outlier: 3.912A pdb=" N ILE d 24 " --> pdb=" O ILE d 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 14 " --> pdb=" O MET d 22 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '9' and resid 64 through 66 removed outlier: 8.737A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '9' and resid 45 through 50 removed outlier: 5.875A pdb=" N VAL 9 86 " --> pdb=" O TRP 9 46 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU 9 48 " --> pdb=" O VAL 9 86 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE 9 88 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP 9 50 " --> pdb=" O ILE 9 88 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL 9 90 " --> pdb=" O ASP 9 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain '9' and resid 162 through 166 removed outlier: 6.482A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL 9 281 " --> pdb=" O ILE 9 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV 760 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2492 hydrogen bonds 3934 hydrogen bond angles 0 basepair planarities 979 basepair parallelities 1519 stacking parallelities Total time for adding SS restraints: 161.72 Time building geometry restraints manager: 39.36 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: 15888 1.33 - 1.46: 41822 1.46 - 1.58: 36978 1.58 - 1.70: 6032 1.70 - 1.82: 168 Bond restraints: 100888 Sorted by residual: bond pdb=" N3B GNP 9 402 " pdb=" PG GNP 9 402 " ideal model delta sigma weight residual 1.801 1.709 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O5' GNP 9 402 " pdb=" PA GNP 9 402 " ideal model delta sigma weight residual 1.660 1.574 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA LYS 9 31 " pdb=" CB LYS 9 31 " ideal model delta sigma weight residual 1.528 1.587 -0.059 2.61e-02 1.47e+03 5.07e+00 bond pdb=" O3A GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.687 1.643 0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" N3B GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.681 1.639 0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 100883 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.25: 14040 105.25 - 112.43: 58162 112.43 - 119.61: 32275 119.61 - 126.79: 38356 126.79 - 133.97: 8345 Bond angle restraints: 151178 Sorted by residual: angle pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " ideal model delta sigma weight residual 110.28 118.17 -7.89 1.55e+00 4.16e-01 2.59e+01 angle pdb=" CB ARG Y 23 " pdb=" CG ARG Y 23 " pdb=" CD ARG Y 23 " ideal model delta sigma weight residual 111.30 122.83 -11.53 2.30e+00 1.89e-01 2.51e+01 angle pdb=" C VAL Q 109 " pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " ideal model delta sigma weight residual 120.31 112.96 7.35 1.52e+00 4.33e-01 2.34e+01 angle pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " pdb=" CG GLU Q 110 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CB MET 0 14 " pdb=" CG MET 0 14 " pdb=" SD MET 0 14 " ideal model delta sigma weight residual 112.70 101.69 11.01 3.00e+00 1.11e-01 1.35e+01 ... (remaining 151173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 52130 35.66 - 71.33: 1424 71.33 - 106.99: 124 106.99 - 142.66: 5 142.66 - 178.32: 10 Dihedral angle restraints: 53693 sinusoidal: 43512 harmonic: 10181 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 53.66 146.34 1 1.50e+01 4.44e-03 7.82e+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 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+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 50.31 -178.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 53690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 18341 0.054 - 0.109: 888 0.109 - 0.163: 114 0.163 - 0.218: 7 0.218 - 0.272: 1 Chirality restraints: 19351 Sorted by residual: 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 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 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 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG Y 23 " pdb=" N ARG Y 23 " pdb=" C ARG Y 23 " pdb=" CB ARG Y 23 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 19348 not shown) Planarity restraints: 7924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.031 2.00e-02 2.50e+03 1.69e-02 6.41e+00 pdb=" N1 U A1736 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 643 " -0.029 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A A 643 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 643 " -0.000 2.00e-02 2.50e+03 pdb=" N6 A A 643 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 643 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 643 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 100 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C ASN G 100 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN G 100 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL G 101 " 0.012 2.00e-02 2.50e+03 ... (remaining 7921 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 5251 2.67 - 3.23: 81646 3.23 - 3.79: 191011 3.79 - 4.34: 245200 4.34 - 4.90: 323028 Nonbonded interactions: 846136 Sorted by model distance: nonbonded pdb="MG MG 9 401 " pdb=" O2G GNP 9 402 " model vdw 2.117 2.170 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 2.126 2.440 nonbonded pdb=" O2' C A2258 " pdb=" OP2 C A2427 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR O 31 " pdb=" O HIS O 34 " model vdw 2.154 2.440 nonbonded pdb=" N2 G A1171 " pdb=" O2 C A1178 " model vdw 2.157 2.496 ... (remaining 846131 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 2 5.21 5 S 94 5.16 5 C 46425 2.51 5 N 17251 2.21 5 O 25977 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 group one per residue 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: 0.620 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: 0.060 Extract box with map and model: 9.540 Check model and map are aligned: 1.010 Convert atoms to be neutral: 0.580 Process input model: 345.150 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 362.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.092 100888 Z= 0.098 Angle : 0.423 11.526 151178 Z= 0.226 Chirality : 0.025 0.272 19351 Planarity : 0.003 0.052 7924 Dihedral : 13.165 178.319 47145 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer Outliers : 0.07 % 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: -0.28 (0.14), residues: 3538 helix: 0.52 (0.18), residues: 858 sheet: 0.89 (0.21), residues: 672 loop : -0.89 (0.13), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.8877 time to fit residues: 247.0124 Evaluate side-chains 129 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 4.832 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7769 time to fit residues: 5.8168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 545 optimal weight: 40.0000 chunk 489 optimal weight: 40.0000 chunk 271 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 330 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 506 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 chunk 307 optimal weight: 30.0000 chunk 376 optimal weight: 40.0000 chunk 586 optimal weight: 40.0000 overall best weight: 19.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 152 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 135 GLN N 11 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN S 7 HIS S 31 GLN T 59 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 2 6 GLN K 3 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.154 100888 Z= 0.449 Angle : 0.771 11.859 151178 Z= 0.383 Chirality : 0.037 0.332 19351 Planarity : 0.006 0.070 7924 Dihedral : 13.875 179.942 40157 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 32.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.06 % Rotamer Outliers : 0.86 % 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: -0.61 (0.14), residues: 3538 helix: 0.17 (0.18), residues: 890 sheet: 0.21 (0.19), residues: 721 loop : -0.89 (0.14), residues: 1927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 155 average time/residue: 0.9086 time to fit residues: 251.7796 Evaluate side-chains 134 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 4.001 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7439 time to fit residues: 16.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 326 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 488 optimal weight: 30.0000 chunk 399 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 587 optimal weight: 30.0000 chunk 634 optimal weight: 20.0000 chunk 523 optimal weight: 50.0000 chunk 582 optimal weight: 30.0000 chunk 200 optimal weight: 50.0000 chunk 471 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- 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** C 142 ASN D 36 GLN D 67 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 41 GLN ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 63 GLN G 72 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN L 104 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN V 75 GLN Y 25 GLN 1 18 HIS 2 29 GLN K 3 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN 9 71 GLN ** 9 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 HIS ** 9 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.143 100888 Z= 0.539 Angle : 0.889 19.662 151178 Z= 0.444 Chirality : 0.044 0.363 19351 Planarity : 0.007 0.071 7924 Dihedral : 16.116 176.600 40157 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 52.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.01 % Favored : 92.91 % Rotamer Outliers : 2.43 % 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: -1.59 (0.13), residues: 3538 helix: -0.85 (0.16), residues: 889 sheet: -0.50 (0.19), residues: 748 loop : -1.36 (0.13), residues: 1901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 128 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 25 residues processed: 182 average time/residue: 0.8002 time to fit residues: 261.5485 Evaluate side-chains 135 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 4.030 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.7771 time to fit residues: 38.8871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 580 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 chunk 305 optimal weight: 40.0000 chunk 65 optimal weight: 30.0000 chunk 280 optimal weight: 7.9990 chunk 394 optimal weight: 30.0000 chunk 589 optimal weight: 20.0000 chunk 624 optimal weight: 0.9980 chunk 308 optimal weight: 20.0000 chunk 558 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 overall best weight: 11.3992 ------------------------------------------------------------------------------- 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** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 100888 Z= 0.260 Angle : 0.610 13.498 151178 Z= 0.311 Chirality : 0.034 0.329 19351 Planarity : 0.004 0.044 7924 Dihedral : 15.712 176.945 40157 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.18 % Rotamer Outliers : 1.82 % 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: -1.15 (0.14), residues: 3538 helix: -0.14 (0.18), residues: 888 sheet: -0.35 (0.19), residues: 724 loop : -1.21 (0.14), residues: 1926 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 17 residues processed: 175 average time/residue: 0.8061 time to fit residues: 253.0082 Evaluate side-chains 139 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 3.946 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.7385 time to fit residues: 26.9282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 520 optimal weight: 50.0000 chunk 354 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 464 optimal weight: 40.0000 chunk 257 optimal weight: 9.9990 chunk 532 optimal weight: 40.0000 chunk 431 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 318 optimal weight: 30.0000 chunk 560 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 overall best weight: 16.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN 3 25 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 100888 Z= 0.372 Angle : 0.679 11.997 151178 Z= 0.344 Chirality : 0.036 0.341 19351 Planarity : 0.005 0.088 7924 Dihedral : 15.945 177.942 40157 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 40.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Rotamer Outliers : 1.99 % 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: -1.31 (0.14), residues: 3538 helix: -0.31 (0.17), residues: 896 sheet: -0.55 (0.19), residues: 734 loop : -1.24 (0.14), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 123 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 23 residues processed: 173 average time/residue: 0.8314 time to fit residues: 263.1951 Evaluate side-chains 144 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7068 time to fit residues: 35.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 210 optimal weight: 0.9990 chunk 562 optimal weight: 40.0000 chunk 123 optimal weight: 50.0000 chunk 366 optimal weight: 30.0000 chunk 154 optimal weight: 40.0000 chunk 625 optimal weight: 0.0870 chunk 518 optimal weight: 50.0000 chunk 289 optimal weight: 40.0000 chunk 51 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 328 optimal weight: 30.0000 overall best weight: 14.2170 ------------------------------------------------------------------------------- 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** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 100888 Z= 0.299 Angle : 0.620 14.230 151178 Z= 0.316 Chirality : 0.035 0.349 19351 Planarity : 0.005 0.047 7924 Dihedral : 15.988 176.904 40157 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 34.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer Outliers : 1.37 % 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: -1.26 (0.14), residues: 3538 helix: -0.17 (0.18), residues: 901 sheet: -0.64 (0.19), residues: 706 loop : -1.22 (0.14), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 158 average time/residue: 0.8236 time to fit residues: 235.6662 Evaluate side-chains 132 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 4.040 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7245 time to fit residues: 21.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 602 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 356 optimal weight: 30.0000 chunk 456 optimal weight: 30.0000 chunk 353 optimal weight: 20.0000 chunk 526 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 622 optimal weight: 5.9990 chunk 389 optimal weight: 30.0000 chunk 379 optimal weight: 30.0000 chunk 287 optimal weight: 30.0000 overall best weight: 18.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS J 136 GLN N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN 9 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.095 100888 Z= 0.406 Angle : 0.725 12.776 151178 Z= 0.364 Chirality : 0.038 0.347 19351 Planarity : 0.005 0.047 7924 Dihedral : 16.358 177.338 40157 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 44.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.62 % Favored : 91.29 % Rotamer Outliers : 1.13 % 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: -1.52 (0.14), residues: 3538 helix: -0.44 (0.17), residues: 894 sheet: -0.85 (0.18), residues: 757 loop : -1.32 (0.14), residues: 1887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 155 average time/residue: 0.8508 time to fit residues: 238.3223 Evaluate side-chains 138 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 4.075 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.7559 time to fit residues: 26.3736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 385 optimal weight: 30.0000 chunk 248 optimal weight: 10.0000 chunk 371 optimal weight: 30.0000 chunk 187 optimal weight: 30.0000 chunk 122 optimal weight: 40.0000 chunk 120 optimal weight: 50.0000 chunk 395 optimal weight: 40.0000 chunk 424 optimal weight: 30.0000 chunk 307 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 489 optimal weight: 30.0000 overall best weight: 20.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.089 100888 Z= 0.415 Angle : 0.746 14.452 151178 Z= 0.375 Chirality : 0.039 0.364 19351 Planarity : 0.005 0.062 7924 Dihedral : 16.848 177.307 40157 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 46.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.59 % Favored : 91.29 % Rotamer Outliers : 0.99 % 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: -1.72 (0.14), residues: 3538 helix: -0.62 (0.17), residues: 873 sheet: -1.13 (0.18), residues: 749 loop : -1.35 (0.14), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 150 average time/residue: 0.9054 time to fit residues: 246.9136 Evaluate side-chains 135 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.7699 time to fit residues: 25.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 566 optimal weight: 30.0000 chunk 596 optimal weight: 30.0000 chunk 544 optimal weight: 30.0000 chunk 580 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 455 optimal weight: 30.0000 chunk 178 optimal weight: 10.0000 chunk 524 optimal weight: 70.0000 chunk 548 optimal weight: 30.0000 chunk 578 optimal weight: 30.0000 overall best weight: 22.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN 9 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.100 100888 Z= 0.461 Angle : 0.793 14.923 151178 Z= 0.396 Chirality : 0.041 0.391 19351 Planarity : 0.006 0.062 7924 Dihedral : 17.088 179.287 40157 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 52.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.72 % Favored : 90.16 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.01 (0.13), residues: 3538 helix: -0.88 (0.17), residues: 904 sheet: -1.29 (0.19), residues: 711 loop : -1.54 (0.14), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 134 average time/residue: 0.8958 time to fit residues: 217.3604 Evaluate side-chains 122 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 4.095 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6938 time to fit residues: 13.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 381 optimal weight: 30.0000 chunk 613 optimal weight: 50.0000 chunk 374 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 426 optimal weight: 30.0000 chunk 643 optimal weight: 30.0000 chunk 592 optimal weight: 20.0000 chunk 512 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 395 optimal weight: 40.0000 chunk 314 optimal weight: 30.0000 overall best weight: 21.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 100888 Z= 0.434 Angle : 0.772 12.932 151178 Z= 0.387 Chirality : 0.041 0.551 19351 Planarity : 0.006 0.065 7924 Dihedral : 17.245 179.278 40157 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 49.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.33 % Favored : 90.56 % Rotamer Outliers : 0.27 % 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: -2.04 (0.13), residues: 3538 helix: -0.90 (0.17), residues: 894 sheet: -1.42 (0.18), residues: 715 loop : -1.52 (0.14), residues: 1929 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 0.9152 time to fit residues: 203.1769 Evaluate side-chains 120 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 4.062 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7425 time to fit residues: 8.4482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 407 optimal weight: 20.0000 chunk 545 optimal weight: 30.0000 chunk 157 optimal weight: 8.9990 chunk 472 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 513 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 chunk 527 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN H 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.023223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.018665 restraints weight = 2013237.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.019099 restraints weight = 727749.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.019318 restraints weight = 411078.612| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 100888 Z= 0.252 Angle : 0.630 14.308 151178 Z= 0.320 Chirality : 0.035 0.347 19351 Planarity : 0.005 0.051 7924 Dihedral : 16.771 179.226 40157 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 35.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.17 % Favored : 91.78 % Rotamer Outliers : 0.17 % 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: -1.70 (0.14), residues: 3538 helix: -0.50 (0.17), residues: 896 sheet: -1.18 (0.19), residues: 703 loop : -1.38 (0.14), residues: 1939 =============================================================================== Job complete usr+sys time: 8759.92 seconds wall clock time: 166 minutes 5.75 seconds (9965.75 seconds total)