Starting phenix.real_space_refine (version: dev) on Tue May 17 07:34:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl5_12218/05_2022/7bl5_12218_updated.pdb" } resolution = 3.3 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= 0.789 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 None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 98927 Number of models: 1 Model: "" Number of chains: 46 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: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "G" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1281 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} 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: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} 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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 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: "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: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} 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: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "7" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 23, 'TRANS': 293} Chain breaks: 1 Chain: "8" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1281 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: "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: "A" Number of atoms: 62534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2913, 62534 Classifications: {'RNA': 2913} Modifications used: {'rna3p_pyr': 1077, 'rna2p_pur': 274, 'rna3p_pur': 1406, 'rna2p_pyr': 156} Link IDs: {'rna3p': 2482, 'rna2p': 430} Chain breaks: 1 Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "e" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: "b" 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: "9" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'GDP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" 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 98635 SG CYS b 16 79.008 16.543 86.917 1.00241.22 S ATOM 98647 SG CYS b 18 81.272 13.966 87.816 1.00237.97 S ATOM 98789 SG CYS b 37 78.821 16.632 90.288 1.00237.10 S ATOM 98810 SG CYS b 40 79.991 14.096 90.093 1.00239.59 S Time building chain proxies: 41.27, per 1000 atoms: 0.42 Number of scatterers: 98927 At special positions: 0 Unit cell: (230.64, 225.68, 261.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 3033 15.00 Mg 2 11.99 O 27193 8.00 N 18357 7.00 C 50225 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.38 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN b 100 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 37 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 18 " pdb="ZN ZN b 100 " - pdb=" SG CYS b 16 " Number of angles added : 6 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 51 sheets defined 25.9% alpha, 15.3% beta 978 base pairs and 1556 stacking pairs defined. Time for finding SS restraints: 44.71 Creating SS restraints... Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' 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 207 through 213 removed outlier: 3.585A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.623A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' 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 141 Processing helix chain 'E' and resid 155 through 161 Processing helix chain 'E' and resid 179 through 182 No H-bonds generated for 'chain 'E' and resid 179 through 182' Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 60 through 75 removed outlier: 3.523A pdb=" N GLN G 63 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 68 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.714A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 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 106 removed outlier: 3.531A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Proline residue: J 97 - end of helix removed outlier: 4.462A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.946A 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 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' 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 129 through 138 removed outlier: 3.591A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 46 removed outlier: 4.239A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 56 removed outlier: 3.759A pdb=" N ILE N 52 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) 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 86 No H-bonds generated for 'chain 'N' and resid 83 through 86' Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.110A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 removed outlier: 4.172A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 113 removed outlier: 3.710A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) 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 71 removed outlier: 4.291A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (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 removed outlier: 3.518A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 23 removed outlier: 3.553A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 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 9 removed outlier: 3.881A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 25 removed outlier: 4.418A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.843A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) 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 23 removed outlier: 3.791A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 52 removed outlier: 3.821A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 removed outlier: 4.001A 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 73 Processing helix chain 'Y' and resid 5 through 7 No H-bonds generated for 'chain 'Y' and resid 5 through 7' Processing helix chain 'Y' and resid 10 through 23 removed outlier: 3.539A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 27 through 33 removed outlier: 3.770A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 27 through 33' Processing helix chain 'Y' and resid 41 through 54 removed outlier: 4.092A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 50 removed outlier: 3.721A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 15 removed outlier: 3.564A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 9 through 16 removed outlier: 3.532A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 21 No H-bonds generated for 'chain '2' and resid 18 through 21' Processing helix chain '2' and resid 25 through 37 Processing helix chain 'I' and resid 35 through 38 removed outlier: 4.074A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 77 through 80 removed outlier: 3.887A pdb=" N LYS I 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 80' Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 5 through 11 removed outlier: 4.054A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 5 through 11' 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: 3.600A 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 '6' and resid 3 through 17 removed outlier: 3.850A pdb=" N ASP 6 12 " --> pdb=" O ASP 6 8 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS 6 13 " --> pdb=" O PHE 6 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 61 removed outlier: 3.631A pdb=" N ALA 6 61 " --> pdb=" O GLN 6 57 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 97 removed outlier: 4.070A pdb=" N ARG 6 96 " --> pdb=" O GLU 6 92 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 97' Processing helix chain '7' and resid 20 through 27 removed outlier: 3.594A pdb=" N LEU 7 24 " --> pdb=" O LEU 7 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 7 25 " --> pdb=" O ASP 7 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU 7 26 " --> pdb=" O GLN 7 22 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET 7 27 " --> pdb=" O ALA 7 23 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 20 through 27' Processing helix chain '7' and resid 33 through 41 removed outlier: 3.915A pdb=" N TRP 7 39 " --> pdb=" O ARG 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 122 Processing helix chain '7' and resid 124 through 128 removed outlier: 3.959A pdb=" N ALA 7 127 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 130 through 133 Processing helix chain '7' and resid 152 through 164 Processing helix chain '7' and resid 235 through 241 Processing helix chain '7' and resid 265 through 273 Processing helix chain '7' and resid 303 through 319 Processing helix chain '8' and resid 29 through 47 Processing helix chain '8' and resid 51 through 56 removed outlier: 3.832A pdb=" N ASP 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS 8 56 " --> pdb=" O ASN 8 52 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 51 through 56' Processing helix chain '8' and resid 61 through 72 removed outlier: 3.688A pdb=" N LEU 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN 8 71 " --> pdb=" O ILE 8 67 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG 8 72 " --> pdb=" O GLU 8 68 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 90 removed outlier: 3.502A pdb=" N MET 8 88 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 104 Processing helix chain '8' and resid 109 through 126 removed outlier: 3.720A pdb=" N ARG 8 122 " --> pdb=" O LEU 8 118 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP 8 123 " --> pdb=" O GLU 8 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG 8 124 " --> pdb=" O ASN 8 120 " (cutoff:3.500A) Processing helix chain '8' and resid 133 through 139 Processing helix chain '8' and resid 145 through 160 removed outlier: 4.031A pdb=" N THR 8 150 " --> pdb=" O GLN 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 180 removed outlier: 3.662A pdb=" N PHE 8 172 " --> pdb=" O ALA 8 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU 8 180 " --> pdb=" O ARG 8 176 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 61 Processing helix chain '9' and resid 128 through 130 No H-bonds generated for 'chain '9' and resid 128 through 130' Processing helix chain '9' and resid 172 through 176 Processing helix chain '9' and resid 229 through 234 removed outlier: 5.018A pdb=" N HIS 9 234 " --> pdb=" O ARG 9 230 " (cutoff:3.500A) Processing helix chain '9' and resid 258 through 267 removed outlier: 4.273A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 9 266 " --> pdb=" O ILE 9 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 9 267 " --> pdb=" O ILE 9 263 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 292 through 303 removed outlier: 4.013A pdb=" N LYS 9 296 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA 9 297 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA 9 301 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.086A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.688A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.218A 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 58 removed outlier: 3.593A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 74 removed outlier: 3.520A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (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 'e' and resid 5 through 20 removed outlier: 3.725A pdb=" N ALA e 19 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 40 removed outlier: 3.569A pdb=" N THR e 39 " --> pdb=" O VAL e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 64 through 66 No H-bonds generated for 'chain 'e' and resid 64 through 66' Processing helix chain 'e' and resid 72 through 78 removed outlier: 4.222A pdb=" N PHE e 76 " --> pdb=" O LYS e 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL e 77 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY e 78 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 101 removed outlier: 4.034A pdb=" N PHE e 99 " --> pdb=" O PHE e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 113 No H-bonds generated for 'chain 'e' and resid 111 through 113' Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 19 removed outlier: 3.577A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.629A pdb=" N ARG F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'C' and resid 100 through 104 removed outlier: 5.762A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= D, first strand: chain 'C' and resid 180 through 184 removed outlier: 4.089A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.563A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 78 through 83 removed outlier: 3.929A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 167 through 171 removed outlier: 7.166A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS E 185 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 149 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL E 187 " --> pdb=" O ILE E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 17 through 19 removed outlier: 4.373A pdb=" N VAL G 22 " --> pdb=" O ASN G 19 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.643A pdb=" N PHE G 82 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 86 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 130 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= K, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.616A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= M, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.493A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= O, first strand: chain 'O' and resid 25 through 27 Processing sheet with id= P, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.531A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.132A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.303A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.141A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 81 through 87 removed outlier: 3.992A pdb=" N MET S 82 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS S 98 " --> pdb=" O MET S 82 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.398A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= W, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.774A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= Y, first strand: chain 'U' and resid 24 through 27 removed outlier: 7.001A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.973A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE V 91 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR V 31 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU V 41 " --> pdb=" O GLU V 7 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AB, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AC, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AD, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.718A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id= AF, first strand: chain '1' and resid 6 through 11 Processing sheet with id= AG, first strand: chain '1' and resid 35 through 39 removed outlier: 3.528A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 98 through 101 Processing sheet with id= AI, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.739A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'P' and resid 82 through 87 removed outlier: 3.781A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '6' and resid 23 through 26 removed outlier: 3.656A pdb=" N ILE 6 23 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL 6 89 " --> pdb=" O ILE 6 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE 6 78 " --> pdb=" O VAL 6 89 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 4 through 10 removed outlier: 4.401A pdb=" N ALA 7 69 " --> pdb=" O VAL 7 5 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 144 through 149 removed outlier: 6.250A pdb=" N ASN 7 97 " --> pdb=" O ILE 7 86 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE 7 86 " --> pdb=" O ASN 7 97 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 169 through 176 removed outlier: 4.292A pdb=" N ARG 7 169 " --> pdb=" O LEU 7 228 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 283 through 287 removed outlier: 3.568A pdb=" N TRP 7 297 " --> pdb=" O LEU 7 284 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 7 286 " --> pdb=" O MET 7 295 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '9' and resid 64 through 66 removed outlier: 8.773A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 9 7 " --> pdb=" O LEU 9 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 9 150 " --> pdb=" O VAL 9 11 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '9' and resid 86 through 91 removed outlier: 3.639A pdb=" N ALA 9 118 " --> pdb=" O VAL 9 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET 9 47 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU 9 116 " --> pdb=" O MET 9 47 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA 9 49 " --> pdb=" O ARG 9 114 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG 9 114 " --> pdb=" O ALA 9 49 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '9' and resid 162 through 166 removed outlier: 5.855A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '9' and resid 199 through 201 Processing sheet with id= AT, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.606A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.621A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU M 90 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.544A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 78 through 82 removed outlier: 4.049A pdb=" N ILE H 80 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 152 through 155 removed outlier: 7.103A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'b' and resid 21 through 24 removed outlier: 3.756A pdb=" N ILE b 24 " --> pdb=" O ILE b 12 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE b 12 " --> pdb=" O ILE b 24 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU b 32 " --> pdb=" O SER b 15 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2474 hydrogen bonds 3866 hydrogen bond angles 0 basepair planarities 978 basepair parallelities 1556 stacking parallelities Total time for adding SS restraints: 160.53 Time building geometry restraints manager: 38.73 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: 17762 1.33 - 1.46: 42727 1.46 - 1.58: 40420 1.58 - 1.70: 6063 1.70 - 1.82: 210 Bond restraints: 107182 Sorted by residual: bond pdb=" C2 C A 106 " pdb=" O2 C A 106 " ideal model delta sigma weight residual 1.240 1.216 0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CA VAL 6 27 " pdb=" C VAL 6 27 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.33e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.25e+00 bond pdb=" C PRO I 21 " pdb=" N PRO I 22 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.16e+00 bond pdb=" C3' U A2249 " pdb=" O3' U A2249 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.16e+00 ... (remaining 107177 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.34: 18100 106.34 - 113.81: 66496 113.81 - 121.28: 47690 121.28 - 128.75: 24383 128.75 - 136.23: 3109 Bond angle restraints: 159778 Sorted by residual: angle pdb=" C PRO V 81 " pdb=" N TYR V 82 " pdb=" CA TYR V 82 " ideal model delta sigma weight residual 121.54 114.09 7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C SER L 68 " pdb=" N ARG L 69 " pdb=" CA ARG L 69 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C3' U A2249 " pdb=" O3' U A2249 " pdb=" P G A2250 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sigma weight residual 120.20 125.07 -4.87 1.50e+00 4.44e-01 1.05e+01 angle pdb=" CB MET 6 49 " pdb=" CG MET 6 49 " pdb=" SD MET 6 49 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.14e+00 ... (remaining 159773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 55576 35.68 - 71.36: 1778 71.36 - 107.03: 177 107.03 - 142.71: 13 142.71 - 178.39: 9 Dihedral angle restraints: 57553 sinusoidal: 45214 harmonic: 12339 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 62.30 137.70 1 1.50e+01 4.44e-03 7.42e+01 dihedral pdb=" O4' C A1914 " pdb=" C1' C A1914 " pdb=" N1 C A1914 " pdb=" C2 C A1914 " ideal model delta sinusoidal sigma weight residual -128.00 50.39 -178.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1915 " pdb=" C1' U A1915 " pdb=" N1 U A1915 " pdb=" C2 U A1915 " ideal model delta sinusoidal sigma weight residual -128.00 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 57550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 18121 0.039 - 0.078: 1616 0.078 - 0.117: 555 0.117 - 0.155: 50 0.155 - 0.194: 6 Chirality restraints: 20348 Sorted by residual: chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" C3' U A2249 " pdb=" C4' U A2249 " pdb=" O3' U A2249 " pdb=" C2' U A2249 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" C1' U A1313 " pdb=" O4' U A1313 " pdb=" C2' U A1313 " pdb=" N1 U A1313 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 20345 not shown) Planarity restraints: 9003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 106 " 0.005 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 C A 106 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A 106 " -0.068 2.00e-02 2.50e+03 pdb=" O2 C A 106 " 0.043 2.00e-02 2.50e+03 pdb=" N3 C A 106 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 106 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C A 106 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 106 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C A 106 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY e 78 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO e 79 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO e 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO e 79 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 81 " -0.005 2.00e-02 2.50e+03 1.30e-02 5.08e+00 pdb=" N9 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G A 81 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 81 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 81 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 81 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G A 81 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 81 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G A 81 " -0.026 2.00e-02 2.50e+03 pdb=" N3 G A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 81 " -0.001 2.00e-02 2.50e+03 ... (remaining 9000 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2101 2.60 - 3.18: 78741 3.18 - 3.75: 197015 3.75 - 4.33: 256457 4.33 - 4.90: 349208 Nonbonded interactions: 883522 Sorted by model distance: nonbonded pdb=" O SER F 117 " pdb=" OH TYR F 127 " model vdw 2.029 2.440 nonbonded pdb=" N2 G A2294 " pdb=" O2 C A2338 " model vdw 2.076 2.496 nonbonded pdb=" O2B GDP 91001 " pdb="MG MG 91002 " model vdw 2.099 2.170 nonbonded pdb=" OG SER 7 34 " pdb=" OP2 U A1923 " model vdw 2.107 2.440 nonbonded pdb=" N2 G A1948 " pdb=" O6 G A1959 " model vdw 2.125 2.520 ... (remaining 883517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3033 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 50225 2.51 5 N 18357 2.21 5 O 27193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 11.430 Check model and map are aligned: 1.090 Convert atoms to be neutral: 0.630 Process input model: 358.020 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 377.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 0.031 107182 Z= 0.109 Angle : 0.451 9.806 159778 Z= 0.242 Chirality : 0.027 0.194 20348 Planarity : 0.003 0.067 9003 Dihedral : 14.152 178.388 49605 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.05 (0.13), residues: 4280 helix: -0.33 (0.16), residues: 1057 sheet: 0.26 (0.20), residues: 744 loop : -1.17 (0.12), residues: 2479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 991 time to evaluate : 4.392 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: 4 outliers final: 1 residues processed: 992 average time/residue: 0.8915 time to fit residues: 1542.0315 Evaluate side-chains 823 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 822 time to evaluate : 4.357 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6886 time to fit residues: 6.1845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 610 optimal weight: 20.0000 chunk 548 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 369 optimal weight: 30.0000 chunk 292 optimal weight: 30.0000 chunk 566 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 656 optimal weight: 10.0000 overall best weight: 7.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 38 GLN O 104 GLN Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN Y 20 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS 2 16 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN 6 20 GLN 6 47 HIS ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 91 GLN 8 154 ASN M 13 HIS H 43 ASN b 41 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.136 107182 Z= 0.370 Angle : 0.708 9.978 159778 Z= 0.358 Chirality : 0.038 0.389 20348 Planarity : 0.006 0.097 9003 Dihedral : 14.298 179.857 41166 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.41 (0.12), residues: 4280 helix: -0.55 (0.15), residues: 1121 sheet: -0.26 (0.19), residues: 758 loop : -1.35 (0.12), residues: 2401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 924 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 93 residues processed: 984 average time/residue: 0.9064 time to fit residues: 1534.3368 Evaluate side-chains 895 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 802 time to evaluate : 4.437 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.6999 time to fit residues: 129.1836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 364 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 657 optimal weight: 10.0000 chunk 710 optimal weight: 20.0000 chunk 585 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 527 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS Q 36 GLN Q 55 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN 0 18 HIS K 3 GLN K 88 ASN 6 20 GLN 6 47 HIS ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 108 HIS ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN b 41 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.309 107182 Z= 0.364 Angle : 0.669 11.723 159778 Z= 0.341 Chirality : 0.038 0.302 20348 Planarity : 0.006 0.094 9003 Dihedral : 14.548 179.705 41166 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.62 (0.12), residues: 4280 helix: -0.55 (0.15), residues: 1133 sheet: -0.43 (0.18), residues: 772 loop : -1.57 (0.12), residues: 2375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 880 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 64 residues processed: 932 average time/residue: 0.9107 time to fit residues: 1469.4503 Evaluate side-chains 860 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 796 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.7086 time to fit residues: 90.7779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 649 optimal weight: 20.0000 chunk 494 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 313 optimal weight: 40.0000 chunk 441 optimal weight: 10.0000 chunk 660 optimal weight: 10.0000 chunk 698 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 625 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN Q 36 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 2 GLN 6 47 HIS ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN H 20 ASN F 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.118 107182 Z= 0.315 Angle : 0.640 10.616 159778 Z= 0.327 Chirality : 0.037 0.364 20348 Planarity : 0.005 0.129 9003 Dihedral : 14.666 178.807 41166 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.74 (0.12), residues: 4280 helix: -0.59 (0.15), residues: 1132 sheet: -0.69 (0.18), residues: 767 loop : -1.61 (0.12), residues: 2381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 877 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 92 residues processed: 941 average time/residue: 0.8805 time to fit residues: 1436.5229 Evaluate side-chains 895 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 803 time to evaluate : 4.444 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.7042 time to fit residues: 128.2501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 582 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 520 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 596 optimal weight: 50.0000 chunk 483 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 627 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN 1 18 HIS K 3 GLN K 88 ASN 6 47 HIS ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 245 HIS ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.159 107182 Z= 0.343 Angle : 0.665 10.825 159778 Z= 0.339 Chirality : 0.038 0.340 20348 Planarity : 0.005 0.113 9003 Dihedral : 14.823 178.750 41166 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -1.85 (0.12), residues: 4280 helix: -0.58 (0.15), residues: 1133 sheet: -0.98 (0.18), residues: 762 loop : -1.65 (0.12), residues: 2385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 869 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 67 residues processed: 933 average time/residue: 0.9204 time to fit residues: 1489.3455 Evaluate side-chains 867 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 800 time to evaluate : 4.429 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7629 time to fit residues: 99.2908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 235 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 138 optimal weight: 0.9980 chunk 410 optimal weight: 10.0000 chunk 172 optimal weight: 0.0970 chunk 699 optimal weight: 40.0000 chunk 580 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 overall best weight: 4.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 104 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 88 ASN ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 288 HIS ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 120 ASN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN H 20 ASN H 133 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 107182 Z= 0.203 Angle : 0.574 14.611 159778 Z= 0.295 Chirality : 0.034 0.342 20348 Planarity : 0.005 0.108 9003 Dihedral : 14.639 177.903 41166 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.68 (0.12), residues: 4280 helix: -0.39 (0.15), residues: 1120 sheet: -0.93 (0.18), residues: 763 loop : -1.54 (0.12), residues: 2397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 878 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 55 residues processed: 924 average time/residue: 0.9017 time to fit residues: 1445.7013 Evaluate side-chains 887 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 832 time to evaluate : 4.476 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.6982 time to fit residues: 78.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 674 optimal weight: 40.0000 chunk 78 optimal weight: 3.9990 chunk 398 optimal weight: 20.0000 chunk 510 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 696 optimal weight: 10.0000 chunk 436 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 overall best weight: 8.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN 6 47 HIS ** 7 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.195 107182 Z= 0.374 Angle : 0.694 11.844 159778 Z= 0.352 Chirality : 0.039 0.350 20348 Planarity : 0.005 0.096 9003 Dihedral : 14.897 178.647 41166 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.87 (0.12), residues: 4280 helix: -0.48 (0.15), residues: 1107 sheet: -1.15 (0.18), residues: 741 loop : -1.65 (0.12), residues: 2432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 858 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 53 residues processed: 896 average time/residue: 0.9175 time to fit residues: 1414.1026 Evaluate side-chains 863 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 810 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.7498 time to fit residues: 80.2243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 431 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 416 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 443 optimal weight: 9.9990 chunk 474 optimal weight: 30.0000 chunk 344 optimal weight: 7.9990 chunk 64 optimal weight: 0.0070 chunk 547 optimal weight: 10.0000 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN 7 105 HIS ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 128 GLN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.151 107182 Z= 0.198 Angle : 0.581 14.086 159778 Z= 0.298 Chirality : 0.034 0.377 20348 Planarity : 0.005 0.110 9003 Dihedral : 14.689 178.475 41166 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.70 (0.12), residues: 4280 helix: -0.33 (0.15), residues: 1104 sheet: -1.11 (0.18), residues: 772 loop : -1.53 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 873 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 37 residues processed: 892 average time/residue: 0.9254 time to fit residues: 1432.4993 Evaluate side-chains 850 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 813 time to evaluate : 4.456 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.7486 time to fit residues: 56.9307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 633 optimal weight: 20.0000 chunk 667 optimal weight: 10.0000 chunk 609 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 509 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 586 optimal weight: 10.0000 chunk 614 optimal weight: 30.0000 chunk 647 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.460 107182 Z= 0.410 Angle : 0.734 73.856 159778 Z= 0.363 Chirality : 0.041 0.325 20348 Planarity : 0.006 0.115 9003 Dihedral : 14.730 178.458 41166 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.85 (0.12), residues: 4280 helix: -0.49 (0.15), residues: 1112 sheet: -1.13 (0.18), residues: 759 loop : -1.63 (0.12), residues: 2409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 833 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 41 residues processed: 854 average time/residue: 0.9030 time to fit residues: 1335.2221 Evaluate side-chains 848 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 807 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.7688 time to fit residues: 63.4145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 426 optimal weight: 10.0000 chunk 686 optimal weight: 3.9990 chunk 419 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 477 optimal weight: 10.0000 chunk 720 optimal weight: 5.9990 chunk 662 optimal weight: 10.0000 chunk 573 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 443 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 99 GLN ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.774 107182 Z= 0.411 Angle : 0.741 72.522 159778 Z= 0.370 Chirality : 0.041 0.325 20348 Planarity : 0.006 0.184 9003 Dihedral : 14.730 178.457 41166 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.85 (0.12), residues: 4280 helix: -0.49 (0.15), residues: 1112 sheet: -1.14 (0.18), residues: 759 loop : -1.63 (0.12), residues: 2409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 812 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 816 average time/residue: 0.9117 time to fit residues: 1287.4011 Evaluate side-chains 813 residues out of total 3542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 806 time to evaluate : 4.428 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.7953 time to fit residues: 15.0495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 455 optimal weight: 20.0000 chunk 610 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 528 optimal weight: 10.0000 chunk 84 optimal weight: 0.0470 chunk 159 optimal weight: 0.5980 chunk 574 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 589 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 ASN ** 9 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.109957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088387 restraints weight = 302489.103| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.06 r_work: 0.3486 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.3474 rms_B_bonded: 1.98 restraints_weight: 0.1250 r_work: 0.3467 rms_B_bonded: 2.03 restraints_weight: 0.0625 r_work: 0.3460 rms_B_bonded: 2.10 restraints_weight: 0.0312 r_work: 0.3453 rms_B_bonded: 2.18 restraints_weight: 0.0156 r_work: 0.3446 rms_B_bonded: 2.29 restraints_weight: 0.0078 r_work: 0.3439 rms_B_bonded: 2.40 restraints_weight: 0.0039 r_work: 0.3431 rms_B_bonded: 2.53 restraints_weight: 0.0020 r_work: 0.3424 rms_B_bonded: 2.68 restraints_weight: 0.0010 r_work: 0.3416 rms_B_bonded: 2.84 restraints_weight: 0.0005 r_work: 0.3407 rms_B_bonded: 3.01 restraints_weight: 0.0002 r_work: 0.3399 rms_B_bonded: 3.20 restraints_weight: 0.0001 r_work: 0.3390 rms_B_bonded: 3.40 restraints_weight: 0.0001 r_work: 0.3380 rms_B_bonded: 3.62 restraints_weight: 0.0000 r_work: 0.3371 rms_B_bonded: 3.86 restraints_weight: 0.0000 r_work: 0.3361 rms_B_bonded: 4.11 restraints_weight: 0.0000 r_work: 0.3350 rms_B_bonded: 4.39 restraints_weight: 0.0000 r_work: 0.3339 rms_B_bonded: 4.68 restraints_weight: 0.0000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.472 107182 Z= 0.237 Angle : 0.616 47.043 159778 Z= 0.313 Chirality : 0.034 0.332 20348 Planarity : 0.005 0.099 9003 Dihedral : 14.680 178.639 41166 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.73 (0.12), residues: 4280 helix: -0.32 (0.15), residues: 1109 sheet: -1.22 (0.18), residues: 770 loop : -1.52 (0.12), residues: 2401 =============================================================================== Job complete usr+sys time: 22142.28 seconds wall clock time: 392 minutes 24.93 seconds (23544.93 seconds total)