Starting phenix.real_space_refine on Mon Sep 14 16:42:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.map" model { file = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d6q_7808/09_2026/6d6q_7808.cif" } resolution = 3.45 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 196 5.16 5 C 19695 2.51 5 N 5611 2.21 5 O 6074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31639 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1859 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "I" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 6856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6856 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 40, 'TRANS': 812} Chain breaks: 6 Chain: "L" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 573 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5648 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 683} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Classifications: {'RNAv2': 13} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'DNA': 13, 'RNAv2': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' C%rna3p_pyr:plan2': 2, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17538 SG CYS K 31 45.162 135.806 78.689 1.00 59.63 S ATOM 17564 SG CYS K 36 45.036 136.870 82.511 1.00 80.34 S ATOM 17580 SG CYS K 39 44.022 133.227 81.287 1.00 84.66 S Time building chain proxies: 6.41, per 1000 atoms: 0.20 Number of scatterers: 31639 At special positions: 0 Unit cell: (164.78, 191.53, 174.41, 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 196 16.00 P 61 15.00 Mg 1 11.99 O 6074 8.00 N 5611 7.00 C 19695 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K2002 " pdb="ZN ZN K2002 " - pdb=" NE2 HIS K 159 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 31 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 39 " pdb="ZN ZN K2002 " - pdb=" SG CYS K 36 " Number of angles added : 3 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 47 sheets defined 35.0% alpha, 21.2% beta 14 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.679A pdb=" N ALA A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.543A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 113 " --> pdb=" O CYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 243 through 277 removed outlier: 3.902A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.059A pdb=" N THR B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.595A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.046A pdb=" N LEU B 114 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.983A pdb=" N ALA B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 208 through 243 removed outlier: 4.293A pdb=" N VAL B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.985A pdb=" N PHE C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 147 through 163 removed outlier: 3.862A pdb=" N ALA C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 245 through 272 removed outlier: 4.216A pdb=" N ASP C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N CYS C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 106 Processing helix chain 'D' and resid 129 through 144 removed outlier: 4.170A pdb=" N ASN D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 202 through 232 Processing helix chain 'E' and resid 8 through 20 Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 147 through 162 Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 250 through 281 removed outlier: 3.738A pdb=" N GLU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 285 Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 118 through 131 Processing helix chain 'F' and resid 157 through 173 Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 233 through 270 Proline residue: F 253 - end of helix Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.589A pdb=" N ILE G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 225 removed outlier: 3.905A pdb=" N GLY G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 257 Processing helix chain 'G' and resid 261 through 274 Processing helix chain 'H' and resid 12 through 16 removed outlier: 4.378A pdb=" N SER H 15 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 12 through 16' Processing helix chain 'H' and resid 124 through 134 removed outlier: 4.920A pdb=" N ARG H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 179 removed outlier: 3.986A pdb=" N VAL H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 4.685A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 263 Processing helix chain 'H' and resid 273 through 293 Processing helix chain 'I' and resid 16 through 20 removed outlier: 3.593A pdb=" N GLY I 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 61 removed outlier: 3.652A pdb=" N SER I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 122 Processing helix chain 'K' and resid 69 through 76 Processing helix chain 'K' and resid 76 through 82 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 102 through 114 removed outlier: 3.576A pdb=" N TYR K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 164 removed outlier: 4.284A pdb=" N SER K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 187 removed outlier: 3.641A pdb=" N LYS K 181 " --> pdb=" O ASP K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 201 removed outlier: 3.619A pdb=" N LEU K 201 " --> pdb=" O TYR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 210 Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.561A pdb=" N LYS K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 437 removed outlier: 4.491A pdb=" N GLU K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 452 removed outlier: 3.517A pdb=" N PHE K 451 " --> pdb=" O ALA K 447 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU K 452 " --> pdb=" O VAL K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 466 removed outlier: 3.879A pdb=" N ASN K 466 " --> pdb=" O ASP K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 512 removed outlier: 3.591A pdb=" N HIS K 511 " --> pdb=" O ASP K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 526 removed outlier: 3.927A pdb=" N GLN K 521 " --> pdb=" O ASN K 517 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG K 526 " --> pdb=" O GLU K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 547 Processing helix chain 'K' and resid 589 through 599 Processing helix chain 'K' and resid 606 through 627 removed outlier: 3.781A pdb=" N LEU K 616 " --> pdb=" O GLY K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 657 through 682 removed outlier: 3.600A pdb=" N SER K 661 " --> pdb=" O ARG K 657 " (cutoff:3.500A) Processing helix chain 'K' and resid 699 through 709 Processing helix chain 'K' and resid 717 through 726 removed outlier: 3.750A pdb=" N LEU K 721 " --> pdb=" O THR K 717 " (cutoff:3.500A) Processing helix chain 'K' and resid 736 through 746 Processing helix chain 'K' and resid 782 through 796 Processing helix chain 'K' and resid 801 through 805 Processing helix chain 'K' and resid 806 through 843 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 16 through 21 removed outlier: 3.610A pdb=" N GLN L 20 " --> pdb=" O MET L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 68 removed outlier: 3.811A pdb=" N CYS L 67 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 92 removed outlier: 3.509A pdb=" N GLU L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 removed outlier: 3.567A pdb=" N ASN M 153 " --> pdb=" O GLN M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 181 Processing helix chain 'M' and resid 192 through 207 Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 254 through 259 removed outlier: 3.624A pdb=" N ASP M 259 " --> pdb=" O TYR M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 273 removed outlier: 4.364A pdb=" N TRP M 266 " --> pdb=" O ARG M 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 301 Processing helix chain 'M' and resid 339 through 354 removed outlier: 3.989A pdb=" N PHE M 343 " --> pdb=" O ARG M 339 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 384 Processing helix chain 'M' and resid 396 through 407 Processing helix chain 'M' and resid 414 through 429 Processing helix chain 'M' and resid 438 through 451 Proline residue: M 446 - end of helix Processing helix chain 'M' and resid 460 through 474 Processing helix chain 'M' and resid 483 through 488 removed outlier: 4.026A pdb=" N MET M 487 " --> pdb=" O GLU M 483 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY M 488 " --> pdb=" O THR M 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 483 through 488' Processing helix chain 'M' and resid 513 through 522 Processing helix chain 'M' and resid 544 through 553 Processing helix chain 'M' and resid 566 through 575 Processing helix chain 'M' and resid 580 through 588 Processing helix chain 'M' and resid 588 through 593 Processing helix chain 'M' and resid 598 through 609 Processing helix chain 'M' and resid 832 through 840 Processing helix chain 'M' and resid 847 through 861 removed outlier: 3.782A pdb=" N LEU M 851 " --> pdb=" O GLN M 847 " (cutoff:3.500A) Processing helix chain 'M' and resid 871 through 878 Processing helix chain 'M' and resid 884 through 893 removed outlier: 3.620A pdb=" N LEU M 888 " --> pdb=" O ASP M 884 " (cutoff:3.500A) Processing helix chain 'M' and resid 901 through 914 removed outlier: 3.949A pdb=" N ALA M 905 " --> pdb=" O SER M 901 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR M 906 " --> pdb=" O ALA M 902 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE M 912 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing helix chain 'M' and resid 925 through 949 Proline residue: M 931 - end of helix removed outlier: 3.731A pdb=" N ALA M 949 " --> pdb=" O VAL M 945 " (cutoff:3.500A) Processing helix chain 'M' and resid 954 through 961 Processing helix chain 'M' and resid 966 through 975 Processing helix chain 'M' and resid 978 through 982 Processing helix chain 'M' and resid 989 through 1015 removed outlier: 4.033A pdb=" N ILE M 993 " --> pdb=" O PHE M 989 " (cutoff:3.500A) Processing helix chain 'M' and resid 1017 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 6.554A pdb=" N PHE A 77 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 136 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN A 79 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU A 138 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU A 81 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.747A pdb=" N MET A 225 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 219 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 233 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 233 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA B 202 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN A 235 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET B 200 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER A 237 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LEU B 198 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 187 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 185 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 200 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN B 183 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.603A pdb=" N ALA B 49 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 40 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS B 46 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN B 119 " --> pdb=" O PRO B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.181A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.976A pdb=" N GLU C 167 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS C 183 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N THR C 169 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N LEU C 181 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N ASN C 171 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N VAL C 179 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.881A pdb=" N VAL C 194 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS C 234 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP C 227 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU C 232 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.038A pdb=" N SER D 115 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.700A pdb=" N VAL D 180 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR D 197 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR D 182 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 195 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.953A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 127 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 133 " --> pdb=" O CYS E 125 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS E 125 " --> pdb=" O TRP E 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.953A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL E 35 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 209 through 212 removed outlier: 4.373A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS E 238 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.786A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS F 61 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG F 95 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL F 146 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU F 97 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA F 148 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP F 99 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 150 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.373A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.373A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.922A pdb=" N VAL G 66 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL G 102 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE L 59 " --> pdb=" O VAL G 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 191 through 192 removed outlier: 3.668A pdb=" N GLY G 191 " --> pdb=" O TYR G 164 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER G 140 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS G 124 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS G 130 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.666A pdb=" N LEU G 227 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 229 " --> pdb=" O MET L 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 26 through 27 removed outlier: 3.532A pdb=" N GLY H 58 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER H 59 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET H 40 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL H 69 " --> pdb=" O MET H 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'H' and resid 164 through 165 removed outlier: 6.837A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU H 109 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL H 91 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS H 97 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.890A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 7 through 8 removed outlier: 3.569A pdb=" N GLY I 39 " --> pdb=" O CYS I 8 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL I 55 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 13 through 15 removed outlier: 6.891A pdb=" N ARG I 13 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER I 35 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS I 15 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 93 through 94 removed outlier: 3.662A pdb=" N MET I 93 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 90 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA I 83 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE I 78 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL I 85 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER I 76 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE I 87 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS I 74 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR I 89 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE I 127 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 93 through 94 removed outlier: 3.662A pdb=" N MET I 93 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 90 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG I 100 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU I 144 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR I 102 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU I 143 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE I 127 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 165 through 168 removed outlier: 3.519A pdb=" N ILE I 167 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 2 through 10 Processing sheet with id=AD6, first strand: chain 'K' and resid 87 through 90 removed outlier: 3.592A pdb=" N TYR K 121 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 174 through 175 Processing sheet with id=AD8, first strand: chain 'K' and resid 274 through 277 removed outlier: 6.904A pdb=" N ILE K 291 " --> pdb=" O ILE K 349 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY K 347 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU K 295 " --> pdb=" O VAL K 345 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL K 345 " --> pdb=" O GLU K 295 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 356 through 361 removed outlier: 6.498A pdb=" N ARG K 384 " --> pdb=" O GLY K 414 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N PHE K 416 " --> pdb=" O ARG K 384 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN K 413 " --> pdb=" O ASP K 403 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE K 399 " --> pdb=" O VAL K 417 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN K 419 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ARG K 397 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG K 396 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU K 360 " --> pdb=" O ARG K 396 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 468 through 469 removed outlier: 6.428A pdb=" N GLU K 468 " --> pdb=" O VAL K 581 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ASN K 583 " --> pdb=" O GLU K 468 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 574 " --> pdb=" O GLU K 565 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 477 through 478 removed outlier: 6.754A pdb=" N SER K 477 " --> pdb=" O LEU K 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 530 through 531 Processing sheet with id=AE4, first strand: chain 'K' and resid 637 through 638 removed outlier: 3.851A pdb=" N GLN K 652 " --> pdb=" O ARG K 638 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 688 through 690 Processing sheet with id=AE6, first strand: chain 'K' and resid 846 through 848 removed outlier: 5.753A pdb=" N VAL K 846 " --> pdb=" O ILE K 911 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 911 " --> pdb=" O VAL K 846 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 851 through 852 Processing sheet with id=AE8, first strand: chain 'K' and resid 887 through 888 Processing sheet with id=AE9, first strand: chain 'M' and resid 99 through 103 removed outlier: 6.713A pdb=" N VAL M 157 " --> pdb=" O PHE M 281 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER M 283 " --> pdb=" O VAL M 157 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL M 159 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG M 184 " --> pdb=" O VAL M 246 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP M 248 " --> pdb=" O ARG M 184 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 329 through 332 removed outlier: 7.477A pdb=" N HIS M 318 " --> pdb=" O VAL M 331 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL M 496 " --> pdb=" O ILE M 536 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N MET M 538 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE M 498 " --> pdb=" O MET M 538 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL M 389 " --> pdb=" O LEU M 479 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA M 481 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE M 391 " --> pdb=" O ALA M 481 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 864 through 865 removed outlier: 3.563A pdb=" N VAL M 869 " --> pdb=" O THR M 865 " (cutoff:3.500A) 1355 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 7.65 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10383 1.34 - 1.45: 4767 1.45 - 1.57: 16726 1.57 - 1.69: 121 1.69 - 1.81: 292 Bond restraints: 32289 Sorted by residual: bond pdb=" P C O 17 " pdb=" OP2 C O 17 " ideal model delta sigma weight residual 1.485 1.679 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O3' DT O 16 " pdb=" P C O 17 " ideal model delta sigma weight residual 1.607 1.705 -0.098 1.20e-02 6.94e+03 6.73e+01 bond pdb=" O3A ANP M2001 " pdb=" PB ANP M2001 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" P C O 17 " pdb=" OP1 C O 17 " ideal model delta sigma weight residual 1.485 1.591 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 43241 2.57 - 5.15: 604 5.15 - 7.72: 22 7.72 - 10.30: 3 10.30 - 12.87: 2 Bond angle restraints: 43872 Sorted by residual: angle pdb=" CA PRO K 648 " pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 112.00 99.13 12.87 1.40e+00 5.10e-01 8.46e+01 angle pdb=" C3' DT O 16 " pdb=" O3' DT O 16 " pdb=" P C O 17 " ideal model delta sigma weight residual 119.70 111.67 8.03 1.20e+00 6.94e-01 4.48e+01 angle pdb=" N3 DT O 16 " pdb=" C4 DT O 16 " pdb=" O4 DT O 16 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT O 8 " pdb=" C4 DT O 8 " pdb=" O4 DT O 8 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT O 13 " pdb=" C4 DT O 13 " pdb=" O4 DT O 13 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.63e+01 ... (remaining 43867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 19434 33.75 - 67.50: 203 67.50 - 101.26: 20 101.26 - 135.01: 1 135.01 - 168.76: 1 Dihedral angle restraints: 19659 sinusoidal: 8434 harmonic: 11225 Sorted by residual: dihedral pdb=" C4' C O 49 " pdb=" C3' C O 49 " pdb=" C2' C O 49 " pdb=" C1' C O 49 " ideal model delta sinusoidal sigma weight residual 36.34 -36.36 72.70 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A O 53 " pdb=" C3' A O 53 " pdb=" C2' A O 53 " pdb=" C1' A O 53 " ideal model delta sinusoidal sigma weight residual 36.35 -36.17 72.52 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' A O 62 " pdb=" C3' A O 62 " pdb=" C2' A O 62 " pdb=" C1' A O 62 " ideal model delta sinusoidal sigma weight residual 36.34 -35.60 71.95 1 3.10e+00 1.04e-01 6.89e+02 ... (remaining 19656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 5045 0.262 - 0.525: 8 0.525 - 0.787: 0 0.787 - 1.049: 0 1.049 - 1.311: 1 Chirality restraints: 5054 Sorted by residual: chirality pdb=" P C O 17 " pdb=" OP1 C O 17 " pdb=" OP2 C O 17 " pdb=" O5' C O 17 " both_signs ideal model delta sigma weight residual True 2.17 -3.48 -1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" C3' C O 45 " pdb=" C4' C O 45 " pdb=" O3' C O 45 " pdb=" C2' C O 45 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C2' C O 17 " pdb=" C3' C O 17 " pdb=" O2' C O 17 " pdb=" C1' C O 17 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 5051 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C O 45 " -0.039 2.00e-02 2.50e+03 1.90e-02 8.08e+00 pdb=" N1 C O 45 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C O 45 " 0.010 2.00e-02 2.50e+03 pdb=" O2 C O 45 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C O 45 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C O 45 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C O 45 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C O 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 45 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 60 " 0.036 2.00e-02 2.50e+03 1.62e-02 7.20e+00 pdb=" N9 A O 60 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A O 60 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A O 60 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A O 60 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A O 60 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A O 60 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 42 " 0.036 2.00e-02 2.50e+03 1.77e-02 7.02e+00 pdb=" N1 C O 42 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C O 42 " -0.017 2.00e-02 2.50e+03 pdb=" O2 C O 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C O 42 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C O 42 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C O 42 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C O 42 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C O 42 " -0.010 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 126 2.40 - 3.03: 20355 3.03 - 3.65: 44793 3.65 - 4.28: 67823 4.28 - 4.90: 114866 Nonbonded interactions: 247963 Sorted by model distance: nonbonded pdb=" OH TYR M 237 " pdb=" OE2 GLU M 268 " model vdw 1.778 3.040 nonbonded pdb=" O2' C O 42 " pdb=" O5' A O 43 " model vdw 1.823 3.040 nonbonded pdb=" OG SER B 7 " pdb=" OE1 GLN B 9 " model vdw 1.922 3.040 nonbonded pdb=" OG SER M 189 " pdb=" OG SER M 195 " model vdw 1.957 3.040 nonbonded pdb=" OE2 GLU M 267 " pdb=" OG SER M 561 " model vdw 1.963 3.040 ... (remaining 247958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 4.200 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 35.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.194 32293 Z= 0.285 Angle : 0.751 12.873 43875 Z= 0.407 Chirality : 0.056 1.311 5054 Planarity : 0.004 0.052 5456 Dihedral : 10.612 168.761 12395 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.11), residues: 3839 helix: -1.96 (0.12), residues: 1237 sheet: -2.41 (0.17), residues: 776 loop : -4.01 (0.10), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 108 TYR 0.035 0.002 TYR M 279 PHE 0.029 0.003 PHE C 154 TRP 0.020 0.002 TRP G 101 HIS 0.012 0.002 HIS M 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 (32289) covalent geometry : angle 0.75099 / 0.41 (43872) hydrogen bonds : bond 0.12166 / 8.08 ( 1377) hydrogen bonds : angle 6.27849 / 4.35 ( 3871) metal coordination : bond 0.10742 / 5.26 ( 4) metal coordination : angle 0.69753 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 859 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8001 (m-30) cc_final: 0.7731 (m-30) REVERT: B 125 GLN cc_start: 0.7574 (tp40) cc_final: 0.6790 (tp40) REVERT: C 226 MET cc_start: 0.6982 (tpt) cc_final: 0.6626 (tpt) REVERT: D 72 ASN cc_start: 0.8754 (p0) cc_final: 0.8549 (p0) REVERT: D 164 THR cc_start: 0.7792 (m) cc_final: 0.6878 (p) REVERT: E 125 CYS cc_start: 0.6732 (t) cc_final: 0.6278 (p) REVERT: E 233 LYS cc_start: 0.8056 (mptp) cc_final: 0.7607 (mttp) REVERT: G 224 LEU cc_start: 0.6070 (mp) cc_final: 0.5839 (mt) REVERT: H 33 ILE cc_start: 0.8281 (mm) cc_final: 0.8025 (mm) REVERT: H 83 ILE cc_start: 0.8607 (pp) cc_final: 0.8328 (mp) REVERT: K 156 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: K 185 ILE cc_start: 0.7990 (mp) cc_final: 0.7776 (mm) REVERT: K 566 MET cc_start: 0.6595 (mtt) cc_final: 0.6374 (mtm) REVERT: K 578 THR cc_start: 0.7655 (p) cc_final: 0.7420 (t) REVERT: K 610 LEU cc_start: 0.7965 (mt) cc_final: 0.7178 (mp) REVERT: L 91 MET cc_start: 0.7633 (mmt) cc_final: 0.7369 (mpp) outliers start: 2 outliers final: 0 residues processed: 861 average time/residue: 0.2372 time to fit residues: 312.2967 Evaluate side-chains 384 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 156 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS E 44 ASN E 114 ASN E 131 HIS G 246 GLN H 266 HIS I 97 ASN I 178 HIS ** K 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN K 266 HIS K 284 ASN K 569 ASN K 821 HIS K 902 HIS ** K 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 920 HIS M 197 GLN M 291 GLN M 300 HIS M 317 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.158660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123351 restraints weight = 51478.493| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.55 r_work: 0.3424 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32293 Z= 0.197 Angle : 0.810 18.081 43875 Z= 0.392 Chirality : 0.062 1.567 5054 Planarity : 0.005 0.061 5456 Dihedral : 9.682 166.455 4921 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 10.70 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.13), residues: 3839 helix: -0.13 (0.14), residues: 1260 sheet: -1.64 (0.18), residues: 767 loop : -2.91 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 689 TYR 0.028 0.002 TYR M 279 PHE 0.030 0.002 PHE M 563 TRP 0.023 0.002 TRP G 101 HIS 0.006 0.001 HIS K 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (32289) covalent geometry : angle 0.80932 / 0.39 (43872) hydrogen bonds : bond 0.05151 / 3.45 ( 1377) hydrogen bonds : angle 5.22755 / 3.60 ( 3871) metal coordination : bond 0.01993 / 1.00 ( 4) metal coordination : angle 3.94086 / 2.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7284 (t80) cc_final: 0.6583 (t80) REVERT: A 168 GLN cc_start: 0.8457 (mt0) cc_final: 0.8080 (mp10) REVERT: A 240 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6678 (pt) REVERT: B 92 ASP cc_start: 0.7914 (t0) cc_final: 0.7619 (m-30) REVERT: C 164 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: C 226 MET cc_start: 0.8031 (tpt) cc_final: 0.7741 (tpt) REVERT: D 72 ASN cc_start: 0.8919 (p0) cc_final: 0.8653 (p0) REVERT: D 143 ASP cc_start: 0.8491 (t70) cc_final: 0.8153 (t0) REVERT: D 190 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8517 (mtt90) REVERT: E 125 CYS cc_start: 0.7603 (t) cc_final: 0.6666 (p) REVERT: E 162 ASN cc_start: 0.8547 (t0) cc_final: 0.8285 (t0) REVERT: E 233 LYS cc_start: 0.8641 (mptp) cc_final: 0.8030 (mttp) REVERT: G 174 MET cc_start: 0.8104 (ttm) cc_final: 0.7851 (mtp) REVERT: H 33 ILE cc_start: 0.8682 (mm) cc_final: 0.8437 (mm) REVERT: H 290 GLU cc_start: 0.6953 (pp20) cc_final: 0.6298 (pt0) REVERT: I 86 HIS cc_start: 0.8082 (m170) cc_final: 0.6917 (m-70) REVERT: I 126 ASP cc_start: 0.8066 (p0) cc_final: 0.7865 (p0) REVERT: K 156 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: K 163 MET cc_start: 0.7373 (ttt) cc_final: 0.7067 (ttt) REVERT: K 465 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7464 (mttp) REVERT: K 501 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6501 (mm-30) REVERT: K 525 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7060 (mtm110) REVERT: K 564 TRP cc_start: 0.5606 (m-90) cc_final: 0.4912 (m-90) REVERT: K 566 MET cc_start: 0.7158 (mtt) cc_final: 0.6885 (mtm) REVERT: K 578 THR cc_start: 0.8260 (p) cc_final: 0.7952 (t) REVERT: K 749 MET cc_start: 0.8462 (mmp) cc_final: 0.7897 (mmm) REVERT: K 823 MET cc_start: 0.8447 (mmp) cc_final: 0.8231 (mmt) REVERT: K 925 MET cc_start: 0.7449 (mtt) cc_final: 0.6931 (mtt) REVERT: L 20 GLN cc_start: 0.7704 (mm110) cc_final: 0.7381 (mp10) REVERT: L 45 TYR cc_start: 0.8379 (m-80) cc_final: 0.8133 (m-80) REVERT: M 348 GLN cc_start: 0.8272 (mm110) cc_final: 0.8023 (mm-40) REVERT: M 494 ARG cc_start: 0.5886 (ttt90) cc_final: 0.5455 (ttm110) REVERT: M 529 MET cc_start: 0.7190 (mpp) cc_final: 0.6939 (mpp) outliers start: 59 outliers final: 28 residues processed: 495 average time/residue: 0.2139 time to fit residues: 169.2653 Evaluate side-chains 377 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 346 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 558 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 313 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 308 optimal weight: 0.0170 chunk 295 optimal weight: 6.9990 chunk 360 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 143 optimal weight: 0.0050 chunk 97 optimal weight: 0.7980 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN E 275 HIS H 266 HIS ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS M 300 HIS M 317 GLN M 318 HIS M 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123142 restraints weight = 50633.161| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.64 r_work: 0.3413 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32293 Z= 0.147 Angle : 0.697 19.814 43875 Z= 0.339 Chirality : 0.056 1.506 5054 Planarity : 0.004 0.063 5456 Dihedral : 9.481 168.359 4921 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.59 % Allowed : 12.45 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 3839 helix: 0.47 (0.15), residues: 1271 sheet: -1.24 (0.18), residues: 763 loop : -2.44 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 6 TYR 0.023 0.002 TYR A 175 PHE 0.020 0.002 PHE M 394 TRP 0.020 0.002 TRP G 101 HIS 0.009 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (32289) covalent geometry : angle 0.69603 / 0.34 (43872) hydrogen bonds : bond 0.04611 / 3.08 ( 1377) hydrogen bonds : angle 4.85869 / 3.35 ( 3871) metal coordination : bond 0.01196 / 0.60 ( 4) metal coordination : angle 3.34164 / 1.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 391 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7256 (t80) cc_final: 0.6908 (t80) REVERT: A 180 ARG cc_start: 0.7448 (mtt90) cc_final: 0.7198 (mtp85) REVERT: A 240 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6655 (pt) REVERT: B 92 ASP cc_start: 0.7871 (t0) cc_final: 0.7626 (m-30) REVERT: C 178 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7777 (pm20) REVERT: C 226 MET cc_start: 0.8043 (tpt) cc_final: 0.7718 (tpt) REVERT: D 72 ASN cc_start: 0.8884 (p0) cc_final: 0.8629 (p0) REVERT: D 143 ASP cc_start: 0.8669 (t70) cc_final: 0.8351 (t0) REVERT: D 190 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8519 (mtt90) REVERT: E 125 CYS cc_start: 0.7549 (t) cc_final: 0.6834 (p) REVERT: E 162 ASN cc_start: 0.8543 (t0) cc_final: 0.8214 (t0) REVERT: E 233 LYS cc_start: 0.8672 (mptp) cc_final: 0.8086 (mttp) REVERT: H 6 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8270 (ptp-110) REVERT: H 33 ILE cc_start: 0.8667 (mm) cc_final: 0.8447 (mm) REVERT: H 290 GLU cc_start: 0.7187 (pp20) cc_final: 0.6899 (pt0) REVERT: I 86 HIS cc_start: 0.8126 (m170) cc_final: 0.7057 (m-70) REVERT: I 126 ASP cc_start: 0.8151 (p0) cc_final: 0.7940 (p0) REVERT: K 156 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: K 163 MET cc_start: 0.7485 (ttt) cc_final: 0.7080 (ttt) REVERT: K 465 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7366 (mttp) REVERT: K 495 LEU cc_start: 0.1801 (OUTLIER) cc_final: 0.1585 (tt) REVERT: K 501 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6410 (mm-30) REVERT: K 525 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7219 (mtm110) REVERT: K 554 ASP cc_start: 0.7721 (t70) cc_final: 0.7358 (m-30) REVERT: K 564 TRP cc_start: 0.5541 (m-90) cc_final: 0.5094 (m-90) REVERT: K 566 MET cc_start: 0.7242 (mtt) cc_final: 0.7032 (mtm) REVERT: K 578 THR cc_start: 0.8322 (p) cc_final: 0.7917 (p) REVERT: K 723 GLU cc_start: 0.8304 (mp0) cc_final: 0.7981 (mt-10) REVERT: K 749 MET cc_start: 0.8595 (mmp) cc_final: 0.8084 (mmm) REVERT: K 925 MET cc_start: 0.7372 (mtt) cc_final: 0.6877 (mtt) REVERT: L 20 GLN cc_start: 0.7770 (mm110) cc_final: 0.7446 (mp10) REVERT: L 45 TYR cc_start: 0.8392 (m-80) cc_final: 0.8131 (m-80) REVERT: M 536 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8124 (mm) REVERT: M 543 MET cc_start: 0.7597 (mmm) cc_final: 0.7284 (mmm) outliers start: 86 outliers final: 49 residues processed: 449 average time/residue: 0.1997 time to fit residues: 146.6447 Evaluate side-chains 386 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 253 ASP Chi-restraints excluded: chain I residue 40 CYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 799 CYS Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 1014 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 353 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 147 ASN C 259 HIS E 19 GLN F 5 HIS H 266 HIS ** K 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN M 317 GLN M 894 ASN M 898 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111003 restraints weight = 51231.384| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.56 r_work: 0.3229 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 32293 Z= 0.324 Angle : 0.842 20.780 43875 Z= 0.420 Chirality : 0.059 1.555 5054 Planarity : 0.006 0.075 5456 Dihedral : 9.665 177.108 4921 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.92 % Allowed : 12.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3839 helix: 0.27 (0.14), residues: 1269 sheet: -1.00 (0.18), residues: 761 loop : -2.34 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 285 TYR 0.032 0.003 TYR F 252 PHE 0.034 0.003 PHE D 31 TRP 0.016 0.002 TRP H 96 HIS 0.011 0.002 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.32 (32289) covalent geometry : angle 0.84129 / 0.42 (43872) hydrogen bonds : bond 0.05571 / 3.68 ( 1377) hydrogen bonds : angle 5.09751 / 3.53 ( 3871) metal coordination : bond 0.02469 / 1.23 ( 4) metal coordination : angle 3.71989 / 1.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 341 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8746 (t0) cc_final: 0.8520 (t0) REVERT: A 168 GLN cc_start: 0.8328 (mt0) cc_final: 0.8020 (mp10) REVERT: A 180 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7553 (mtp85) REVERT: A 240 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7097 (pt) REVERT: B 92 ASP cc_start: 0.7984 (t0) cc_final: 0.7768 (m-30) REVERT: B 119 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8550 (mm110) REVERT: B 186 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8136 (pt) REVERT: C 33 ARG cc_start: 0.8766 (ptt180) cc_final: 0.8488 (mtm180) REVERT: C 226 MET cc_start: 0.8534 (tpt) cc_final: 0.8043 (tpt) REVERT: D 190 ARG cc_start: 0.8872 (mtt180) cc_final: 0.8443 (mtt90) REVERT: E 107 ASN cc_start: 0.8595 (m110) cc_final: 0.8371 (m-40) REVERT: E 233 LYS cc_start: 0.8740 (mptp) cc_final: 0.8235 (mttp) REVERT: F 120 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7509 (mtp180) REVERT: G 130 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: G 173 ASP cc_start: 0.8484 (m-30) cc_final: 0.8271 (m-30) REVERT: G 266 LYS cc_start: 0.7303 (ttmt) cc_final: 0.6936 (mmtm) REVERT: H 33 ILE cc_start: 0.8803 (mm) cc_final: 0.8530 (mt) REVERT: H 107 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9105 (m) REVERT: H 291 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7681 (pp30) REVERT: I 86 HIS cc_start: 0.8275 (m170) cc_final: 0.7077 (m-70) REVERT: K 163 MET cc_start: 0.7686 (ttt) cc_final: 0.7288 (ttt) REVERT: K 455 MET cc_start: 0.5841 (tpt) cc_final: 0.5387 (tpp) REVERT: K 465 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7526 (mttp) REVERT: K 554 ASP cc_start: 0.7687 (t70) cc_final: 0.7235 (m-30) REVERT: K 566 MET cc_start: 0.7336 (mtt) cc_final: 0.7100 (mtm) REVERT: K 723 GLU cc_start: 0.8230 (mp0) cc_final: 0.7970 (mt-10) REVERT: K 739 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7756 (tt) REVERT: K 749 MET cc_start: 0.8469 (mmp) cc_final: 0.8035 (mtp) REVERT: K 925 MET cc_start: 0.7476 (mtt) cc_final: 0.7048 (mtt) REVERT: L 45 TYR cc_start: 0.8391 (m-80) cc_final: 0.8178 (m-80) REVERT: M 227 MET cc_start: 0.8179 (ptt) cc_final: 0.7830 (ptt) REVERT: M 422 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7324 (mm-30) REVERT: M 536 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8217 (mm) outliers start: 130 outliers final: 73 residues processed: 439 average time/residue: 0.2042 time to fit residues: 146.2365 Evaluate side-chains 381 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 497 ASN Chi-restraints excluded: chain K residue 560 PHE Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain K residue 739 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 185 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 149 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 377 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 285 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS A 188 HIS E 131 HIS ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS H 266 HIS ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS M 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115023 restraints weight = 50751.219| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.61 r_work: 0.3295 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32293 Z= 0.139 Angle : 0.673 16.957 43875 Z= 0.329 Chirality : 0.051 1.149 5054 Planarity : 0.004 0.064 5456 Dihedral : 9.525 178.523 4921 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.77 % Allowed : 14.38 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3839 helix: 0.76 (0.15), residues: 1269 sheet: -0.86 (0.18), residues: 742 loop : -2.05 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 285 TYR 0.015 0.001 TYR H 252 PHE 0.019 0.002 PHE B 106 TRP 0.018 0.001 TRP H 96 HIS 0.006 0.001 HIS F 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (32289) covalent geometry : angle 0.67242 / 0.33 (43872) hydrogen bonds : bond 0.04452 / 2.96 ( 1377) hydrogen bonds : angle 4.69857 / 3.25 ( 3871) metal coordination : bond 0.01198 / 0.60 ( 4) metal coordination : angle 3.14911 / 1.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 345 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8559 (tp-100) REVERT: A 240 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6744 (pt) REVERT: B 110 ILE cc_start: 0.8653 (tp) cc_final: 0.8396 (tp) REVERT: C 226 MET cc_start: 0.8487 (tpt) cc_final: 0.8108 (tpt) REVERT: E 233 LYS cc_start: 0.8585 (mptp) cc_final: 0.8121 (mttp) REVERT: E 285 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6874 (tp-100) REVERT: F 120 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7119 (mmm-85) REVERT: G 130 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (mtpp) REVERT: G 158 GLN cc_start: 0.7535 (pm20) cc_final: 0.7118 (pm20) REVERT: G 161 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: G 182 ASP cc_start: 0.8071 (t0) cc_final: 0.7862 (t0) REVERT: G 266 LYS cc_start: 0.7315 (ttmt) cc_final: 0.7029 (mmtm) REVERT: H 33 ILE cc_start: 0.8753 (mm) cc_final: 0.8537 (mt) REVERT: I 86 HIS cc_start: 0.8101 (m170) cc_final: 0.7216 (m-70) REVERT: K 156 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: K 163 MET cc_start: 0.7612 (ttt) cc_final: 0.7251 (ttt) REVERT: K 554 ASP cc_start: 0.7634 (t70) cc_final: 0.7220 (m-30) REVERT: K 566 MET cc_start: 0.7466 (mtt) cc_final: 0.7125 (mtm) REVERT: K 610 LEU cc_start: 0.8237 (mt) cc_final: 0.7896 (mt) REVERT: K 712 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: K 713 ILE cc_start: 0.5983 (mm) cc_final: 0.5764 (tp) REVERT: K 723 GLU cc_start: 0.8122 (mp0) cc_final: 0.7891 (mt-10) REVERT: K 739 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7643 (tt) REVERT: K 748 MET cc_start: 0.7068 (mpp) cc_final: 0.6380 (pmm) REVERT: K 749 MET cc_start: 0.8324 (mmp) cc_final: 0.7726 (mtp) REVERT: K 803 GLU cc_start: 0.7297 (mp0) cc_final: 0.6303 (tt0) REVERT: K 925 MET cc_start: 0.7649 (mtt) cc_final: 0.7267 (mtt) REVERT: L 17 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7239 (mtpp) REVERT: L 45 TYR cc_start: 0.8271 (m-80) cc_final: 0.8064 (m-80) REVERT: M 318 HIS cc_start: 0.6890 (m-70) cc_final: 0.6687 (m-70) REVERT: M 406 MET cc_start: 0.5749 (mmt) cc_final: 0.5497 (mmt) REVERT: M 495 THR cc_start: 0.7748 (m) cc_final: 0.7214 (p) REVERT: M 536 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8080 (mm) outliers start: 92 outliers final: 55 residues processed: 414 average time/residue: 0.1944 time to fit residues: 133.4239 Evaluate side-chains 374 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 712 GLU Chi-restraints excluded: chain K residue 739 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 1014 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 375 optimal weight: 0.0170 chunk 167 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 311 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 ASN K 902 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116476 restraints weight = 50702.956| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.59 r_work: 0.3316 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.003 0.043 32293 Z= 0.130 Angle : 0.643 12.771 43875 Z= 0.313 Chirality : 0.048 0.603 5054 Planarity : 0.004 0.063 5456 Dihedral : 9.450 174.736 4921 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.98 % Allowed : 14.83 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3839 helix: 1.03 (0.15), residues: 1269 sheet: -0.67 (0.19), residues: 736 loop : -1.89 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 471 TYR 0.022 0.001 TYR A 175 PHE 0.016 0.001 PHE B 106 TRP 0.017 0.001 TRP H 96 HIS 0.006 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (32289) covalent geometry : angle 0.64281 / 0.31 (43872) hydrogen bonds : bond 0.04155 / 2.75 ( 1377) hydrogen bonds : angle 4.51742 / 3.12 ( 3871) metal coordination : bond 0.00973 / 0.49 ( 4) metal coordination : angle 2.56759 / 1.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 343 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7699 (mp0) REVERT: A 240 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6940 (pt) REVERT: B 110 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 233 LYS cc_start: 0.8683 (mptp) cc_final: 0.8202 (mttp) REVERT: E 285 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6894 (tp-100) REVERT: F 120 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7269 (mtp180) REVERT: G 130 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: G 161 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: G 266 LYS cc_start: 0.7301 (ttmt) cc_final: 0.6927 (mmtm) REVERT: H 291 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7467 (pp30) REVERT: I 86 HIS cc_start: 0.8135 (m170) cc_final: 0.7346 (m-70) REVERT: K 156 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: K 163 MET cc_start: 0.7656 (ttt) cc_final: 0.7318 (ttt) REVERT: K 465 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7518 (mttp) REVERT: K 554 ASP cc_start: 0.7838 (t70) cc_final: 0.7381 (m-30) REVERT: K 566 MET cc_start: 0.7514 (mtt) cc_final: 0.7047 (mtm) REVERT: K 598 ASP cc_start: 0.6034 (p0) cc_final: 0.5265 (t0) REVERT: K 610 LEU cc_start: 0.8225 (mt) cc_final: 0.7896 (mt) REVERT: K 739 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7734 (tt) REVERT: K 749 MET cc_start: 0.8362 (mmp) cc_final: 0.8051 (mtp) REVERT: K 803 GLU cc_start: 0.7233 (mp0) cc_final: 0.6239 (tt0) REVERT: K 925 MET cc_start: 0.7628 (mtt) cc_final: 0.7240 (mtt) REVERT: L 17 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7236 (tttp) REVERT: L 45 TYR cc_start: 0.8319 (m-80) cc_final: 0.8105 (m-80) REVERT: M 406 MET cc_start: 0.5870 (mmt) cc_final: 0.5612 (mmt) REVERT: M 536 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (mm) REVERT: M 569 MET cc_start: 0.8700 (ttt) cc_final: 0.8426 (ttt) REVERT: M 1007 MET cc_start: 0.8495 (mmm) cc_final: 0.7973 (mmm) outliers start: 99 outliers final: 60 residues processed: 418 average time/residue: 0.1922 time to fit residues: 132.1461 Evaluate side-chains 374 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 739 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 1033 ASP Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 133 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 279 optimal weight: 0.0000 chunk 222 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 318 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.154511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117587 restraints weight = 50950.458| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.56 r_work: 0.3335 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32293 Z= 0.118 Angle : 0.634 12.522 43875 Z= 0.309 Chirality : 0.047 0.569 5054 Planarity : 0.004 0.061 5456 Dihedral : 9.379 173.395 4921 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.83 % Allowed : 15.55 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 3839 helix: 1.22 (0.15), residues: 1270 sheet: -0.53 (0.19), residues: 743 loop : -1.78 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 471 TYR 0.014 0.001 TYR K 106 PHE 0.023 0.001 PHE K 775 TRP 0.018 0.001 TRP H 96 HIS 0.010 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (32289) covalent geometry : angle 0.63391 / 0.31 (43872) hydrogen bonds : bond 0.03920 / 2.60 ( 1377) hydrogen bonds : angle 4.40135 / 3.04 ( 3871) metal coordination : bond 0.00783 / 0.39 ( 4) metal coordination : angle 2.06983 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 337 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7658 (mp0) REVERT: A 77 PHE cc_start: 0.7761 (t80) cc_final: 0.7306 (t80) REVERT: A 240 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6862 (pp) REVERT: B 110 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 233 LYS cc_start: 0.8667 (mptp) cc_final: 0.8186 (mttp) REVERT: E 285 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6977 (tp-100) REVERT: F 120 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7242 (mtp180) REVERT: G 24 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7769 (pp) REVERT: G 130 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: G 161 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: G 266 LYS cc_start: 0.7318 (ttmt) cc_final: 0.6974 (mmtm) REVERT: H 279 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: I 86 HIS cc_start: 0.8061 (m170) cc_final: 0.7421 (m-70) REVERT: K 156 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: K 163 MET cc_start: 0.7577 (ttt) cc_final: 0.7255 (ttt) REVERT: K 554 ASP cc_start: 0.7739 (t70) cc_final: 0.7316 (m-30) REVERT: K 566 MET cc_start: 0.7444 (mtt) cc_final: 0.7038 (mtm) REVERT: K 610 LEU cc_start: 0.8222 (mt) cc_final: 0.7861 (mt) REVERT: K 739 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7733 (tt) REVERT: K 803 GLU cc_start: 0.7317 (mp0) cc_final: 0.6371 (tt0) REVERT: K 925 MET cc_start: 0.7664 (mtt) cc_final: 0.7320 (mtt) REVERT: L 17 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7239 (tttp) REVERT: L 20 GLN cc_start: 0.7389 (mm110) cc_final: 0.7099 (mp10) REVERT: L 45 TYR cc_start: 0.8308 (m-80) cc_final: 0.8090 (m-80) REVERT: M 404 LEU cc_start: 0.8282 (pp) cc_final: 0.7893 (mm) REVERT: M 433 ASP cc_start: 0.7886 (p0) cc_final: 0.7373 (p0) REVERT: M 536 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8258 (mm) REVERT: M 1007 MET cc_start: 0.8521 (mmm) cc_final: 0.8130 (mmm) outliers start: 94 outliers final: 57 residues processed: 404 average time/residue: 0.1908 time to fit residues: 127.1234 Evaluate side-chains 374 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 739 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 1033 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 221 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 chunk 356 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 0.0980 chunk 246 optimal weight: 0.8980 chunk 367 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS M 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117255 restraints weight = 50897.048| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.55 r_work: 0.3330 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32293 Z= 0.124 Angle : 0.632 12.328 43875 Z= 0.307 Chirality : 0.046 0.539 5054 Planarity : 0.004 0.060 5456 Dihedral : 9.330 172.937 4921 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.71 % Allowed : 16.09 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 3839 helix: 1.30 (0.15), residues: 1270 sheet: -0.44 (0.19), residues: 745 loop : -1.73 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 471 TYR 0.017 0.001 TYR K 735 PHE 0.015 0.001 PHE K 666 TRP 0.016 0.001 TRP H 96 HIS 0.007 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (32289) covalent geometry : angle 0.63227 / 0.31 (43872) hydrogen bonds : bond 0.03866 / 2.57 ( 1377) hydrogen bonds : angle 4.34903 / 3.00 ( 3871) metal coordination : bond 0.00757 / 0.38 ( 4) metal coordination : angle 2.10660 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 333 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7613 (mp0) REVERT: A 77 PHE cc_start: 0.7730 (t80) cc_final: 0.7204 (t80) REVERT: A 175 TYR cc_start: 0.8434 (m-10) cc_final: 0.8156 (m-10) REVERT: A 180 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6852 (mtt-85) REVERT: B 110 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 233 LYS cc_start: 0.8681 (mptp) cc_final: 0.8212 (mttp) REVERT: E 285 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7004 (tp-100) REVERT: F 120 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7257 (mtp180) REVERT: G 24 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7881 (pp) REVERT: G 101 TRP cc_start: 0.6943 (p-90) cc_final: 0.6619 (p-90) REVERT: G 130 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8404 (mtpp) REVERT: G 161 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: G 173 ASP cc_start: 0.8190 (m-30) cc_final: 0.7922 (t0) REVERT: H 279 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: I 86 HIS cc_start: 0.8048 (m170) cc_final: 0.7411 (m-70) REVERT: K 156 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: K 163 MET cc_start: 0.7569 (ttt) cc_final: 0.7257 (ttt) REVERT: K 554 ASP cc_start: 0.7751 (t70) cc_final: 0.7346 (m-30) REVERT: K 566 MET cc_start: 0.7438 (mtt) cc_final: 0.7020 (mtm) REVERT: K 610 LEU cc_start: 0.8151 (mt) cc_final: 0.7885 (mt) REVERT: K 739 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7727 (tt) REVERT: K 925 MET cc_start: 0.7703 (mtt) cc_final: 0.7359 (mtt) REVERT: L 17 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7136 (tttp) REVERT: L 20 GLN cc_start: 0.7382 (mm110) cc_final: 0.7102 (mp10) REVERT: M 243 MET cc_start: 0.7411 (mmp) cc_final: 0.7063 (ptm) REVERT: M 404 LEU cc_start: 0.8343 (pp) cc_final: 0.7939 (mm) REVERT: M 536 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8255 (mm) REVERT: M 1007 MET cc_start: 0.8551 (mmm) cc_final: 0.8176 (mmm) outliers start: 90 outliers final: 69 residues processed: 398 average time/residue: 0.1865 time to fit residues: 123.2200 Evaluate side-chains 388 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 311 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 739 LEU Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 443 HIS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 536 ILE Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 1033 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 192 HIS ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN K 902 HIS ** M 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.151779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113747 restraints weight = 51091.635| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.60 r_work: 0.3265 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32293 Z= 0.183 Angle : 0.670 12.319 43875 Z= 0.328 Chirality : 0.047 0.472 5054 Planarity : 0.004 0.057 5456 Dihedral : 9.350 172.528 4921 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.92 % Allowed : 16.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 3839 helix: 1.24 (0.15), residues: 1269 sheet: -0.46 (0.18), residues: 763 loop : -1.75 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.015 0.001 TYR F 252 PHE 0.027 0.002 PHE K 775 TRP 0.014 0.001 TRP K 564 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (32289) covalent geometry : angle 0.66946 / 0.33 (43872) hydrogen bonds : bond 0.04191 / 2.77 ( 1377) hydrogen bonds : angle 4.43829 / 3.06 ( 3871) metal coordination : bond 0.00939 / 0.47 ( 4) metal coordination : angle 2.12246 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 330 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 77 PHE cc_start: 0.7566 (t80) cc_final: 0.7041 (t80) REVERT: A 240 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6892 (pt) REVERT: B 110 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8367 (tp) REVERT: D 68 LYS cc_start: 0.8080 (mtmp) cc_final: 0.7841 (mtpt) REVERT: E 233 LYS cc_start: 0.8666 (mptp) cc_final: 0.8221 (mttp) REVERT: E 285 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6940 (tp-100) REVERT: G 101 TRP cc_start: 0.6898 (p-90) cc_final: 0.6586 (p-90) REVERT: G 130 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8238 (mtpp) REVERT: G 161 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: G 173 ASP cc_start: 0.8176 (m-30) cc_final: 0.7907 (t0) REVERT: I 86 HIS cc_start: 0.8035 (m170) cc_final: 0.7396 (m-70) REVERT: K 163 MET cc_start: 0.7554 (ttt) cc_final: 0.7256 (ttt) REVERT: K 566 MET cc_start: 0.7469 (mtt) cc_final: 0.7024 (mtm) REVERT: K 610 LEU cc_start: 0.8054 (mt) cc_final: 0.7827 (mt) REVERT: K 803 GLU cc_start: 0.7119 (mp0) cc_final: 0.6130 (tt0) REVERT: K 925 MET cc_start: 0.7497 (mtt) cc_final: 0.7175 (mtt) REVERT: L 17 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7110 (tttp) REVERT: L 20 GLN cc_start: 0.7381 (mm110) cc_final: 0.7123 (mp10) REVERT: M 397 LYS cc_start: 0.8439 (mtpm) cc_final: 0.8210 (ttmm) REVERT: M 1007 MET cc_start: 0.8437 (mmm) cc_final: 0.8023 (mmm) outliers start: 97 outliers final: 79 residues processed: 398 average time/residue: 0.1927 time to fit residues: 127.2148 Evaluate side-chains 396 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 313 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 97 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 359 MET Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 443 HIS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 482 THR Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 182 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 359 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS M 197 GLN ** M 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.152253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115106 restraints weight = 50772.218| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.52 r_work: 0.3295 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32293 Z= 0.147 Angle : 0.651 12.225 43875 Z= 0.318 Chirality : 0.046 0.460 5054 Planarity : 0.004 0.058 5456 Dihedral : 9.332 172.086 4921 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.53 % Allowed : 16.76 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 3839 helix: 1.39 (0.15), residues: 1263 sheet: -0.41 (0.19), residues: 760 loop : -1.68 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 471 TYR 0.025 0.001 TYR K 735 PHE 0.018 0.001 PHE B 106 TRP 0.015 0.001 TRP K 564 HIS 0.006 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (32289) covalent geometry : angle 0.65045 / 0.32 (43872) hydrogen bonds : bond 0.03991 / 2.64 ( 1377) hydrogen bonds : angle 4.36570 / 3.01 ( 3871) metal coordination : bond 0.00744 / 0.37 ( 4) metal coordination : angle 2.17909 / 1.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 321 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7682 (mp0) REVERT: A 77 PHE cc_start: 0.7808 (t80) cc_final: 0.7279 (t80) REVERT: A 240 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6997 (pp) REVERT: B 110 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (tp) REVERT: C 75 ASP cc_start: 0.7218 (p0) cc_final: 0.6954 (p0) REVERT: E 233 LYS cc_start: 0.8771 (mptp) cc_final: 0.8312 (mttp) REVERT: E 285 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7007 (tp-100) REVERT: G 101 TRP cc_start: 0.6861 (p-90) cc_final: 0.6558 (p-90) REVERT: G 130 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8380 (mtpp) REVERT: G 161 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: G 173 ASP cc_start: 0.8245 (m-30) cc_final: 0.7985 (t0) REVERT: I 29 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7805 (tpm170) REVERT: I 86 HIS cc_start: 0.8092 (m170) cc_final: 0.7434 (m-70) REVERT: K 156 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: K 163 MET cc_start: 0.7584 (ttt) cc_final: 0.7298 (ttt) REVERT: K 566 MET cc_start: 0.7488 (mtt) cc_final: 0.7029 (mtm) REVERT: K 610 LEU cc_start: 0.8094 (mt) cc_final: 0.7791 (mt) REVERT: K 662 MET cc_start: 0.7750 (ptp) cc_final: 0.7453 (ptp) REVERT: K 925 MET cc_start: 0.7555 (mtt) cc_final: 0.7223 (mtt) REVERT: L 17 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7096 (tttp) REVERT: L 20 GLN cc_start: 0.7384 (mm110) cc_final: 0.7125 (mp10) REVERT: M 243 MET cc_start: 0.7597 (mmp) cc_final: 0.7205 (ptt) REVERT: M 397 LYS cc_start: 0.8450 (mtpm) cc_final: 0.8240 (ttmm) REVERT: M 404 LEU cc_start: 0.8284 (pp) cc_final: 0.7819 (mm) REVERT: M 892 MET cc_start: 0.8205 (mtm) cc_final: 0.7901 (mtm) REVERT: M 1007 MET cc_start: 0.8511 (mmm) cc_final: 0.7883 (mmm) outliers start: 84 outliers final: 73 residues processed: 380 average time/residue: 0.1941 time to fit residues: 122.6728 Evaluate side-chains 389 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 125 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain I residue 29 ARG Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 631 VAL Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 194 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 564 TRP Chi-restraints excluded: chain K residue 838 LEU Chi-restraints excluded: chain K residue 842 SER Chi-restraints excluded: chain K residue 853 LEU Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 46 optimal weight: 0.5980 chunk 317 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 902 HIS M 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115687 restraints weight = 51080.838| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.56 r_work: 0.3304 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32293 Z= 0.133 Angle : 0.651 14.085 43875 Z= 0.317 Chirality : 0.046 0.481 5054 Planarity : 0.004 0.058 5456 Dihedral : 9.289 171.549 4921 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.65 % Allowed : 16.88 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 3839 helix: 1.47 (0.15), residues: 1263 sheet: -0.35 (0.19), residues: 737 loop : -1.66 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 180 TYR 0.016 0.001 TYR A 175 PHE 0.028 0.001 PHE K 775 TRP 0.016 0.001 TRP K 564 HIS 0.005 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (32289) covalent geometry : angle 0.65035 / 0.32 (43872) hydrogen bonds : bond 0.03895 / 2.58 ( 1377) hydrogen bonds : angle 4.33048 / 2.98 ( 3871) metal coordination : bond 0.00706 / 0.35 ( 4) metal coordination : angle 2.10927 / 1.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9567.04 seconds wall clock time: 164 minutes 8.20 seconds (9848.20 seconds total)