Starting phenix.real_space_refine on Sat Sep 12 14:40:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.map" model { file = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ww7_21929/09_2026/6ww7_21929.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 10610 2.51 5 N 2853 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s 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: 16576 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7347 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 883} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2306 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 276} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1707 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 67 Classifications: {'peptide': 14} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 11} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 774 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 884 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1462 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 2 Chain: "I" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1150 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16576 At special positions: 0 Unit cell: (94.468, 124.564, 213.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 3051 8.00 N 2853 7.00 C 10610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.04 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG I 301 " - " ASN I 182 " " NAG J 1 " - " ASN A 818 " " NAG K 1 " - " ASN A 913 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 732.4 milliseconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3898 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 23 sheets defined 33.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 480 through 500 Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 906 through 908 No H-bonds generated for 'chain 'A' and resid 906 through 908' Processing helix chain 'A' and resid 962 through 992 removed outlier: 4.079A pdb=" N PHE A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.789A pdb=" N ASP B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.590A pdb=" N VAL B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 69 through 82 removed outlier: 4.557A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 79 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.932A pdb=" N GLN B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.781A pdb=" N ILE B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.749A pdb=" N ARG B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 removed outlier: 4.055A pdb=" N HIS B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.538A pdb=" N ALA B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.768A pdb=" N LYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 Processing helix chain 'B' and resid 247 through 274 removed outlier: 3.701A pdb=" N GLN B 263 " --> pdb=" O TRP B 259 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 removed outlier: 3.762A pdb=" N ALA B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL B 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU B 286 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 38 removed outlier: 3.900A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix removed outlier: 3.757A pdb=" N GLY C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 63 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.860A pdb=" N LYS C 90 " --> pdb=" O PHE C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 115 through 131 Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 146 through 152 Proline residue: C 150 - end of helix Processing helix chain 'C' and resid 168 through 186 removed outlier: 3.897A pdb=" N ARG C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 removed outlier: 4.281A pdb=" N LYS C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'E' and resid 6 through 34 Processing helix chain 'E' and resid 43 through 63 removed outlier: 3.551A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 removed outlier: 4.268A pdb=" N LEU E 76 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'F' and resid 16 through 44 removed outlier: 3.836A pdb=" N GLY F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 70 removed outlier: 3.553A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 56 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 107 removed outlier: 3.777A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 removed outlier: 4.011A pdb=" N THR F 86 " --> pdb=" O PRO F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 61 Processing helix chain 'H' and resid 8 through 20 Processing helix chain 'H' and resid 68 through 85 removed outlier: 3.546A pdb=" N LEU H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR H 76 " --> pdb=" O GLU H 72 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 118 removed outlier: 3.724A pdb=" N ARG H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 176 Processing helix chain 'H' and resid 179 through 182 Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 200 through 207 removed outlier: 3.839A pdb=" N ALA H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 104 Processing helix chain 'I' and resid 134 through 140 Processing helix chain 'I' and resid 175 through 178 Processing helix chain 'I' and resid 199 through 205 Processing helix chain 'F' and resid 74 through 77 Processing sheet with id=A, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=B, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.948A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A 75 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.654A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 128 through 134 removed outlier: 6.732A pdb=" N LEU A 146 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 131 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA A 144 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 133 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 142 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.800A pdb=" N LEU A 189 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 178 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=G, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.681A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 391 through 394 removed outlier: 3.772A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS A 338 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR A 319 " --> pdb=" O CYS A 338 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 444 through 446 removed outlier: 4.484A pdb=" N LEU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'A' and resid 452 through 459 removed outlier: 6.892A pdb=" N VAL A 539 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 455 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 537 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 457 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A 535 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.546A pdb=" N THR A 588 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL A 574 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 572 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 592 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE A 570 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'A' and resid 649 through 652 removed outlier: 3.979A pdb=" N VAL A 639 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'D' and resid 176 through 181 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 176 through 181 current: chain 'A' and resid 670 through 675 removed outlier: 6.001A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=O, first strand: chain 'A' and resid 705 through 711 removed outlier: 6.756A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 756 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'A' and resid 784 through 786 removed outlier: 3.922A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=R, first strand: chain 'G' and resid 83 through 86 removed outlier: 6.481A pdb=" N LEU G 138 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'G' and resid 74 through 76 Processing sheet with id=T, first strand: chain 'H' and resid 92 through 94 Processing sheet with id=U, first strand: chain 'H' and resid 56 through 62 removed outlier: 3.533A pdb=" N ASP H 56 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASN H 27 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'I' and resid 128 through 133 removed outlier: 5.844A pdb=" N HIS I 58 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS I 70 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR I 82 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'I' and resid 182 through 188 675 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2692 1.31 - 1.44: 4603 1.44 - 1.57: 9549 1.57 - 1.70: 0 1.70 - 1.83: 103 Bond restraints: 16947 Sorted by residual: bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C7 NAG A1001 " pdb=" N2 NAG A1001 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C7 NAG I 301 " pdb=" N2 NAG I 301 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 16942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 21965 1.21 - 2.41: 807 2.41 - 3.62: 148 3.62 - 4.83: 41 4.83 - 6.03: 18 Bond angle restraints: 22979 Sorted by residual: angle pdb=" N ILE B 128 " pdb=" CA ILE B 128 " pdb=" C ILE B 128 " ideal model delta sigma weight residual 113.42 108.76 4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" C VAL A 230 " pdb=" N ASP A 231 " pdb=" CA ASP A 231 " ideal model delta sigma weight residual 120.82 125.61 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" N SER C 40 " pdb=" CA SER C 40 " pdb=" C SER C 40 " ideal model delta sigma weight residual 108.07 112.51 -4.44 1.59e+00 3.96e-01 7.80e+00 angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 112.96 110.28 2.68 1.00e+00 1.00e+00 7.19e+00 angle pdb=" N ASP A 231 " pdb=" CA ASP A 231 " pdb=" C ASP A 231 " ideal model delta sigma weight residual 111.37 115.77 -4.40 1.65e+00 3.67e-01 7.12e+00 ... (remaining 22974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 8940 17.57 - 35.15: 894 35.15 - 52.72: 166 52.72 - 70.29: 45 70.29 - 87.86: 17 Dihedral angle restraints: 10062 sinusoidal: 4026 harmonic: 6036 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 368 " pdb=" CB CYS A 368 " ideal model delta sinusoidal sigma weight residual -86.00 -134.12 48.12 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA VAL A 230 " pdb=" C VAL A 230 " pdb=" N ASP A 231 " pdb=" CA ASP A 231 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS A 227 " pdb=" SG CYS A 227 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual 93.00 59.72 33.28 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 10059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1647 0.032 - 0.065: 659 0.065 - 0.097: 175 0.097 - 0.130: 108 0.130 - 0.162: 9 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C5 NAG A1001 " pdb=" C4 NAG A1001 " pdb=" C6 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.41 -2.57 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C5 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" C6 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" C5 NAG I 301 " pdb=" C4 NAG I 301 " pdb=" C6 NAG I 301 " pdb=" O5 NAG I 301 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2595 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 18 " -0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 19 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 19 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 19 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 565 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.42e+00 pdb=" N PRO A 566 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 132 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO I 133 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " -0.016 5.00e-02 4.00e+02 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 407 2.70 - 3.25: 15803 3.25 - 3.80: 25438 3.80 - 4.35: 34222 4.35 - 4.90: 57973 Nonbonded interactions: 133843 Sorted by model distance: nonbonded pdb=" O SER A 927 " pdb=" OG SER A 927 " model vdw 2.145 3.040 nonbonded pdb=" O THR C 137 " pdb=" OH TYR F 110 " model vdw 2.145 3.040 nonbonded pdb=" O TRP A 992 " pdb=" OG SER B 86 " model vdw 2.175 3.040 nonbonded pdb=" O PRO C 141 " pdb=" OG1 THR F 47 " model vdw 2.192 3.040 nonbonded pdb=" O ALA A 975 " pdb=" OG1 THR A 979 " model vdw 2.221 3.040 ... (remaining 133838 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 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' } 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.250 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.005 0.112 16955 Z= 0.231 Angle : 0.584 6.653 23001 Z= 0.336 Chirality : 0.042 0.162 2598 Planarity : 0.003 0.041 2917 Dihedral : 14.872 87.865 6158 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 12.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.34 (0.17), residues: 2030 helix: -1.13 (0.18), residues: 663 sheet: -1.42 (0.21), residues: 506 loop : -1.83 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 706 TYR 0.010 0.001 TYR A 938 PHE 0.013 0.001 PHE A 202 TRP 0.008 0.001 TRP A 163 HIS 0.005 0.001 HIS I 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (16947) covalent geometry : angle 0.57950 / 0.34 (22979) SS BOND : bond 0.00533 / 0.27 ( 2) SS BOND : angle 2.60558 / 1.45 ( 4) hydrogen bonds : bond 0.09187 / 6.15 ( 675) hydrogen bonds : angle 4.95831 / 3.43 ( 1911) link_BETA1-4 : bond 0.01166 / 0.61 ( 2) link_BETA1-4 : angle 3.10410 / 1.73 ( 6) link_NAG-ASN : bond 0.00169 / 0.09 ( 4) link_NAG-ASN : angle 1.59965 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8228 (pttt) cc_final: 0.7944 (pttp) REVERT: A 84 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 137 GLN cc_start: 0.8494 (mt0) cc_final: 0.8058 (tm-30) REVERT: A 258 GLN cc_start: 0.7803 (tt0) cc_final: 0.7454 (tt0) REVERT: A 446 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 142 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7065 (tpm170) REVERT: B 254 MET cc_start: 0.5543 (mtp) cc_final: 0.5211 (tmm) REVERT: B 255 LYS cc_start: 0.7368 (ttmt) cc_final: 0.7084 (ttpp) REVERT: C 73 PHE cc_start: 0.8700 (t80) cc_final: 0.8382 (t80) REVERT: E 32 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7726 (ptp90) REVERT: E 70 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: F 81 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (ttp-170) REVERT: F 83 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: H 72 GLU cc_start: 0.7741 (pt0) cc_final: 0.6750 (mm-30) REVERT: H 97 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7149 (mm-30) REVERT: H 114 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.6973 (tpt90) REVERT: H 191 ASP cc_start: 0.6538 (m-30) cc_final: 0.6321 (m-30) REVERT: I 145 GLN cc_start: 0.8597 (tt0) cc_final: 0.8288 (tt0) outliers start: 52 outliers final: 36 residues processed: 360 average time/residue: 0.1638 time to fit residues: 82.0199 Evaluate side-chains 268 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 304 GLN A 408 GLN A 424 GLN A 466 GLN A 501 HIS A 989 ASN B 194 GLN C 39 GLN E 27 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS I 87 GLN I 105 ASN I 171 HIS I 186 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116123 restraints weight = 22295.400| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.37 r_work: 0.3121 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16955 Z= 0.207 Angle : 0.582 12.197 23001 Z= 0.293 Chirality : 0.044 0.173 2598 Planarity : 0.004 0.044 2917 Dihedral : 6.152 55.153 2324 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.54 % Allowed : 15.99 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.48 (0.18), residues: 2030 helix: -0.13 (0.20), residues: 666 sheet: -1.10 (0.22), residues: 508 loop : -1.48 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 275 TYR 0.022 0.002 TYR B 44 PHE 0.017 0.002 PHE A 324 TRP 0.009 0.001 TRP C 171 HIS 0.008 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (16947) covalent geometry : angle 0.57656 / 0.29 (22979) SS BOND : bond 0.00260 / 0.13 ( 2) SS BOND : angle 2.45711 / 1.44 ( 4) hydrogen bonds : bond 0.03597 / 2.46 ( 675) hydrogen bonds : angle 4.55235 / 3.14 ( 1911) link_BETA1-4 : bond 0.01087 / 0.57 ( 2) link_BETA1-4 : angle 3.15489 / 1.77 ( 6) link_NAG-ASN : bond 0.00486 / 0.25 ( 4) link_NAG-ASN : angle 2.15393 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 0.590 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: A 52 LYS cc_start: 0.8421 (pttt) cc_final: 0.8112 (ptpp) REVERT: A 137 GLN cc_start: 0.8864 (mt0) cc_final: 0.8062 (tm-30) REVERT: A 295 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7905 (mt) REVERT: B 142 ARG cc_start: 0.7701 (ttp80) cc_final: 0.6896 (tpm170) REVERT: B 254 MET cc_start: 0.5701 (mtp) cc_final: 0.5278 (tmm) REVERT: F 83 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8629 (Cg_endo) REVERT: H 72 GLU cc_start: 0.7987 (pt0) cc_final: 0.6464 (mm-30) REVERT: H 77 LEU cc_start: 0.8416 (tt) cc_final: 0.8136 (mp) REVERT: H 97 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7099 (mm-30) REVERT: H 147 HIS cc_start: 0.4214 (OUTLIER) cc_final: 0.2762 (p90) REVERT: I 145 GLN cc_start: 0.8978 (tt0) cc_final: 0.8622 (tt0) outliers start: 63 outliers final: 43 residues processed: 297 average time/residue: 0.1530 time to fit residues: 64.8386 Evaluate side-chains 267 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 105 ASN I 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119564 restraints weight = 22413.137| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.46 r_work: 0.3048 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16955 Z= 0.124 Angle : 0.517 9.234 23001 Z= 0.262 Chirality : 0.042 0.168 2598 Planarity : 0.003 0.044 2917 Dihedral : 5.163 51.438 2290 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.54 % Allowed : 16.84 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.86 (0.18), residues: 2030 helix: 0.49 (0.21), residues: 667 sheet: -0.80 (0.22), residues: 510 loop : -1.18 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.028 0.001 TYR G 148 PHE 0.019 0.001 PHE A 324 TRP 0.009 0.001 TRP C 171 HIS 0.008 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (16947) covalent geometry : angle 0.51234 / 0.26 (22979) SS BOND : bond 0.00501 / 0.24 ( 2) SS BOND : angle 2.89839 / 1.60 ( 4) hydrogen bonds : bond 0.03134 / 2.14 ( 675) hydrogen bonds : angle 4.40314 / 3.04 ( 1911) link_BETA1-4 : bond 0.01247 / 0.65 ( 2) link_BETA1-4 : angle 2.92914 / 1.64 ( 6) link_NAG-ASN : bond 0.00189 / 0.10 ( 4) link_NAG-ASN : angle 1.71424 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.572 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: A 52 LYS cc_start: 0.8445 (pttt) cc_final: 0.8104 (ptpp) REVERT: A 96 ASP cc_start: 0.8974 (m-30) cc_final: 0.8772 (m-30) REVERT: A 112 THR cc_start: 0.8777 (p) cc_final: 0.8569 (p) REVERT: A 137 GLN cc_start: 0.8855 (mt0) cc_final: 0.8047 (tm-30) REVERT: A 295 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7948 (mt) REVERT: B 124 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8193 (mtp85) REVERT: B 142 ARG cc_start: 0.7709 (ttp80) cc_final: 0.6882 (tpm170) REVERT: B 254 MET cc_start: 0.5637 (mtp) cc_final: 0.5276 (tmm) REVERT: H 72 GLU cc_start: 0.7790 (pt0) cc_final: 0.6475 (mm-30) REVERT: H 97 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7077 (mm-30) REVERT: H 147 HIS cc_start: 0.4286 (OUTLIER) cc_final: 0.2807 (p90) REVERT: I 145 GLN cc_start: 0.8941 (tt0) cc_final: 0.8586 (tt0) outliers start: 63 outliers final: 42 residues processed: 291 average time/residue: 0.1467 time to fit residues: 61.0720 Evaluate side-chains 259 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 169 optimal weight: 0.0670 chunk 16 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117850 restraints weight = 22440.497| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.37 r_work: 0.3133 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16955 Z= 0.140 Angle : 0.525 7.738 23001 Z= 0.264 Chirality : 0.043 0.167 2598 Planarity : 0.003 0.043 2917 Dihedral : 4.830 49.353 2278 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.26 % Allowed : 17.28 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.59 (0.19), residues: 2030 helix: 0.72 (0.21), residues: 669 sheet: -0.67 (0.22), residues: 525 loop : -1.02 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.018 0.001 TYR G 148 PHE 0.017 0.001 PHE A 324 TRP 0.009 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (16947) covalent geometry : angle 0.52093 / 0.26 (22979) SS BOND : bond 0.00932 / 0.49 ( 2) SS BOND : angle 2.32268 / 1.34 ( 4) hydrogen bonds : bond 0.03131 / 2.13 ( 675) hydrogen bonds : angle 4.39246 / 3.02 ( 1911) link_BETA1-4 : bond 0.01223 / 0.64 ( 2) link_BETA1-4 : angle 2.95686 / 1.66 ( 6) link_NAG-ASN : bond 0.00269 / 0.14 ( 4) link_NAG-ASN : angle 1.73198 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 0.617 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: A 52 LYS cc_start: 0.8432 (pttt) cc_final: 0.8103 (ptpp) REVERT: A 137 GLN cc_start: 0.8839 (mt0) cc_final: 0.8059 (tm-30) REVERT: A 295 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 642 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9116 (mp) REVERT: B 124 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8303 (mtp85) REVERT: B 142 ARG cc_start: 0.7600 (ttp80) cc_final: 0.6873 (tpm170) REVERT: B 254 MET cc_start: 0.5510 (mtp) cc_final: 0.5233 (tmm) REVERT: C 157 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6191 (pm20) REVERT: F 20 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7762 (mtm180) REVERT: F 81 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8111 (ttp-170) REVERT: H 72 GLU cc_start: 0.7714 (pt0) cc_final: 0.6533 (mm-30) REVERT: H 77 LEU cc_start: 0.8413 (tt) cc_final: 0.8116 (mt) REVERT: H 97 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7112 (mm-30) REVERT: H 147 HIS cc_start: 0.4242 (OUTLIER) cc_final: 0.2771 (p90) REVERT: I 145 GLN cc_start: 0.8989 (tt0) cc_final: 0.8630 (tt0) outliers start: 76 outliers final: 50 residues processed: 285 average time/residue: 0.1440 time to fit residues: 58.5058 Evaluate side-chains 264 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 428 HIS A 657 ASN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115091 restraints weight = 22400.713| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.54 r_work: 0.3085 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16955 Z= 0.247 Angle : 0.608 8.642 23001 Z= 0.307 Chirality : 0.045 0.156 2598 Planarity : 0.004 0.050 2917 Dihedral : 5.152 57.582 2277 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.71 % Allowed : 18.07 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.67 (0.19), residues: 2030 helix: 0.62 (0.21), residues: 666 sheet: -0.74 (0.22), residues: 521 loop : -0.99 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 212 TYR 0.023 0.002 TYR A 175 PHE 0.018 0.002 PHE A 202 TRP 0.019 0.002 TRP A 187 HIS 0.004 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (16947) covalent geometry : angle 0.60259 / 0.31 (22979) SS BOND : bond 0.00658 / 0.34 ( 2) SS BOND : angle 2.53448 / 1.47 ( 4) hydrogen bonds : bond 0.03645 / 2.49 ( 675) hydrogen bonds : angle 4.64044 / 3.18 ( 1911) link_BETA1-4 : bond 0.01220 / 0.64 ( 2) link_BETA1-4 : angle 3.18403 / 1.78 ( 6) link_NAG-ASN : bond 0.00614 / 0.31 ( 4) link_NAG-ASN : angle 2.42767 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8470 (pttt) cc_final: 0.8104 (ptpp) REVERT: A 137 GLN cc_start: 0.8874 (mt0) cc_final: 0.8142 (tm-30) REVERT: A 642 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9113 (mp) REVERT: B 124 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8389 (mtp85) REVERT: B 142 ARG cc_start: 0.7640 (ttp80) cc_final: 0.6806 (tpm170) REVERT: B 254 MET cc_start: 0.5634 (mtp) cc_final: 0.5321 (tmm) REVERT: C 157 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6132 (pm20) REVERT: C 219 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7559 (mmtt) REVERT: E 32 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7638 (ptp90) REVERT: H 72 GLU cc_start: 0.7932 (pt0) cc_final: 0.6806 (mm-30) REVERT: H 97 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7508 (tm-30) REVERT: H 147 HIS cc_start: 0.4345 (OUTLIER) cc_final: 0.3082 (p90) outliers start: 84 outliers final: 55 residues processed: 293 average time/residue: 0.1476 time to fit residues: 62.0882 Evaluate side-chains 270 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 HIS ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118889 restraints weight = 22075.536| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.35 r_work: 0.3148 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16955 Z= 0.109 Angle : 0.526 7.987 23001 Z= 0.266 Chirality : 0.042 0.242 2598 Planarity : 0.003 0.044 2917 Dihedral : 4.796 57.902 2275 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.65 % Allowed : 19.70 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.29 (0.19), residues: 2030 helix: 0.98 (0.21), residues: 667 sheet: -0.51 (0.23), residues: 514 loop : -0.84 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.018 0.001 TYR B 44 PHE 0.017 0.001 PHE A 324 TRP 0.014 0.001 TRP A 187 HIS 0.004 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16947) covalent geometry : angle 0.52293 / 0.26 (22979) SS BOND : bond 0.00459 / 0.24 ( 2) SS BOND : angle 1.68728 / 0.99 ( 4) hydrogen bonds : bond 0.03041 / 2.07 ( 675) hydrogen bonds : angle 4.39557 / 3.02 ( 1911) link_BETA1-4 : bond 0.01215 / 0.64 ( 2) link_BETA1-4 : angle 2.81178 / 1.58 ( 6) link_NAG-ASN : bond 0.00143 / 0.07 ( 4) link_NAG-ASN : angle 1.66310 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 230 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8406 (pttt) cc_final: 0.8071 (ptpp) REVERT: A 137 GLN cc_start: 0.8830 (mt0) cc_final: 0.8085 (tm-30) REVERT: A 642 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 142 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6796 (tpm170) REVERT: B 254 MET cc_start: 0.5444 (mtp) cc_final: 0.5224 (tmm) REVERT: C 157 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6177 (pm20) REVERT: C 219 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7515 (mmtt) REVERT: C 251 MET cc_start: 0.6573 (ppp) cc_final: 0.4041 (ttp) REVERT: E 32 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7797 (ptp90) REVERT: F 20 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7859 (mtm180) REVERT: F 81 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8167 (ttp-170) REVERT: H 72 GLU cc_start: 0.7815 (pt0) cc_final: 0.6670 (mm-30) REVERT: H 97 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7582 (tm-30) REVERT: H 147 HIS cc_start: 0.4397 (OUTLIER) cc_final: 0.3095 (p90) REVERT: H 197 TRP cc_start: 0.7653 (p90) cc_final: 0.6899 (p90) outliers start: 65 outliers final: 47 residues processed: 282 average time/residue: 0.1533 time to fit residues: 61.5607 Evaluate side-chains 266 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 45 optimal weight: 0.0980 chunk 200 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118454 restraints weight = 22200.994| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.29 r_work: 0.3147 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16955 Z= 0.115 Angle : 0.535 8.855 23001 Z= 0.266 Chirality : 0.042 0.219 2598 Planarity : 0.003 0.042 2917 Dihedral : 4.683 53.205 2275 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.87 % Allowed : 19.75 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.17 (0.19), residues: 2030 helix: 1.06 (0.21), residues: 671 sheet: -0.40 (0.23), residues: 511 loop : -0.79 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 212 TYR 0.022 0.001 TYR A 179 PHE 0.015 0.001 PHE I 201 TRP 0.014 0.001 TRP H 164 HIS 0.004 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (16947) covalent geometry : angle 0.53175 / 0.26 (22979) SS BOND : bond 0.00388 / 0.20 ( 2) SS BOND : angle 1.70577 / 1.00 ( 4) hydrogen bonds : bond 0.02993 / 2.04 ( 675) hydrogen bonds : angle 4.35664 / 3.00 ( 1911) link_BETA1-4 : bond 0.01316 / 0.69 ( 2) link_BETA1-4 : angle 2.87046 / 1.61 ( 6) link_NAG-ASN : bond 0.00187 / 0.09 ( 4) link_NAG-ASN : angle 1.61051 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8413 (pttt) cc_final: 0.8126 (ptpp) REVERT: A 137 GLN cc_start: 0.8825 (mt0) cc_final: 0.8095 (tm-30) REVERT: A 642 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 951 LYS cc_start: 0.8495 (mttt) cc_final: 0.7973 (mmmt) REVERT: B 142 ARG cc_start: 0.7572 (ttp80) cc_final: 0.6806 (tpm170) REVERT: B 254 MET cc_start: 0.5418 (mtp) cc_final: 0.5203 (tmm) REVERT: C 76 ARG cc_start: 0.7723 (mpt-90) cc_final: 0.7476 (mtt-85) REVERT: C 157 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: C 219 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7480 (mmtt) REVERT: C 251 MET cc_start: 0.6664 (ppp) cc_final: 0.4879 (ptt) REVERT: E 32 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7813 (ptp90) REVERT: F 20 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7820 (mtm180) REVERT: F 81 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8143 (ttp-170) REVERT: H 65 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4144 (mm) REVERT: H 72 GLU cc_start: 0.7751 (pt0) cc_final: 0.6670 (mm-30) REVERT: H 77 LEU cc_start: 0.8368 (tt) cc_final: 0.7977 (mt) REVERT: H 97 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7106 (mm-30) REVERT: H 147 HIS cc_start: 0.4524 (OUTLIER) cc_final: 0.3204 (p90) REVERT: H 197 TRP cc_start: 0.7642 (p90) cc_final: 0.6872 (p90) outliers start: 69 outliers final: 48 residues processed: 273 average time/residue: 0.1529 time to fit residues: 59.9736 Evaluate side-chains 267 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 166 GLU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 32 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115251 restraints weight = 22484.155| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.38 r_work: 0.3105 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16955 Z= 0.221 Angle : 0.617 12.406 23001 Z= 0.307 Chirality : 0.045 0.225 2598 Planarity : 0.004 0.047 2917 Dihedral : 4.917 49.393 2273 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.98 % Allowed : 20.03 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.33 (0.19), residues: 2030 helix: 0.92 (0.21), residues: 668 sheet: -0.49 (0.23), residues: 517 loop : -0.86 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 275 TYR 0.023 0.002 TYR A 179 PHE 0.017 0.002 PHE A 324 TRP 0.015 0.002 TRP H 164 HIS 0.003 0.001 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (16947) covalent geometry : angle 0.61010 / 0.30 (22979) SS BOND : bond 0.00840 / 0.41 ( 2) SS BOND : angle 4.51251 / 2.41 ( 4) hydrogen bonds : bond 0.03447 / 2.36 ( 675) hydrogen bonds : angle 4.57684 / 3.14 ( 1911) link_BETA1-4 : bond 0.01344 / 0.71 ( 2) link_BETA1-4 : angle 3.08182 / 1.73 ( 6) link_NAG-ASN : bond 0.00519 / 0.26 ( 4) link_NAG-ASN : angle 2.27237 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8463 (pttt) cc_final: 0.8113 (ptpp) REVERT: A 137 GLN cc_start: 0.8877 (mt0) cc_final: 0.8128 (tm-30) REVERT: A 488 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7432 (mt) REVERT: A 642 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9066 (mp) REVERT: A 661 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: A 951 LYS cc_start: 0.8535 (mttt) cc_final: 0.8045 (mmmt) REVERT: B 142 ARG cc_start: 0.7621 (ttp80) cc_final: 0.6739 (tpm170) REVERT: B 208 LEU cc_start: 0.8051 (mm) cc_final: 0.7612 (pp) REVERT: B 254 MET cc_start: 0.5562 (mtp) cc_final: 0.5301 (tmm) REVERT: C 157 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: C 219 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7453 (mmtt) REVERT: C 251 MET cc_start: 0.6725 (ppp) cc_final: 0.5002 (ptt) REVERT: E 32 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7689 (ptp90) REVERT: F 20 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7797 (mtm180) REVERT: F 81 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8156 (ttp-170) REVERT: H 65 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4148 (mm) REVERT: H 72 GLU cc_start: 0.7920 (pt0) cc_final: 0.6826 (mm-30) REVERT: H 97 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7104 (mm-30) REVERT: H 145 GLU cc_start: 0.6392 (mm-30) cc_final: 0.5950 (mm-30) REVERT: H 147 HIS cc_start: 0.4510 (OUTLIER) cc_final: 0.3188 (p90) REVERT: H 197 TRP cc_start: 0.7746 (p90) cc_final: 0.6871 (p90) outliers start: 71 outliers final: 53 residues processed: 277 average time/residue: 0.1501 time to fit residues: 59.4276 Evaluate side-chains 276 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 166 GLU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 151 optimal weight: 0.0270 chunk 188 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117760 restraints weight = 22340.225| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.44 r_work: 0.3130 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16955 Z= 0.127 Angle : 0.569 11.843 23001 Z= 0.281 Chirality : 0.043 0.215 2598 Planarity : 0.003 0.043 2917 Dihedral : 4.743 50.582 2272 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 20.93 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.13 (0.19), residues: 2030 helix: 1.10 (0.21), residues: 669 sheet: -0.38 (0.23), residues: 511 loop : -0.77 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 275 TYR 0.024 0.001 TYR A 179 PHE 0.017 0.001 PHE A 324 TRP 0.016 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16947) covalent geometry : angle 0.56489 / 0.28 (22979) SS BOND : bond 0.00627 / 0.31 ( 2) SS BOND : angle 3.40786 / 1.86 ( 4) hydrogen bonds : bond 0.03058 / 2.08 ( 675) hydrogen bonds : angle 4.44220 / 3.06 ( 1911) link_BETA1-4 : bond 0.01284 / 0.68 ( 2) link_BETA1-4 : angle 2.78529 / 1.56 ( 6) link_NAG-ASN : bond 0.00147 / 0.07 ( 4) link_NAG-ASN : angle 1.68652 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8431 (pttt) cc_final: 0.8105 (ptpp) REVERT: A 137 GLN cc_start: 0.8863 (mt0) cc_final: 0.8110 (tm-30) REVERT: A 258 GLN cc_start: 0.7954 (tt0) cc_final: 0.7627 (tt0) REVERT: A 642 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9079 (mp) REVERT: A 951 LYS cc_start: 0.8522 (mttt) cc_final: 0.8003 (mmmt) REVERT: B 142 ARG cc_start: 0.7592 (ttp80) cc_final: 0.6733 (tpm170) REVERT: B 254 MET cc_start: 0.5457 (mtp) cc_final: 0.5252 (tmm) REVERT: C 76 ARG cc_start: 0.7835 (mpt-90) cc_final: 0.7560 (mtt-85) REVERT: C 157 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.5990 (pm20) REVERT: C 219 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7415 (mmtt) REVERT: C 251 MET cc_start: 0.6698 (ppp) cc_final: 0.5021 (ptt) REVERT: E 32 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: F 20 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7802 (mtm180) REVERT: F 81 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8105 (ttp-170) REVERT: G 117 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8537 (mtpt) REVERT: H 65 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.3996 (mm) REVERT: H 72 GLU cc_start: 0.7798 (pt0) cc_final: 0.6711 (mm-30) REVERT: H 97 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7092 (mm-30) REVERT: H 147 HIS cc_start: 0.4588 (OUTLIER) cc_final: 0.3301 (p90) outliers start: 55 outliers final: 46 residues processed: 269 average time/residue: 0.1507 time to fit residues: 57.5817 Evaluate side-chains 273 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 27 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116898 restraints weight = 22334.007| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.28 r_work: 0.3142 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16955 Z= 0.133 Angle : 0.563 11.677 23001 Z= 0.279 Chirality : 0.043 0.212 2598 Planarity : 0.003 0.044 2917 Dihedral : 4.704 51.653 2272 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.25 % Allowed : 20.65 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.09 (0.19), residues: 2030 helix: 1.18 (0.21), residues: 670 sheet: -0.35 (0.23), residues: 504 loop : -0.80 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 275 TYR 0.025 0.001 TYR A 179 PHE 0.016 0.001 PHE A 324 TRP 0.016 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (16947) covalent geometry : angle 0.55869 / 0.28 (22979) SS BOND : bond 0.00543 / 0.27 ( 2) SS BOND : angle 3.15822 / 1.74 ( 4) hydrogen bonds : bond 0.03072 / 2.09 ( 675) hydrogen bonds : angle 4.40401 / 3.03 ( 1911) link_BETA1-4 : bond 0.01153 / 0.61 ( 2) link_BETA1-4 : angle 2.84569 / 1.59 ( 6) link_NAG-ASN : bond 0.00229 / 0.11 ( 4) link_NAG-ASN : angle 1.71157 / 0.89 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8439 (pttt) cc_final: 0.8136 (ptpp) REVERT: A 137 GLN cc_start: 0.8842 (mt0) cc_final: 0.8109 (tm-30) REVERT: A 642 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9001 (mp) REVERT: A 951 LYS cc_start: 0.8496 (mttt) cc_final: 0.7982 (mmmt) REVERT: B 142 ARG cc_start: 0.7583 (ttp80) cc_final: 0.6729 (tpm170) REVERT: C 70 LYS cc_start: 0.6898 (tptt) cc_final: 0.6683 (tptt) REVERT: C 157 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: C 219 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7424 (mmtt) REVERT: C 251 MET cc_start: 0.6683 (ppp) cc_final: 0.4993 (ptt) REVERT: E 32 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7857 (ptp90) REVERT: F 20 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7798 (mtm180) REVERT: F 73 ARG cc_start: 0.8275 (ptm160) cc_final: 0.7772 (ttp-110) REVERT: F 81 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8066 (ttp-170) REVERT: G 117 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8532 (mtpt) REVERT: H 65 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4072 (mm) REVERT: H 72 GLU cc_start: 0.7794 (pt0) cc_final: 0.6737 (mm-30) REVERT: H 77 LEU cc_start: 0.8440 (tt) cc_final: 0.7995 (mt) REVERT: H 97 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7092 (mm-30) REVERT: H 147 HIS cc_start: 0.4518 (OUTLIER) cc_final: 0.3246 (p90) outliers start: 58 outliers final: 50 residues processed: 279 average time/residue: 0.1571 time to fit residues: 62.1850 Evaluate side-chains 276 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 123 optimal weight: 0.0050 chunk 195 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118427 restraints weight = 22342.339| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.34 r_work: 0.3158 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16955 Z= 0.116 Angle : 0.556 11.654 23001 Z= 0.275 Chirality : 0.043 0.210 2598 Planarity : 0.003 0.043 2917 Dihedral : 4.645 52.504 2272 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.14 % Allowed : 20.76 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.01 (0.19), residues: 2030 helix: 1.30 (0.21), residues: 669 sheet: -0.38 (0.23), residues: 508 loop : -0.74 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 275 TYR 0.025 0.001 TYR A 179 PHE 0.016 0.001 PHE H 61 TRP 0.016 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16947) covalent geometry : angle 0.55194 / 0.27 (22979) SS BOND : bond 0.00554 / 0.28 ( 2) SS BOND : angle 2.85705 / 1.58 ( 4) hydrogen bonds : bond 0.02969 / 2.02 ( 675) hydrogen bonds : angle 4.35269 / 3.00 ( 1911) link_BETA1-4 : bond 0.01185 / 0.62 ( 2) link_BETA1-4 : angle 2.77827 / 1.56 ( 6) link_NAG-ASN : bond 0.00148 / 0.07 ( 4) link_NAG-ASN : angle 1.54096 / 0.80 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.13 seconds wall clock time: 77 minutes 15.14 seconds (4635.14 seconds total)