Starting phenix.real_space_refine on Sat Jun 14 03:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053.map" model { file = "/net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q0g_18053/06_2025/8q0g_18053_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 46 5.16 5 C 9871 2.51 5 N 2790 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15819 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6041 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2784 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain: "C" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1090 Classifications: {'peptide': 174} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 63} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 181 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "F" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1920 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 1520 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 1515 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 218} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 845 Unresolved non-hydrogen angles: 1089 Unresolved non-hydrogen dihedrals: 722 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 Conformer: "B" Number of residues, atoms: 299, 1515 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 218} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 845 Unresolved non-hydrogen angles: 1089 Unresolved non-hydrogen dihedrals: 722 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 bond proxies already assigned to first conformer: 1512 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR P1150 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTYR P1150 " occ=0.50 Time building chain proxies: 10.23, per 1000 atoms: 0.65 Number of scatterers: 15819 At special positions: 0 Unit cell: (134.68, 153.18, 147.26, 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 46 16.00 O 3112 8.00 N 2790 7.00 C 9871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.3 seconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 26.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.523A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 removed outlier: 3.531A pdb=" N PHE A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.664A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.761A pdb=" N SER A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.804A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.908A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.765A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 4.077A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.992A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.507A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.615A pdb=" N LEU C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Proline residue: C 118 - end of helix Processing helix chain 'C' and resid 191 through 210 removed outlier: 3.981A pdb=" N MET C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.669A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 4.378A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.969A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.827A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.662A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 Processing helix chain 'F' and resid 65 through 86 removed outlier: 4.310A pdb=" N GLY F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.293A pdb=" N LYS F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 150 removed outlier: 3.919A pdb=" N GLN F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 134 " --> pdb=" O ASN F 130 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET F 136 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.549A pdb=" N SER F 159 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 209 removed outlier: 3.807A pdb=" N GLU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER F 197 " --> pdb=" O ASN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.845A pdb=" N LEU F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.761A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 396 through 420 removed outlier: 4.152A pdb=" N ARG F 404 " --> pdb=" O MET F 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1022 Processing helix chain 'P' and resid 1136 through 1139 removed outlier: 4.210A pdb=" N LEU P1139 " --> pdb=" O PHE P1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1136 through 1139' Processing helix chain 'P' and resid 1185 through 1189 Processing helix chain 'P' and resid 1282 through 1287 removed outlier: 4.177A pdb=" N TYR P1286 " --> pdb=" O ALA P1282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.660A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 7.548A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.796A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 256 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.633A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.633A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.049A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.753A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 428 " --> pdb=" O PHE P1296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.779A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 700 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.637A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.152A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 111 through 118 removed outlier: 3.690A pdb=" N GLY B 125 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 115 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 123 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 117 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 126 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.012A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.390A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 7.292A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.287A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 4.150A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.322A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'F' and resid 36 through 38 removed outlier: 6.525A pdb=" N VAL F 37 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 234 removed outlier: 5.706A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS F 269 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 1040 through 1051 removed outlier: 4.106A pdb=" N THR P1080 " --> pdb=" O LYS P1069 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL P1103 " --> pdb=" O HIS P1127 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS P1147 " --> pdb=" O SER P1179 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER P1179 " --> pdb=" O HIS P1147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 1040 through 1051 removed outlier: 4.106A pdb=" N THR P1080 " --> pdb=" O LYS P1069 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL P1103 " --> pdb=" O HIS P1127 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS P1147 " --> pdb=" O SER P1179 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER P1179 " --> pdb=" O HIS P1147 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY P1204 " --> pdb=" O ASP P1232 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP P1232 " --> pdb=" O GLY P1204 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR P1206 " --> pdb=" O GLN P1230 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN P1230 " --> pdb=" O THR P1206 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL P1208 " --> pdb=" O GLY P1228 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY P1228 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL P1210 " --> pdb=" O GLY P1226 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY P1226 " --> pdb=" O VAL P1210 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 1194 through 1195 862 hydrogen bonds defined for protein. 2408 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: 6.18 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5001 1.33 - 1.46: 3584 1.46 - 1.58: 7422 1.58 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 16095 Sorted by residual: bond pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.24e-02 6.50e+03 8.33e+00 bond pdb=" N ASN E 106 " pdb=" CA ASN E 106 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.61e+00 bond pdb=" N ILE A 806 " pdb=" CA ILE A 806 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" N VAL F 192 " pdb=" CA VAL F 192 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.47e+00 bond pdb=" N THR C 130 " pdb=" CA THR C 130 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.30e+00 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 21440 2.13 - 4.25: 404 4.25 - 6.38: 42 6.38 - 8.50: 8 8.50 - 10.63: 2 Bond angle restraints: 21896 Sorted by residual: angle pdb=" N GLU B 222 " pdb=" CA GLU B 222 " pdb=" CB GLU B 222 " ideal model delta sigma weight residual 114.17 109.32 4.85 1.14e+00 7.69e-01 1.81e+01 angle pdb=" C MET F 87 " pdb=" N GLY F 88 " pdb=" CA GLY F 88 " ideal model delta sigma weight residual 121.41 128.84 -7.43 1.96e+00 2.60e-01 1.44e+01 angle pdb=" CB MET F 402 " pdb=" CG MET F 402 " pdb=" SD MET F 402 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA ILE C 131 " pdb=" C ILE C 131 " pdb=" O ILE C 131 " ideal model delta sigma weight residual 121.64 118.28 3.36 9.80e-01 1.04e+00 1.18e+01 angle pdb=" N TYR C 129 " pdb=" CA TYR C 129 " pdb=" C TYR C 129 " ideal model delta sigma weight residual 112.86 108.85 4.01 1.22e+00 6.72e-01 1.08e+01 ... (remaining 21891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8746 17.91 - 35.82: 657 35.82 - 53.72: 96 53.72 - 71.63: 23 71.63 - 89.54: 15 Dihedral angle restraints: 9537 sinusoidal: 3349 harmonic: 6188 Sorted by residual: dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N GLY B 265 " pdb=" CA GLY B 265 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASP D 84 " pdb=" C ASP D 84 " pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N ASP A 582 " pdb=" CA ASP A 582 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 9534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1856 0.050 - 0.100: 502 0.100 - 0.151: 98 0.151 - 0.201: 9 0.201 - 0.251: 2 Chirality restraints: 2467 Sorted by residual: chirality pdb=" CB ILE A 430 " pdb=" CA ILE A 430 " pdb=" CG1 ILE A 430 " pdb=" CG2 ILE A 430 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL D 108 " pdb=" CA VAL D 108 " pdb=" CG1 VAL D 108 " pdb=" CG2 VAL D 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2464 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 186 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO C 187 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 187 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 187 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 257 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO F 258 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 258 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 258 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 223 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" CD GLN F 223 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN F 223 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN F 223 " -0.013 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 553 2.70 - 3.25: 16561 3.25 - 3.80: 24702 3.80 - 4.35: 30188 4.35 - 4.90: 50506 Nonbonded interactions: 122510 Sorted by model distance: nonbonded pdb=" O SER C 32 " pdb=" OH TYR D 77 " model vdw 2.149 3.040 nonbonded pdb=" O ARG F 404 " pdb=" OG SER F 407 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASN B 294 " pdb=" NH1 ARG B 295 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 432 " pdb=" O GLU P1277 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR B 333 " pdb=" O GLY B 376 " model vdw 2.172 3.040 ... (remaining 122505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.080 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 0.045 16096 Z= 0.242 Angle : 0.709 10.630 21898 Z= 0.391 Chirality : 0.046 0.251 2467 Planarity : 0.005 0.063 2926 Dihedral : 13.480 89.539 5582 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.45 % Rotamer: Outliers : 0.13 % Allowed : 0.86 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2143 helix: 0.50 (0.23), residues: 506 sheet: -0.66 (0.20), residues: 622 loop : -1.72 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 48 HIS 0.004 0.001 HIS A 196 PHE 0.023 0.002 PHE A 663 TYR 0.018 0.002 TYR D 222 ARG 0.010 0.001 ARG F 260 Details of bonding type rmsd hydrogen bonds : bond 0.14541 ( 775) hydrogen bonds : angle 6.48663 ( 2408) SS BOND : bond 0.00147 ( 1) SS BOND : angle 2.26213 ( 2) covalent geometry : bond 0.00488 (16095) covalent geometry : angle 0.70859 (21896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 1.668 Fit side-chains REVERT: A 369 MET cc_start: 0.8231 (mmm) cc_final: 0.7928 (mmm) REVERT: A 674 TYR cc_start: 0.6132 (m-10) cc_final: 0.5816 (m-10) REVERT: C 82 ILE cc_start: 0.8995 (mm) cc_final: 0.8693 (tp) REVERT: C 195 GLN cc_start: 0.7291 (tp-100) cc_final: 0.6753 (pt0) REVERT: C 199 THR cc_start: 0.7895 (p) cc_final: 0.7449 (p) REVERT: F 180 LEU cc_start: 0.8165 (tp) cc_final: 0.7789 (tp) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.2252 time to fit residues: 84.2561 Evaluate side-chains 189 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 0.0370 chunk 109 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 194 optimal weight: 30.0000 overall best weight: 6.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078630 restraints weight = 54851.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.077172 restraints weight = 39047.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077130 restraints weight = 45122.061| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16096 Z= 0.316 Angle : 0.741 9.368 21898 Z= 0.399 Chirality : 0.047 0.183 2467 Planarity : 0.006 0.053 2926 Dihedral : 5.380 31.111 2328 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.46 % Allowed : 8.96 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2143 helix: 0.28 (0.22), residues: 523 sheet: -0.65 (0.20), residues: 601 loop : -2.05 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 205 HIS 0.007 0.002 HIS A 196 PHE 0.022 0.002 PHE A 426 TYR 0.021 0.002 TYR B 60 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 775) hydrogen bonds : angle 5.64511 ( 2408) SS BOND : bond 0.00035 ( 1) SS BOND : angle 3.25312 ( 2) covalent geometry : bond 0.00694 (16095) covalent geometry : angle 0.74041 (21896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.6003 (m-10) cc_final: 0.5594 (m-10) REVERT: A 704 ASP cc_start: 0.8218 (p0) cc_final: 0.7757 (p0) REVERT: B 367 PHE cc_start: 0.7273 (m-10) cc_final: 0.6985 (m-10) REVERT: C 82 ILE cc_start: 0.9138 (mm) cc_final: 0.8845 (tp) REVERT: C 195 GLN cc_start: 0.6995 (tp-100) cc_final: 0.6160 (tp-100) REVERT: F 415 GLN cc_start: 0.8198 (tt0) cc_final: 0.7905 (tt0) outliers start: 7 outliers final: 4 residues processed: 238 average time/residue: 0.2293 time to fit residues: 87.6751 Evaluate side-chains 195 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 201 optimal weight: 50.0000 chunk 110 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081106 restraints weight = 54212.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080301 restraints weight = 36024.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080706 restraints weight = 29212.710| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16096 Z= 0.126 Angle : 0.607 7.438 21898 Z= 0.321 Chirality : 0.044 0.206 2467 Planarity : 0.004 0.049 2926 Dihedral : 4.748 30.156 2328 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2143 helix: 0.70 (0.22), residues: 524 sheet: -0.62 (0.20), residues: 638 loop : -1.76 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 233 HIS 0.003 0.001 HIS B 347 PHE 0.017 0.002 PHE A 426 TYR 0.018 0.002 TYR D 184 ARG 0.007 0.001 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 775) hydrogen bonds : angle 5.07993 ( 2408) SS BOND : bond 0.00089 ( 1) SS BOND : angle 2.05479 ( 2) covalent geometry : bond 0.00272 (16095) covalent geometry : angle 0.60622 (21896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.8560 (t) cc_final: 0.8323 (t) REVERT: A 304 MET cc_start: 0.7706 (ttt) cc_final: 0.7445 (ttt) REVERT: A 380 ASP cc_start: 0.8069 (p0) cc_final: 0.7243 (t0) REVERT: A 741 MET cc_start: 0.7996 (tmm) cc_final: 0.7722 (tmm) REVERT: C 195 GLN cc_start: 0.7017 (tp-100) cc_final: 0.6129 (tp-100) REVERT: F 415 GLN cc_start: 0.8152 (tt0) cc_final: 0.7885 (tt0) outliers start: 1 outliers final: 1 residues processed: 271 average time/residue: 0.2911 time to fit residues: 126.9639 Evaluate side-chains 197 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 205 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078669 restraints weight = 54729.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078212 restraints weight = 39456.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078501 restraints weight = 31337.968| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16096 Z= 0.258 Angle : 0.680 8.888 21898 Z= 0.362 Chirality : 0.045 0.151 2467 Planarity : 0.005 0.067 2926 Dihedral : 5.079 32.929 2328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2143 helix: 0.57 (0.22), residues: 522 sheet: -0.49 (0.20), residues: 591 loop : -1.94 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 413 HIS 0.005 0.001 HIS D 139 PHE 0.016 0.002 PHE A 426 TYR 0.026 0.002 TYR C 65 ARG 0.007 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 775) hydrogen bonds : angle 5.24301 ( 2408) SS BOND : bond 0.02385 ( 1) SS BOND : angle 2.34309 ( 2) covalent geometry : bond 0.00574 (16095) covalent geometry : angle 0.67966 (21896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.7648 (ttt) cc_final: 0.7388 (ttt) REVERT: A 368 GLU cc_start: 0.8288 (mp0) cc_final: 0.7915 (mp0) REVERT: A 717 GLU cc_start: 0.8316 (mp0) cc_final: 0.8014 (mp0) REVERT: C 82 ILE cc_start: 0.9142 (mm) cc_final: 0.8800 (tp) REVERT: C 195 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6047 (tp-100) REVERT: F 191 GLN cc_start: 0.7442 (mp10) cc_final: 0.7228 (mp10) REVERT: F 415 GLN cc_start: 0.8212 (tt0) cc_final: 0.7866 (tt0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3386 time to fit residues: 130.0235 Evaluate side-chains 182 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 187 optimal weight: 0.0770 chunk 168 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080258 restraints weight = 54789.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080048 restraints weight = 38579.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080225 restraints weight = 31075.454| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16096 Z= 0.144 Angle : 0.616 8.008 21898 Z= 0.325 Chirality : 0.044 0.296 2467 Planarity : 0.004 0.056 2926 Dihedral : 4.794 33.545 2328 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2143 helix: 0.79 (0.23), residues: 521 sheet: -0.33 (0.21), residues: 591 loop : -1.88 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 PHE 0.015 0.002 PHE A 426 TYR 0.017 0.001 TYR D 184 ARG 0.005 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 775) hydrogen bonds : angle 4.93931 ( 2408) SS BOND : bond 0.00245 ( 1) SS BOND : angle 3.00580 ( 2) covalent geometry : bond 0.00321 (16095) covalent geometry : angle 0.61572 (21896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLU cc_start: 0.8191 (mp0) cc_final: 0.7969 (mp0) REVERT: C 195 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6412 (pt0) REVERT: C 199 THR cc_start: 0.7551 (p) cc_final: 0.7155 (p) REVERT: D 225 MET cc_start: 0.8322 (mtm) cc_final: 0.8060 (mtm) REVERT: F 415 GLN cc_start: 0.8185 (tt0) cc_final: 0.7935 (tt0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2330 time to fit residues: 92.1603 Evaluate side-chains 191 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 136 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 209 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 108 optimal weight: 0.2980 chunk 158 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080650 restraints weight = 55316.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079005 restraints weight = 40243.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079190 restraints weight = 44376.798| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16096 Z= 0.201 Angle : 0.642 8.797 21898 Z= 0.343 Chirality : 0.045 0.247 2467 Planarity : 0.005 0.057 2926 Dihedral : 4.882 32.182 2328 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2143 helix: 0.76 (0.23), residues: 522 sheet: -0.26 (0.21), residues: 572 loop : -1.98 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 PHE 0.014 0.002 PHE A 426 TYR 0.019 0.002 TYR B 60 ARG 0.009 0.001 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 775) hydrogen bonds : angle 5.01915 ( 2408) SS BOND : bond 0.00045 ( 1) SS BOND : angle 2.74052 ( 2) covalent geometry : bond 0.00448 (16095) covalent geometry : angle 0.64164 (21896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7648 (p0) cc_final: 0.7441 (p0) REVERT: A 368 GLU cc_start: 0.7925 (mp0) cc_final: 0.7705 (mp0) REVERT: A 380 ASP cc_start: 0.8109 (p0) cc_final: 0.7394 (t0) REVERT: A 717 GLU cc_start: 0.8329 (mp0) cc_final: 0.7949 (mp0) REVERT: C 195 GLN cc_start: 0.6857 (tp-100) cc_final: 0.6410 (pt0) REVERT: C 199 THR cc_start: 0.7582 (p) cc_final: 0.7196 (p) REVERT: D 225 MET cc_start: 0.8384 (mtm) cc_final: 0.8119 (mtm) REVERT: F 415 GLN cc_start: 0.8220 (tt0) cc_final: 0.8002 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2305 time to fit residues: 84.3918 Evaluate side-chains 183 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 185 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078751 restraints weight = 55055.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077817 restraints weight = 39009.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078160 restraints weight = 33725.903| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16096 Z= 0.232 Angle : 0.672 8.995 21898 Z= 0.358 Chirality : 0.045 0.232 2467 Planarity : 0.005 0.073 2926 Dihedral : 5.097 31.927 2328 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2143 helix: 0.65 (0.22), residues: 521 sheet: -0.37 (0.21), residues: 562 loop : -2.02 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 413 HIS 0.005 0.001 HIS D 139 PHE 0.014 0.002 PHE A 802 TYR 0.029 0.002 TYR C 65 ARG 0.007 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 775) hydrogen bonds : angle 5.12783 ( 2408) SS BOND : bond 0.00120 ( 1) SS BOND : angle 3.00352 ( 2) covalent geometry : bond 0.00512 (16095) covalent geometry : angle 0.67148 (21896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7631 (p0) cc_final: 0.7420 (p0) REVERT: A 674 TYR cc_start: 0.5739 (m-10) cc_final: 0.5522 (m-10) REVERT: A 704 ASP cc_start: 0.8357 (p0) cc_final: 0.8099 (p0) REVERT: A 717 GLU cc_start: 0.8278 (mp0) cc_final: 0.7882 (mp0) REVERT: C 195 GLN cc_start: 0.6892 (tp-100) cc_final: 0.6469 (pt0) REVERT: C 199 THR cc_start: 0.7594 (p) cc_final: 0.7191 (p) REVERT: D 225 MET cc_start: 0.8339 (mtm) cc_final: 0.8094 (mtm) REVERT: E 91 LEU cc_start: 0.9429 (tp) cc_final: 0.9200 (tt) REVERT: F 415 GLN cc_start: 0.8252 (tt0) cc_final: 0.7952 (tt0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2298 time to fit residues: 84.6764 Evaluate side-chains 182 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 14 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078273 restraints weight = 55612.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076049 restraints weight = 38703.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076250 restraints weight = 38623.064| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16096 Z= 0.297 Angle : 0.748 9.979 21898 Z= 0.399 Chirality : 0.047 0.207 2467 Planarity : 0.005 0.081 2926 Dihedral : 5.464 33.324 2328 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2143 helix: 0.40 (0.22), residues: 520 sheet: -0.69 (0.20), residues: 595 loop : -2.19 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 413 HIS 0.007 0.001 HIS B 121 PHE 0.018 0.002 PHE A 426 TYR 0.031 0.002 TYR B 60 ARG 0.008 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 775) hydrogen bonds : angle 5.41679 ( 2408) SS BOND : bond 0.00183 ( 1) SS BOND : angle 2.78358 ( 2) covalent geometry : bond 0.00658 (16095) covalent geometry : angle 0.74762 (21896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7728 (p0) cc_final: 0.7457 (p0) REVERT: A 614 ASP cc_start: 0.8105 (t0) cc_final: 0.7815 (t0) REVERT: A 704 ASP cc_start: 0.8414 (p0) cc_final: 0.8177 (p0) REVERT: A 717 GLU cc_start: 0.8395 (mp0) cc_final: 0.8046 (mp0) REVERT: B 189 MET cc_start: 0.7471 (mtm) cc_final: 0.7213 (mtm) REVERT: B 332 LEU cc_start: 0.8012 (mt) cc_final: 0.7582 (tt) REVERT: C 82 ILE cc_start: 0.9104 (mm) cc_final: 0.8840 (tp) REVERT: C 195 GLN cc_start: 0.6836 (tp-100) cc_final: 0.6481 (pt0) REVERT: C 199 THR cc_start: 0.7512 (p) cc_final: 0.7124 (p) REVERT: F 85 GLN cc_start: 0.7651 (tt0) cc_final: 0.7384 (pt0) REVERT: F 268 LEU cc_start: 0.7691 (mt) cc_final: 0.7226 (pp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2281 time to fit residues: 83.3361 Evaluate side-chains 177 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 171 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 205 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 135 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079277 restraints weight = 55178.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077681 restraints weight = 37208.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077921 restraints weight = 39246.652| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16096 Z= 0.186 Angle : 0.673 9.076 21898 Z= 0.355 Chirality : 0.045 0.187 2467 Planarity : 0.004 0.057 2926 Dihedral : 5.132 33.224 2328 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2143 helix: 0.65 (0.23), residues: 520 sheet: -0.48 (0.21), residues: 570 loop : -2.06 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 PHE 0.018 0.002 PHE P1296 TYR 0.018 0.002 TYR D 184 ARG 0.016 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 775) hydrogen bonds : angle 5.11191 ( 2408) SS BOND : bond 0.00109 ( 1) SS BOND : angle 3.33571 ( 2) covalent geometry : bond 0.00413 (16095) covalent geometry : angle 0.67190 (21896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7648 (p0) cc_final: 0.7353 (p0) REVERT: A 369 MET cc_start: 0.8195 (mmm) cc_final: 0.7808 (mmm) REVERT: A 380 ASP cc_start: 0.8202 (p0) cc_final: 0.7971 (p0) REVERT: A 614 ASP cc_start: 0.8060 (t0) cc_final: 0.7757 (t0) REVERT: A 704 ASP cc_start: 0.8290 (p0) cc_final: 0.8089 (p0) REVERT: B 58 ASN cc_start: 0.8306 (m110) cc_final: 0.7558 (p0) REVERT: B 189 MET cc_start: 0.7428 (mtm) cc_final: 0.7205 (mtm) REVERT: B 332 LEU cc_start: 0.8041 (mt) cc_final: 0.7491 (tt) REVERT: C 195 GLN cc_start: 0.6896 (tp-100) cc_final: 0.6048 (tp-100) REVERT: F 85 GLN cc_start: 0.7628 (tt0) cc_final: 0.7190 (pt0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2162 time to fit residues: 83.3212 Evaluate side-chains 178 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 122 optimal weight: 40.0000 chunk 32 optimal weight: 0.7980 overall best weight: 3.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079589 restraints weight = 55286.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077805 restraints weight = 40711.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078118 restraints weight = 37982.988| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16096 Z= 0.191 Angle : 0.667 9.190 21898 Z= 0.353 Chirality : 0.045 0.217 2467 Planarity : 0.005 0.066 2926 Dihedral : 5.063 32.754 2328 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2143 helix: 0.69 (0.23), residues: 520 sheet: -0.45 (0.21), residues: 565 loop : -2.02 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 PHE 0.015 0.002 PHE A 718 TYR 0.022 0.002 TYR D 184 ARG 0.006 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 775) hydrogen bonds : angle 5.07088 ( 2408) SS BOND : bond 0.00120 ( 1) SS BOND : angle 3.50794 ( 2) covalent geometry : bond 0.00426 (16095) covalent geometry : angle 0.66668 (21896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7656 (p0) cc_final: 0.7378 (p0) REVERT: A 380 ASP cc_start: 0.8224 (p0) cc_final: 0.7981 (p0) REVERT: A 614 ASP cc_start: 0.8091 (t0) cc_final: 0.7675 (t0) REVERT: B 58 ASN cc_start: 0.8338 (m110) cc_final: 0.7550 (p0) REVERT: B 332 LEU cc_start: 0.8043 (mt) cc_final: 0.7453 (tt) REVERT: C 195 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6139 (tp-100) REVERT: E 91 LEU cc_start: 0.9394 (tp) cc_final: 0.8981 (tt) REVERT: F 85 GLN cc_start: 0.7652 (tt0) cc_final: 0.7216 (pt0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2109 time to fit residues: 77.2220 Evaluate side-chains 184 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079931 restraints weight = 54828.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079336 restraints weight = 33810.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079621 restraints weight = 27713.010| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16096 Z= 0.119 Angle : 0.626 8.489 21898 Z= 0.327 Chirality : 0.044 0.213 2467 Planarity : 0.004 0.067 2926 Dihedral : 4.681 32.620 2328 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2143 helix: 1.03 (0.23), residues: 513 sheet: -0.21 (0.21), residues: 559 loop : -1.79 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 PHE 0.015 0.001 PHE A 67 TYR 0.020 0.001 TYR A 522 ARG 0.005 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 775) hydrogen bonds : angle 4.75151 ( 2408) SS BOND : bond 0.00111 ( 1) SS BOND : angle 3.36844 ( 2) covalent geometry : bond 0.00262 (16095) covalent geometry : angle 0.62529 (21896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6749.42 seconds wall clock time: 119 minutes 30.26 seconds (7170.26 seconds total)