Starting phenix.real_space_refine on Sun Aug 24 00:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q0g_18053/08_2025/8q0g_18053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q0g_18053/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q0g_18053/08_2025/8q0g_18053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q0g_18053/08_2025/8q0g_18053_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q0g_18053/08_2025/8q0g_18053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q0g_18053/08_2025/8q0g_18053.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 6, 'GLU:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'TYR:plan': 4} 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: {'ARG:plan': 1, 'GLN:plan1': 2, '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: {'GLU:plan': 15, 'ARG:plan': 12, 'PHE:plan': 13, 'ASP:plan': 24, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 8, 'GLN:plan1': 5} 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: {'GLU:plan': 15, 'ARG:plan': 12, 'PHE:plan': 13, 'ASP:plan': 24, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 8, 'GLN:plan1': 5} 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: 3.84, per 1000 atoms: 0.24 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: 1.16 Conformation dependent library (CDL) restraints added in 885.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.59 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: 3.09 Time building geometry restraints manager: 1.54 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: 1.800 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: 0.360 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- 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 : 15.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG F 260 TYR 0.018 0.002 TYR D 222 PHE 0.023 0.002 PHE A 663 TRP 0.017 0.002 TRP D 48 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00488 (16095) covalent geometry : angle 0.70859 (21896) SS BOND : bond 0.00147 ( 1) SS BOND : angle 2.26213 ( 2) hydrogen bonds : bond 0.14541 ( 775) hydrogen bonds : angle 6.48663 ( 2408) *********************** 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 : 0.451 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: 0.0851 time to fit residues: 32.3590 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 : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080519 restraints weight = 54835.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078638 restraints weight = 41839.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078732 restraints weight = 41530.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078913 restraints weight = 36109.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079148 restraints weight = 29940.180| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16096 Z= 0.208 Angle : 0.648 9.471 21898 Z= 0.349 Chirality : 0.044 0.189 2467 Planarity : 0.005 0.051 2926 Dihedral : 4.902 28.314 2328 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.40 % Allowed : 6.44 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 2143 helix: 0.62 (0.22), residues: 523 sheet: -0.57 (0.20), residues: 629 loop : -1.81 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 260 TYR 0.017 0.002 TYR D 184 PHE 0.018 0.002 PHE A 426 TRP 0.011 0.002 TRP F 413 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00455 (16095) covalent geometry : angle 0.64795 (21896) SS BOND : bond 0.00115 ( 1) SS BOND : angle 2.78254 ( 2) hydrogen bonds : bond 0.04454 ( 775) hydrogen bonds : angle 5.42530 ( 2408) *********************** 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 244 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: C 82 ILE cc_start: 0.9074 (mm) cc_final: 0.8736 (tp) REVERT: C 195 GLN cc_start: 0.7051 (tp-100) cc_final: 0.6260 (tp-100) REVERT: F 415 GLN cc_start: 0.8188 (tt0) cc_final: 0.7844 (tt0) outliers start: 6 outliers final: 3 residues processed: 243 average time/residue: 0.0979 time to fit residues: 38.1145 Evaluate side-chains 194 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 11 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 201 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080587 restraints weight = 55660.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.079374 restraints weight = 43758.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078953 restraints weight = 44926.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079320 restraints weight = 36856.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079946 restraints weight = 29767.616| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16096 Z= 0.233 Angle : 0.659 8.224 21898 Z= 0.354 Chirality : 0.045 0.186 2467 Planarity : 0.005 0.054 2926 Dihedral : 5.016 32.201 2328 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 2143 helix: 0.55 (0.22), residues: 523 sheet: -0.64 (0.20), residues: 618 loop : -1.91 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 148 TYR 0.018 0.002 TYR B 60 PHE 0.019 0.002 PHE A 426 TRP 0.019 0.002 TRP F 233 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00514 (16095) covalent geometry : angle 0.65905 (21896) SS BOND : bond 0.00014 ( 1) SS BOND : angle 2.09739 ( 2) hydrogen bonds : bond 0.04207 ( 775) hydrogen bonds : angle 5.32291 ( 2408) *********************** 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 247 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.8518 (t) cc_final: 0.8268 (t) REVERT: A 304 MET cc_start: 0.7731 (ttt) cc_final: 0.7477 (ttt) REVERT: A 368 GLU cc_start: 0.8251 (mp0) cc_final: 0.7886 (mp0) REVERT: A 380 ASP cc_start: 0.8197 (p0) cc_final: 0.7974 (p0) REVERT: A 595 LEU cc_start: 0.8764 (tt) cc_final: 0.8528 (tt) REVERT: C 195 GLN cc_start: 0.7082 (tp-100) cc_final: 0.6243 (tp-100) REVERT: F 400 MET cc_start: 0.5116 (tpt) cc_final: 0.4838 (tpt) REVERT: F 415 GLN cc_start: 0.8177 (tt0) cc_final: 0.7954 (tt0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1036 time to fit residues: 40.2916 Evaluate side-chains 188 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 194 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 190 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080946 restraints weight = 55172.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079237 restraints weight = 41901.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079605 restraints weight = 36784.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079862 restraints weight = 30472.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079937 restraints weight = 27245.994| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16096 Z= 0.175 Angle : 0.633 8.003 21898 Z= 0.334 Chirality : 0.044 0.186 2467 Planarity : 0.005 0.052 2926 Dihedral : 4.853 33.469 2328 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2143 helix: 0.68 (0.22), residues: 521 sheet: -0.36 (0.20), residues: 596 loop : -1.93 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 547 TYR 0.020 0.002 TYR A 522 PHE 0.014 0.002 PHE A 426 TRP 0.013 0.002 TRP F 413 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00386 (16095) covalent geometry : angle 0.63195 (21896) SS BOND : bond 0.00050 ( 1) SS BOND : angle 2.85358 ( 2) hydrogen bonds : bond 0.03788 ( 775) hydrogen bonds : angle 5.06031 ( 2408) *********************** 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 248 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8539 (t) cc_final: 0.8284 (t) REVERT: A 368 GLU cc_start: 0.8327 (mp0) cc_final: 0.8000 (mp0) REVERT: A 380 ASP cc_start: 0.8300 (p0) cc_final: 0.8046 (p0) REVERT: A 674 TYR cc_start: 0.5825 (m-10) cc_final: 0.5546 (m-10) REVERT: A 704 ASP cc_start: 0.8023 (p0) cc_final: 0.7774 (p0) REVERT: B 70 ASN cc_start: 0.8246 (m-40) cc_final: 0.8019 (t0) REVERT: C 82 ILE cc_start: 0.9064 (mm) cc_final: 0.8772 (tp) REVERT: C 195 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6047 (tp-100) REVERT: E 91 LEU cc_start: 0.9391 (tp) cc_final: 0.9173 (tt) REVERT: F 26 ASP cc_start: 0.1028 (t70) cc_final: 0.0415 (t70) REVERT: F 415 GLN cc_start: 0.8140 (tt0) cc_final: 0.7914 (tt0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1099 time to fit residues: 42.7579 Evaluate side-chains 190 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 3 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 105 optimal weight: 0.0270 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 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 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** ** 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 = 0.3730 r_free = 0.3730 target = 0.105852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079871 restraints weight = 54791.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078944 restraints weight = 43159.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079209 restraints weight = 32509.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079429 restraints weight = 27273.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079596 restraints weight = 25435.402| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 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 = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1755 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= 0.170 Angle : 0.627 8.269 21898 Z= 0.332 Chirality : 0.044 0.158 2467 Planarity : 0.004 0.052 2926 Dihedral : 4.798 33.582 2328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.94 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2143 helix: 0.71 (0.22), residues: 521 sheet: -0.22 (0.21), residues: 583 loop : -1.93 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 370 TYR 0.017 0.001 TYR D 184 PHE 0.016 0.002 PHE A 426 TRP 0.013 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00378 (16095) covalent geometry : angle 0.62662 (21896) SS BOND : bond 0.00126 ( 1) SS BOND : angle 3.12871 ( 2) hydrogen bonds : bond 0.03673 ( 775) hydrogen bonds : angle 4.94482 ( 2408) *********************** 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 252 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.8549 (t) cc_final: 0.8312 (t) REVERT: A 368 GLU cc_start: 0.8162 (mp0) cc_final: 0.7914 (mp0) REVERT: A 674 TYR cc_start: 0.5692 (m-10) cc_final: 0.5466 (m-10) REVERT: A 704 ASP cc_start: 0.8089 (p0) cc_final: 0.7617 (p0) REVERT: B 70 ASN cc_start: 0.8224 (m-40) cc_final: 0.7999 (t0) REVERT: C 195 GLN cc_start: 0.6926 (tp-100) cc_final: 0.6417 (pt0) REVERT: C 199 THR cc_start: 0.7582 (p) cc_final: 0.7188 (p) REVERT: E 91 LEU cc_start: 0.9393 (tp) cc_final: 0.9174 (tt) REVERT: F 409 GLU cc_start: 0.8391 (tp30) cc_final: 0.8036 (tp30) REVERT: F 415 GLN cc_start: 0.8176 (tt0) cc_final: 0.7946 (tt0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1044 time to fit residues: 41.1773 Evaluate side-chains 192 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 188 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 12 optimal weight: 0.0870 chunk 139 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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 264 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 403 ASN ** 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 = 0.3715 r_free = 0.3715 target = 0.105103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080385 restraints weight = 55099.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078594 restraints weight = 41951.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078779 restraints weight = 39398.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079090 restraints weight = 30430.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079518 restraints weight = 27261.305| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 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 = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16096 Z= 0.208 Angle : 0.654 8.898 21898 Z= 0.349 Chirality : 0.045 0.309 2467 Planarity : 0.005 0.055 2926 Dihedral : 4.919 33.079 2328 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2143 helix: 0.66 (0.23), residues: 522 sheet: -0.23 (0.21), residues: 572 loop : -1.99 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 148 TYR 0.022 0.002 TYR C 65 PHE 0.015 0.002 PHE D 64 TRP 0.023 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00462 (16095) covalent geometry : angle 0.65339 (21896) SS BOND : bond 0.00025 ( 1) SS BOND : angle 3.01377 ( 2) hydrogen bonds : bond 0.03839 ( 775) hydrogen bonds : angle 5.03508 ( 2408) *********************** 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 239 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8538 (t) cc_final: 0.8277 (t) REVERT: A 368 GLU cc_start: 0.8279 (mp0) cc_final: 0.7904 (mp0) REVERT: A 380 ASP cc_start: 0.8006 (p0) cc_final: 0.7337 (t0) REVERT: A 674 TYR cc_start: 0.5692 (m-10) cc_final: 0.5487 (m-10) REVERT: A 704 ASP cc_start: 0.8038 (p0) cc_final: 0.7678 (p0) REVERT: B 70 ASN cc_start: 0.8245 (m-40) cc_final: 0.8030 (t0) REVERT: C 82 ILE cc_start: 0.9089 (mm) cc_final: 0.8780 (tp) REVERT: C 195 GLN cc_start: 0.6912 (tp-100) cc_final: 0.6445 (pt0) REVERT: C 199 THR cc_start: 0.7596 (p) cc_final: 0.7217 (p) REVERT: E 91 LEU cc_start: 0.9386 (tp) cc_final: 0.9162 (tt) REVERT: F 409 GLU cc_start: 0.8405 (tp30) cc_final: 0.8169 (tp30) REVERT: F 415 GLN cc_start: 0.8212 (tt0) cc_final: 0.7987 (tt0) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0936 time to fit residues: 35.4609 Evaluate side-chains 187 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 0.0070 chunk 19 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 209 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** 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** ** F 403 ASN ** 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 = 0.3720 r_free = 0.3720 target = 0.105447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080300 restraints weight = 54694.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078722 restraints weight = 43419.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078993 restraints weight = 40419.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.079273 restraints weight = 31834.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079389 restraints weight = 28640.561| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16096 Z= 0.180 Angle : 0.636 9.396 21898 Z= 0.337 Chirality : 0.044 0.244 2467 Planarity : 0.004 0.053 2926 Dihedral : 4.847 32.319 2328 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.18), residues: 2143 helix: 0.77 (0.23), residues: 521 sheet: -0.23 (0.21), residues: 561 loop : -1.94 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 370 TYR 0.018 0.002 TYR D 184 PHE 0.014 0.002 PHE A 426 TRP 0.018 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00399 (16095) covalent geometry : angle 0.63591 (21896) SS BOND : bond 0.00000 ( 1) SS BOND : angle 2.84121 ( 2) hydrogen bonds : bond 0.03688 ( 775) hydrogen bonds : angle 4.93873 ( 2408) *********************** 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 242 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8556 (t) cc_final: 0.8316 (t) REVERT: A 358 ASP cc_start: 0.7608 (p0) cc_final: 0.7402 (p0) REVERT: A 368 GLU cc_start: 0.8312 (mp0) cc_final: 0.7930 (mp0) REVERT: A 380 ASP cc_start: 0.8152 (p0) cc_final: 0.7430 (t0) REVERT: A 704 ASP cc_start: 0.8059 (p0) cc_final: 0.7828 (p0) REVERT: B 70 ASN cc_start: 0.8270 (m-40) cc_final: 0.8056 (t0) REVERT: C 195 GLN cc_start: 0.6886 (tp-100) cc_final: 0.6460 (pt0) REVERT: C 199 THR cc_start: 0.7559 (p) cc_final: 0.7157 (p) REVERT: E 91 LEU cc_start: 0.9388 (tp) cc_final: 0.9157 (tt) REVERT: F 409 GLU cc_start: 0.8447 (tp30) cc_final: 0.8175 (tp30) REVERT: F 415 GLN cc_start: 0.8236 (tt0) cc_final: 0.7933 (tt0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0982 time to fit residues: 38.1828 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 : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 158 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 104 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.106285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079851 restraints weight = 54687.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079580 restraints weight = 36897.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079812 restraints weight = 27992.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080020 restraints weight = 24161.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080138 restraints weight = 22231.315| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 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 = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2221 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= 0.143 Angle : 0.623 8.639 21898 Z= 0.329 Chirality : 0.044 0.236 2467 Planarity : 0.004 0.058 2926 Dihedral : 4.668 31.344 2328 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.18), residues: 2143 helix: 0.91 (0.23), residues: 521 sheet: -0.16 (0.21), residues: 573 loop : -1.85 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.019 0.002 TYR C 65 PHE 0.012 0.001 PHE A 802 TRP 0.020 0.001 TRP F 413 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00319 (16095) covalent geometry : angle 0.62297 (21896) SS BOND : bond 0.00032 ( 1) SS BOND : angle 2.66163 ( 2) hydrogen bonds : bond 0.03509 ( 775) hydrogen bonds : angle 4.83851 ( 2408) *********************** 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 257 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8538 (t) cc_final: 0.8275 (t) REVERT: A 358 ASP cc_start: 0.7603 (p0) cc_final: 0.7316 (p0) REVERT: A 368 GLU cc_start: 0.8303 (mp0) cc_final: 0.7886 (mp0) REVERT: A 369 MET cc_start: 0.8149 (mmm) cc_final: 0.7882 (mmm) REVERT: B 70 ASN cc_start: 0.8272 (m-40) cc_final: 0.8039 (t0) REVERT: C 195 GLN cc_start: 0.6860 (tp-100) cc_final: 0.6440 (pt0) REVERT: C 199 THR cc_start: 0.7493 (p) cc_final: 0.7120 (p) REVERT: E 91 LEU cc_start: 0.9381 (tp) cc_final: 0.9150 (tt) REVERT: F 409 GLU cc_start: 0.8472 (tp30) cc_final: 0.8232 (tp30) REVERT: F 415 GLN cc_start: 0.8232 (tt0) cc_final: 0.7988 (tt0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.0890 time to fit residues: 37.4979 Evaluate side-chains 195 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 209 optimal weight: 40.0000 chunk 189 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 0.0470 chunk 210 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 104 ASN ** 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 = 0.3714 r_free = 0.3714 target = 0.105009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079215 restraints weight = 54932.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077586 restraints weight = 35095.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078142 restraints weight = 32400.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078315 restraints weight = 25187.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078424 restraints weight = 23497.968| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16096 Z= 0.191 Angle : 0.658 9.200 21898 Z= 0.347 Chirality : 0.045 0.231 2467 Planarity : 0.005 0.054 2926 Dihedral : 4.824 34.017 2328 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 2143 helix: 0.90 (0.23), residues: 519 sheet: -0.17 (0.21), residues: 570 loop : -1.87 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 243 TYR 0.019 0.002 TYR D 184 PHE 0.013 0.002 PHE A 802 TRP 0.020 0.002 TRP A 546 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00424 (16095) covalent geometry : angle 0.65727 (21896) SS BOND : bond 0.00912 ( 1) SS BOND : angle 3.18599 ( 2) hydrogen bonds : bond 0.03749 ( 775) hydrogen bonds : angle 4.88694 ( 2408) *********************** 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 243 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8577 (t) cc_final: 0.8365 (t) REVERT: A 358 ASP cc_start: 0.7659 (p0) cc_final: 0.7389 (p0) REVERT: A 368 GLU cc_start: 0.8315 (mp0) cc_final: 0.7907 (mp0) REVERT: A 614 ASP cc_start: 0.7964 (t0) cc_final: 0.7704 (t0) REVERT: A 724 PHE cc_start: 0.6771 (m-10) cc_final: 0.6509 (m-80) REVERT: B 70 ASN cc_start: 0.8305 (m-40) cc_final: 0.8075 (t0) REVERT: C 195 GLN cc_start: 0.6945 (tp-100) cc_final: 0.6562 (pt0) REVERT: C 199 THR cc_start: 0.7526 (p) cc_final: 0.7155 (p) REVERT: E 91 LEU cc_start: 0.9398 (tp) cc_final: 0.9178 (tt) REVERT: F 409 GLU cc_start: 0.8480 (tp30) cc_final: 0.8226 (tp30) REVERT: F 415 GLN cc_start: 0.8223 (tt0) cc_final: 0.7959 (tt0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0919 time to fit residues: 36.6445 Evaluate side-chains 190 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 30.0000 chunk 156 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 120 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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** D 30 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.105477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079221 restraints weight = 54882.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079055 restraints weight = 36631.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079285 restraints weight = 27624.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079537 restraints weight = 24252.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079601 restraints weight = 22117.453| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 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 = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16096 Z= 0.163 Angle : 0.646 8.912 21898 Z= 0.338 Chirality : 0.044 0.234 2467 Planarity : 0.004 0.054 2926 Dihedral : 4.740 32.415 2328 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.18), residues: 2143 helix: 0.93 (0.23), residues: 520 sheet: -0.20 (0.21), residues: 569 loop : -1.84 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.024 0.002 TYR D 184 PHE 0.013 0.002 PHE A 802 TRP 0.023 0.002 TRP A 546 HIS 0.004 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00363 (16095) covalent geometry : angle 0.64541 (21896) SS BOND : bond 0.00297 ( 1) SS BOND : angle 3.58167 ( 2) hydrogen bonds : bond 0.03605 ( 775) hydrogen bonds : angle 4.82629 ( 2408) ********************** 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 243 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 274 SER cc_start: 0.8579 (t) cc_final: 0.8336 (t) REVERT: A 358 ASP cc_start: 0.7609 (p0) cc_final: 0.7301 (p0) REVERT: A 368 GLU cc_start: 0.8345 (mp0) cc_final: 0.7936 (mp0) REVERT: A 369 MET cc_start: 0.8157 (mmm) cc_final: 0.7872 (mmm) REVERT: A 380 ASP cc_start: 0.8164 (p0) cc_final: 0.7898 (p0) REVERT: A 614 ASP cc_start: 0.7979 (t0) cc_final: 0.7672 (t0) REVERT: A 724 PHE cc_start: 0.6766 (m-10) cc_final: 0.6518 (m-80) REVERT: C 195 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6583 (pt0) REVERT: C 199 THR cc_start: 0.7555 (p) cc_final: 0.7175 (p) REVERT: E 91 LEU cc_start: 0.9389 (tp) cc_final: 0.9172 (tt) REVERT: F 409 GLU cc_start: 0.8533 (tp30) cc_final: 0.8303 (tp30) REVERT: F 415 GLN cc_start: 0.8249 (tt0) cc_final: 0.7954 (tt0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0914 time to fit residues: 35.8702 Evaluate side-chains 195 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 189 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 0.0060 chunk 177 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.4014 ------------------------------------------------------------------------------- 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 104 ASN ** 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 = 0.106645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079734 restraints weight = 54630.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078843 restraints weight = 34886.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079320 restraints weight = 27365.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079473 restraints weight = 24295.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079549 restraints weight = 22242.176| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16096 Z= 0.120 Angle : 0.620 8.610 21898 Z= 0.323 Chirality : 0.044 0.234 2467 Planarity : 0.004 0.056 2926 Dihedral : 4.512 31.874 2328 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.18), residues: 2143 helix: 1.04 (0.23), residues: 520 sheet: -0.09 (0.21), residues: 576 loop : -1.72 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 120 TYR 0.021 0.001 TYR D 184 PHE 0.012 0.001 PHE A 802 TRP 0.023 0.001 TRP F 413 HIS 0.004 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00265 (16095) covalent geometry : angle 0.61943 (21896) SS BOND : bond 0.00210 ( 1) SS BOND : angle 3.35961 ( 2) hydrogen bonds : bond 0.03322 ( 775) hydrogen bonds : angle 4.64171 ( 2408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.07 seconds wall clock time: 46 minutes 9.14 seconds (2769.14 seconds total)