Starting phenix.real_space_refine on Mon Nov 18 06:55:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0g_18053/11_2024/8q0g_18053_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 9871 2.51 5 N 2790 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15819 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6041 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2784 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain: "C" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1090 Classifications: {'peptide': 174} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 63} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 181 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "F" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1920 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 1520 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 1515 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 218} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 845 Unresolved non-hydrogen angles: 1089 Unresolved non-hydrogen dihedrals: 722 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 Conformer: "B" Number of residues, atoms: 299, 1515 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 218} Link IDs: {'PTRANS': 2, 'TRANS': 296} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 845 Unresolved non-hydrogen angles: 1089 Unresolved non-hydrogen dihedrals: 722 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 509 bond proxies already assigned to first conformer: 1512 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR P1150 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTYR P1150 " occ=0.50 Time building chain proxies: 9.97, per 1000 atoms: 0.63 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: 5.43 Conformation dependent library (CDL) restraints added in 3.9 seconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 26.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.523A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 removed outlier: 3.531A pdb=" N PHE A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.664A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.761A pdb=" N SER A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.804A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.908A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.765A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 4.077A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.992A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.507A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.615A pdb=" N LEU C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Proline residue: C 118 - end of helix Processing helix chain 'C' and resid 191 through 210 removed outlier: 3.981A pdb=" N MET C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.669A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 4.378A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.969A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.827A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.662A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 Processing helix chain 'F' and resid 65 through 86 removed outlier: 4.310A pdb=" N GLY F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.293A pdb=" N LYS F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 150 removed outlier: 3.919A pdb=" N GLN F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 134 " --> pdb=" O ASN F 130 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET F 136 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.549A pdb=" N SER F 159 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 209 removed outlier: 3.807A pdb=" N GLU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER F 197 " --> pdb=" O ASN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.845A pdb=" N LEU F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.761A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 396 through 420 removed outlier: 4.152A pdb=" N ARG F 404 " --> pdb=" O MET F 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1022 Processing helix chain 'P' and resid 1136 through 1139 removed outlier: 4.210A pdb=" N LEU P1139 " --> pdb=" O PHE P1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1136 through 1139' Processing helix chain 'P' and resid 1185 through 1189 Processing helix chain 'P' and resid 1282 through 1287 removed outlier: 4.177A pdb=" N TYR P1286 " --> pdb=" O ALA P1282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.660A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 7.548A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.796A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 256 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.633A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 271 removed outlier: 7.633A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.049A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.753A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 428 " --> pdb=" O PHE P1296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.779A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 700 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.637A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.152A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 111 through 118 removed outlier: 3.690A pdb=" N GLY B 125 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 115 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 123 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 117 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 126 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.012A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.390A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 7.292A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.287A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 4.150A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.322A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'F' and resid 36 through 38 removed outlier: 6.525A pdb=" N VAL F 37 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 234 removed outlier: 5.706A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS F 269 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 1040 through 1051 removed outlier: 4.106A pdb=" N THR P1080 " --> pdb=" O LYS P1069 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL P1103 " --> pdb=" O HIS P1127 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS P1147 " --> pdb=" O SER P1179 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER P1179 " --> pdb=" O HIS P1147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 1040 through 1051 removed outlier: 4.106A pdb=" N THR P1080 " --> pdb=" O LYS P1069 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL P1103 " --> pdb=" O HIS P1127 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS P1147 " --> pdb=" O SER P1179 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER P1179 " --> pdb=" O HIS P1147 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY P1204 " --> pdb=" O ASP P1232 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP P1232 " --> pdb=" O GLY P1204 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR P1206 " --> pdb=" O GLN P1230 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN P1230 " --> pdb=" O THR P1206 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL P1208 " --> pdb=" O GLY P1228 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY P1228 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL P1210 " --> pdb=" O GLY P1226 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY P1226 " --> pdb=" O VAL P1210 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 1194 through 1195 862 hydrogen bonds defined for protein. 2408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 6.00 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: 7.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.940 ------------------------------------------------------------------------------- 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 16095 Z= 0.324 Angle : 0.709 10.630 21896 Z= 0.391 Chirality : 0.046 0.251 2467 Planarity : 0.005 0.063 2926 Dihedral : 13.480 89.539 5582 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.45 % Rotamer: Outliers : 0.13 % Allowed : 0.86 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2143 helix: 0.50 (0.23), residues: 506 sheet: -0.66 (0.20), residues: 622 loop : -1.72 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 48 HIS 0.004 0.001 HIS A 196 PHE 0.023 0.002 PHE A 663 TYR 0.018 0.002 TYR D 222 ARG 0.010 0.001 ARG F 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 1.900 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: 0.2445 time to fit residues: 91.3372 Evaluate side-chains 189 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 0.0370 chunk 109 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 194 optimal weight: 30.0000 overall best weight: 6.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16095 Z= 0.459 Angle : 0.740 9.369 21896 Z= 0.399 Chirality : 0.047 0.183 2467 Planarity : 0.006 0.053 2926 Dihedral : 5.380 31.110 2328 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.46 % Allowed : 8.96 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2143 helix: 0.28 (0.22), residues: 523 sheet: -0.65 (0.20), residues: 601 loop : -2.05 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 205 HIS 0.007 0.002 HIS A 196 PHE 0.022 0.002 PHE A 426 TYR 0.021 0.002 TYR B 60 ARG 0.008 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.6216 (m-10) cc_final: 0.5791 (m-10) REVERT: A 704 ASP cc_start: 0.7921 (p0) cc_final: 0.7450 (p0) REVERT: B 367 PHE cc_start: 0.7210 (m-10) cc_final: 0.6949 (m-10) REVERT: C 82 ILE cc_start: 0.9119 (mm) cc_final: 0.8865 (tp) REVERT: C 195 GLN cc_start: 0.7037 (tp-100) cc_final: 0.6198 (tp-100) REVERT: F 415 GLN cc_start: 0.8187 (tt0) cc_final: 0.7870 (tt0) outliers start: 7 outliers final: 4 residues processed: 238 average time/residue: 0.2382 time to fit residues: 91.0744 Evaluate side-chains 195 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 194 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 276 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16095 Z= 0.312 Angle : 0.653 8.316 21896 Z= 0.350 Chirality : 0.045 0.194 2467 Planarity : 0.005 0.052 2926 Dihedral : 5.107 31.670 2328 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2143 helix: 0.41 (0.22), residues: 522 sheet: -0.73 (0.20), residues: 618 loop : -2.00 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 233 HIS 0.004 0.001 HIS D 139 PHE 0.019 0.002 PHE A 426 TYR 0.028 0.002 TYR C 65 ARG 0.007 0.001 ARG F 148 *********************** 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 248 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.8446 (t) cc_final: 0.8202 (t) REVERT: A 368 GLU cc_start: 0.8006 (mp0) cc_final: 0.7676 (mp0) REVERT: A 380 ASP cc_start: 0.7848 (p0) cc_final: 0.7228 (t0) REVERT: A 614 ASP cc_start: 0.7832 (t0) cc_final: 0.7494 (t0) REVERT: A 674 TYR cc_start: 0.6105 (m-10) cc_final: 0.5767 (m-10) REVERT: A 704 ASP cc_start: 0.7850 (p0) cc_final: 0.7364 (p0) REVERT: C 195 GLN cc_start: 0.7096 (tp-100) cc_final: 0.6211 (tp-100) REVERT: F 400 MET cc_start: 0.4621 (tpt) cc_final: 0.4326 (tpt) REVERT: F 415 GLN cc_start: 0.8153 (tt0) cc_final: 0.7803 (tt0) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2431 time to fit residues: 94.8019 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 : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 50.0000 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 HIS ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16095 Z= 0.221 Angle : 0.617 7.963 21896 Z= 0.326 Chirality : 0.044 0.157 2467 Planarity : 0.004 0.053 2926 Dihedral : 4.840 33.943 2328 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2143 helix: 0.68 (0.22), residues: 520 sheet: -0.49 (0.21), residues: 589 loop : -1.92 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 PHE 0.015 0.001 PHE A 426 TYR 0.017 0.001 TYR D 184 ARG 0.010 0.001 ARG A 547 *********************** 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 247 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.7882 (mp0) cc_final: 0.7619 (mp0) REVERT: A 372 MET cc_start: 0.8135 (mmm) cc_final: 0.7870 (mmm) REVERT: C 195 GLN cc_start: 0.6951 (tp-100) cc_final: 0.6059 (tp-100) REVERT: E 91 LEU cc_start: 0.9342 (tp) cc_final: 0.9105 (tt) REVERT: F 26 ASP cc_start: 0.0586 (t70) cc_final: 0.0015 (t70) REVERT: F 415 GLN cc_start: 0.8145 (tt0) cc_final: 0.7887 (tt0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2727 time to fit residues: 105.8358 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 : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 264 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16095 Z= 0.344 Angle : 0.676 8.861 21896 Z= 0.361 Chirality : 0.046 0.300 2467 Planarity : 0.005 0.057 2926 Dihedral : 5.093 33.630 2328 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2143 helix: 0.51 (0.22), residues: 523 sheet: -0.37 (0.21), residues: 561 loop : -2.04 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 413 HIS 0.004 0.001 HIS B 64 PHE 0.016 0.002 PHE A 426 TYR 0.021 0.002 TYR B 60 ARG 0.007 0.001 ARG A 233 *********************** 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 233 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8053 (mp0) cc_final: 0.7741 (mp0) REVERT: A 380 ASP cc_start: 0.7848 (p0) cc_final: 0.7626 (p0) REVERT: C 195 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6530 (pt0) REVERT: C 199 THR cc_start: 0.7589 (p) cc_final: 0.7190 (p) REVERT: E 91 LEU cc_start: 0.9344 (tp) cc_final: 0.9126 (tt) REVERT: F 415 GLN cc_start: 0.8160 (tt0) cc_final: 0.7845 (tt0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2391 time to fit residues: 88.3830 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 : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.0060 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16095 Z= 0.289 Angle : 0.647 8.829 21896 Z= 0.346 Chirality : 0.045 0.259 2467 Planarity : 0.005 0.058 2926 Dihedral : 5.006 33.573 2328 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2143 helix: 0.60 (0.22), residues: 522 sheet: -0.47 (0.21), residues: 585 loop : -2.05 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 PHE 0.015 0.002 PHE A 426 TYR 0.018 0.002 TYR D 184 ARG 0.010 0.001 ARG F 148 *********************** 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 235 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7535 (p0) cc_final: 0.7293 (p0) REVERT: A 368 GLU cc_start: 0.8078 (mp0) cc_final: 0.7733 (mp0) REVERT: A 380 ASP cc_start: 0.7895 (p0) cc_final: 0.7604 (p0) REVERT: B 332 LEU cc_start: 0.7997 (mt) cc_final: 0.7419 (tt) REVERT: C 195 GLN cc_start: 0.6941 (tp-100) cc_final: 0.6505 (pt0) REVERT: C 199 THR cc_start: 0.7578 (p) cc_final: 0.7165 (p) REVERT: D 227 MET cc_start: 0.7750 (ptp) cc_final: 0.7549 (mtm) REVERT: E 91 LEU cc_start: 0.9334 (tp) cc_final: 0.9108 (tt) REVERT: F 409 GLU cc_start: 0.8377 (tp30) cc_final: 0.8135 (tp30) REVERT: F 415 GLN cc_start: 0.8208 (tt0) cc_final: 0.7894 (tt0) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2495 time to fit residues: 90.7246 Evaluate side-chains 184 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 206 optimal weight: 0.0770 chunk 129 optimal weight: 7.9990 chunk 125 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 overall best weight: 3.3942 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16095 Z= 0.270 Angle : 0.640 8.900 21896 Z= 0.340 Chirality : 0.044 0.212 2467 Planarity : 0.005 0.056 2926 Dihedral : 4.937 33.809 2328 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2143 helix: 0.73 (0.23), residues: 520 sheet: -0.33 (0.21), residues: 551 loop : -1.98 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 413 HIS 0.004 0.001 HIS D 139 PHE 0.012 0.002 PHE A 426 TYR 0.019 0.002 TYR C 65 ARG 0.004 0.000 ARG B 243 *********************** 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 : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7478 (p0) cc_final: 0.7258 (p0) REVERT: A 368 GLU cc_start: 0.8113 (mp0) cc_final: 0.7770 (mp0) REVERT: A 380 ASP cc_start: 0.7945 (p0) cc_final: 0.7658 (p0) REVERT: B 332 LEU cc_start: 0.8026 (mt) cc_final: 0.7440 (tt) REVERT: C 195 GLN cc_start: 0.6953 (tp-100) cc_final: 0.6529 (pt0) REVERT: C 199 THR cc_start: 0.7551 (p) cc_final: 0.7134 (p) REVERT: E 91 LEU cc_start: 0.9310 (tp) cc_final: 0.9085 (tt) REVERT: F 409 GLU cc_start: 0.8379 (tp30) cc_final: 0.8136 (tp30) REVERT: F 415 GLN cc_start: 0.8196 (tt0) cc_final: 0.7867 (tt0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2313 time to fit residues: 90.1111 Evaluate side-chains 191 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 50.0000 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16095 Z= 0.193 Angle : 0.624 8.631 21896 Z= 0.326 Chirality : 0.044 0.234 2467 Planarity : 0.004 0.062 2926 Dihedral : 4.702 32.905 2328 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2143 helix: 0.95 (0.23), residues: 519 sheet: -0.21 (0.21), residues: 571 loop : -1.86 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 PHE 0.011 0.001 PHE A 802 TYR 0.018 0.001 TYR D 184 ARG 0.004 0.000 ARG A 547 *********************** 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 252 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7450 (p0) cc_final: 0.7186 (p0) REVERT: A 368 GLU cc_start: 0.8026 (mp0) cc_final: 0.7766 (mp0) REVERT: A 380 ASP cc_start: 0.7911 (p0) cc_final: 0.7589 (p0) REVERT: B 58 ASN cc_start: 0.8209 (m110) cc_final: 0.7556 (p0) REVERT: B 189 MET cc_start: 0.7521 (mtm) cc_final: 0.7319 (mtm) REVERT: B 250 THR cc_start: 0.9061 (p) cc_final: 0.8858 (p) REVERT: B 332 LEU cc_start: 0.7976 (mt) cc_final: 0.7374 (tt) REVERT: C 195 GLN cc_start: 0.6893 (tp-100) cc_final: 0.6015 (tp-100) REVERT: E 91 LEU cc_start: 0.9294 (tp) cc_final: 0.9050 (tt) REVERT: F 409 GLU cc_start: 0.8403 (tp30) cc_final: 0.8186 (tp30) REVERT: F 415 GLN cc_start: 0.8200 (tt0) cc_final: 0.7940 (tt0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2359 time to fit residues: 95.7942 Evaluate side-chains 200 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 40.0000 chunk 180 optimal weight: 6.9990 chunk 192 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 83 optimal weight: 4.9990 chunk 150 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16095 Z= 0.347 Angle : 0.690 9.653 21896 Z= 0.367 Chirality : 0.046 0.228 2467 Planarity : 0.005 0.056 2926 Dihedral : 5.045 34.990 2328 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % 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 : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2143 helix: 0.76 (0.23), residues: 519 sheet: -0.40 (0.21), residues: 567 loop : -1.95 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 413 HIS 0.005 0.001 HIS B 121 PHE 0.015 0.002 PHE A 426 TYR 0.023 0.002 TYR C 65 ARG 0.005 0.001 ARG B 243 *********************** 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 236 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7541 (p0) cc_final: 0.7292 (p0) REVERT: A 368 GLU cc_start: 0.8219 (mp0) cc_final: 0.7894 (mp0) REVERT: A 380 ASP cc_start: 0.8024 (p0) cc_final: 0.7733 (p0) REVERT: A 614 ASP cc_start: 0.7826 (t0) cc_final: 0.7545 (t0) REVERT: A 704 ASP cc_start: 0.8100 (p0) cc_final: 0.7896 (p0) REVERT: B 58 ASN cc_start: 0.8261 (m110) cc_final: 0.7572 (p0) REVERT: B 250 THR cc_start: 0.9034 (p) cc_final: 0.8815 (p) REVERT: B 332 LEU cc_start: 0.8049 (mt) cc_final: 0.7459 (tt) REVERT: C 195 GLN cc_start: 0.7014 (tp-100) cc_final: 0.6210 (tp-100) REVERT: C 210 ASP cc_start: 0.6052 (m-30) cc_final: 0.5768 (m-30) REVERT: E 91 LEU cc_start: 0.9331 (tp) cc_final: 0.9095 (tt) REVERT: F 409 GLU cc_start: 0.8432 (tp30) cc_final: 0.8183 (tp30) REVERT: F 415 GLN cc_start: 0.8247 (tt0) cc_final: 0.7973 (tt0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2218 time to fit residues: 85.1532 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 : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.3980 chunk 124 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 196 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 324 HIS ** 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** P1295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16095 Z= 0.166 Angle : 0.632 8.404 21896 Z= 0.329 Chirality : 0.044 0.241 2467 Planarity : 0.004 0.059 2926 Dihedral : 4.627 34.432 2328 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2143 helix: 0.99 (0.23), residues: 518 sheet: -0.15 (0.21), residues: 562 loop : -1.76 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 413 HIS 0.003 0.001 HIS D 139 PHE 0.013 0.001 PHE D 127 TYR 0.027 0.001 TYR D 222 ARG 0.006 0.000 ARG B 243 ********************** 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 254 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7370 (p0) cc_final: 0.7098 (p0) REVERT: A 368 GLU cc_start: 0.7975 (mp0) cc_final: 0.7645 (mp0) REVERT: A 369 MET cc_start: 0.8134 (mmm) cc_final: 0.7863 (mmm) REVERT: A 380 ASP cc_start: 0.7897 (p0) cc_final: 0.7668 (p0) REVERT: A 594 ASN cc_start: 0.9182 (t0) cc_final: 0.8956 (t0) REVERT: A 614 ASP cc_start: 0.7778 (t0) cc_final: 0.7576 (t0) REVERT: B 58 ASN cc_start: 0.8149 (m110) cc_final: 0.7493 (p0) REVERT: B 250 THR cc_start: 0.9008 (p) cc_final: 0.8763 (p) REVERT: B 332 LEU cc_start: 0.7955 (mt) cc_final: 0.7348 (tt) REVERT: C 43 GLU cc_start: 0.8097 (mp0) cc_final: 0.7861 (mp0) REVERT: C 195 GLN cc_start: 0.6949 (tp-100) cc_final: 0.6604 (pt0) REVERT: C 199 THR cc_start: 0.7488 (p) cc_final: 0.7139 (p) REVERT: C 210 ASP cc_start: 0.6007 (m-30) cc_final: 0.5686 (m-30) REVERT: D 183 GLU cc_start: 0.7768 (tt0) cc_final: 0.7467 (tt0) REVERT: E 91 LEU cc_start: 0.9265 (tp) cc_final: 0.9026 (tt) REVERT: F 409 GLU cc_start: 0.8441 (tp30) cc_final: 0.8229 (tp30) REVERT: F 415 GLN cc_start: 0.8199 (tt0) cc_final: 0.7923 (tt0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2220 time to fit residues: 90.8266 Evaluate side-chains 202 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 170 optimal weight: 0.0870 chunk 71 optimal weight: 0.0270 chunk 174 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN D 30 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080443 restraints weight = 54538.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080125 restraints weight = 35418.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080357 restraints weight = 27334.985| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16095 Z= 0.172 Angle : 0.629 8.591 21896 Z= 0.328 Chirality : 0.043 0.222 2467 Planarity : 0.004 0.060 2926 Dihedral : 4.467 34.753 2328 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2143 helix: 1.05 (0.23), residues: 520 sheet: -0.10 (0.21), residues: 552 loop : -1.68 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 413 HIS 0.002 0.001 HIS D 139 PHE 0.011 0.001 PHE P1296 TYR 0.019 0.001 TYR D 222 ARG 0.007 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.48 seconds wall clock time: 62 minutes 28.84 seconds (3748.84 seconds total)