Starting phenix.real_space_refine (version: dev) on Wed Mar 15 06:29:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw6_10959/03_2023/6yw6_10959_updated.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "C ARG 142": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13823 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3177 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 26, 'TRANS': 369} Chain breaks: 2 Chain: "C" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2645 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2291 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Chain: "B" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2207 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 2 Chain: "G" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 703 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.95, per 1000 atoms: 0.58 Number of scatterers: 13823 At special positions: 0 Unit cell: (142.04, 104.94, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 2566 8.00 N 2364 7.00 C 8815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 17 sheets defined 32.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.985A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.611A pdb=" N GLU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.526A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.584A pdb=" N TYR A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.501A pdb=" N SER A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 221 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 230 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 231 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.649A pdb=" N TYR A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.955A pdb=" N VAL A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 removed outlier: 4.751A pdb=" N ARG A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix No H-bonds generated for 'chain 'A' and resid 309 through 315' Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.606A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 removed outlier: 4.035A pdb=" N ARG A 374 " --> pdb=" O HIS A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'C' and resid 359 through 362 No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'D' and resid 9 through 12 No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 14 through 23 removed outlier: 4.136A pdb=" N GLU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 64 through 70 removed outlier: 4.557A pdb=" N ALA D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.658A pdb=" N LYS D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 118 through 133 removed outlier: 4.311A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.605A pdb=" N ILE D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 237 through 280 removed outlier: 3.632A pdb=" N ASN D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 64 through 82 removed outlier: 3.530A pdb=" N TYR E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 123 through 143 removed outlier: 3.771A pdb=" N GLU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 148 No H-bonds generated for 'chain 'E' and resid 145 through 148' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.911A pdb=" N TRP B 89 " --> pdb=" O LYS B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.951A pdb=" N LYS B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 228 through 234 removed outlier: 4.163A pdb=" N LEU B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.559A pdb=" N TYR B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 327 removed outlier: 4.242A pdb=" N GLU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.845A pdb=" N GLY B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 361' Processing helix chain 'G' and resid 76 through 85 removed outlier: 3.845A pdb=" N LEU G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 92 through 95 No H-bonds generated for 'chain 'G' and resid 92 through 95' Processing helix chain 'G' and resid 100 through 113 removed outlier: 4.344A pdb=" N ASP G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 removed outlier: 3.634A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 132 " --> pdb=" O TRP G 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 145 No H-bonds generated for 'chain 'G' and resid 142 through 145' Processing helix chain 'F' and resid 5 through 19 removed outlier: 3.812A pdb=" N LEU F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.569A pdb=" N LEU F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE F 90 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 128 through 166 removed outlier: 3.972A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP F 133 " --> pdb=" O HIS F 129 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 16 through 18 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= C, first strand: chain 'A' and resid 178 through 180 Processing sheet with id= D, first strand: chain 'A' and resid 254 through 259 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.801A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY C 349 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 333 " --> pdb=" O CYS C 346 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 348 " --> pdb=" O GLN C 331 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.856A pdb=" N VAL C 32 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.665A pdb=" N LYS C 82 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 66 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 131 through 137 removed outlier: 3.675A pdb=" N CYS C 123 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 103 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 101 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.605A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 270 through 273 removed outlier: 3.736A pdb=" N THR C 271 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 280 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 167 through 170 removed outlier: 5.818A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 247 through 252 removed outlier: 3.737A pdb=" N LEU C 248 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA C 261 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 250 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 259 " --> pdb=" O LEU C 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 32 through 36 removed outlier: 3.582A pdb=" N PHE D 35 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 42 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 143 through 145 Processing sheet with id= O, first strand: chain 'D' and resid 200 through 202 Processing sheet with id= P, first strand: chain 'B' and resid 164 through 169 Processing sheet with id= Q, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.508A pdb=" N ILE F 118 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 915 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: 3.40 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4431 1.34 - 1.46: 3031 1.46 - 1.58: 6547 1.58 - 1.70: 11 1.70 - 1.82: 111 Bond restraints: 14131 Sorted by residual: bond pdb=" CA CYS C 342 " pdb=" C CYS C 342 " ideal model delta sigma weight residual 1.525 1.775 -0.250 2.10e-02 2.27e+03 1.41e+02 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.70e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.22e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.74e+01 ... (remaining 14126 not shown) Histogram of bond angle deviations from ideal: 94.63 - 103.61: 206 103.61 - 112.60: 7344 112.60 - 121.59: 8369 121.59 - 130.58: 3116 130.58 - 139.56: 80 Bond angle restraints: 19115 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.01 16.82 1.00e+00 1.00e+00 2.83e+02 angle pdb=" N LYS C 341 " pdb=" CA LYS C 341 " pdb=" C LYS C 341 " ideal model delta sigma weight residual 110.97 125.51 -14.54 1.09e+00 8.42e-01 1.78e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 127.47 12.40 1.00e+00 1.00e+00 1.54e+02 ... (remaining 19110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 7760 13.99 - 27.98: 549 27.98 - 41.97: 143 41.97 - 55.96: 18 55.96 - 69.95: 6 Dihedral angle restraints: 8476 sinusoidal: 3469 harmonic: 5007 Sorted by residual: dihedral pdb=" C LYS C 341 " pdb=" N LYS C 341 " pdb=" CA LYS C 341 " pdb=" CB LYS C 341 " ideal model delta harmonic sigma weight residual -122.60 -154.46 31.86 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" N LYS C 341 " pdb=" C LYS C 341 " pdb=" CA LYS C 341 " pdb=" CB LYS C 341 " ideal model delta harmonic sigma weight residual 122.80 153.65 -30.85 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" C CYS C 342 " pdb=" N CYS C 342 " pdb=" CA CYS C 342 " pdb=" CB CYS C 342 " ideal model delta harmonic sigma weight residual -122.60 -99.58 -23.02 0 2.50e+00 1.60e-01 8.48e+01 ... (remaining 8473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2103 0.287 - 0.573: 1 0.573 - 0.860: 0 0.860 - 1.146: 0 1.146 - 1.433: 2 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CA LYS C 341 " pdb=" N LYS C 341 " pdb=" C LYS C 341 " pdb=" CB LYS C 341 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA CYS C 342 " pdb=" N CYS C 342 " pdb=" C CYS C 342 " pdb=" CB CYS C 342 " both_signs ideal model delta sigma weight residual False 2.51 3.79 -1.28 2.00e-01 2.50e+01 4.07e+01 chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 2103 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 139 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.58e+00 pdb=" N PRO C 140 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 313 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 314 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " -0.023 2.00e-02 2.50e+03 2.13e-02 7.94e+00 pdb=" CG PHE B 266 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " -0.000 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 824 2.71 - 3.26: 13188 3.26 - 3.81: 23122 3.81 - 4.35: 27640 4.35 - 4.90: 44756 Nonbonded interactions: 109530 Sorted by model distance: nonbonded pdb=" O GLY C 283 " pdb=" N LEU C 285 " model vdw 2.164 2.520 nonbonded pdb=" O LEU C 258 " pdb=" CD1 LEU C 269 " model vdw 2.203 3.460 nonbonded pdb=" OG SER C 343 " pdb=" OD1 ASP C 358 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR A 21 " pdb=" O LEU A 101 " model vdw 2.261 2.440 nonbonded pdb=" O ARG A 198 " pdb=" OG1 THR A 201 " model vdw 2.266 2.440 ... (remaining 109525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 8815 2.51 5 N 2364 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 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: 4.100 Check model and map are aligned: 0.200 Process input model: 35.350 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.250 14131 Z= 0.478 Angle : 1.148 19.484 19115 Z= 0.702 Chirality : 0.071 1.433 2106 Planarity : 0.008 0.073 2439 Dihedral : 10.854 69.952 5238 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.20 % Favored : 93.51 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.53 (0.16), residues: 1694 helix: -4.03 (0.12), residues: 501 sheet: -2.61 (0.26), residues: 309 loop : -2.47 (0.18), residues: 884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 291 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 299 average time/residue: 0.3015 time to fit residues: 124.6766 Evaluate side-chains 155 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3129 time to fit residues: 2.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.0370 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.0270 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 256 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN B 13 ASN B 30 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2668 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: