Starting phenix.real_space_refine on Thu Mar 5 13:29:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.map" model { file = "/net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tju_25932/03_2026/7tju_25932.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.223 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 5 S 29 5.16 5 C 14301 2.51 5 N 3993 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22687 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3555 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3517 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3616 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 461} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3437 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3486 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3524 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1451 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 11, 'GLN:plan1': 8, 'PHE:plan': 8, 'TYR:plan': 4, 'ASN:plan1': 13, 'HIS:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 273 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.43, per 1000 atoms: 0.24 Number of scatterers: 22687 At special positions: 0 Unit cell: (126.828, 128.135, 149.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 10 15.00 Mg 3 11.99 O 4351 8.00 N 3993 7.00 C 14301 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5636 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 20 sheets defined 51.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.506A pdb=" N ALA A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.834A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.564A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.638A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.501A pdb=" N ARG A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.636A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 407 removed outlier: 3.984A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.630A pdb=" N LEU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 478 Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.660A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.952A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.619A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.581A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.563A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.538A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.577A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 454 through 458 removed outlier: 4.116A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.607A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 removed outlier: 4.158A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 503 removed outlier: 3.627A pdb=" N THR B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.536A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.523A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.609A pdb=" N LEU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.882A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.954A pdb=" N LYS C 229 " --> pdb=" O ASP C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.525A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.558A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.900A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.650A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 3.787A pdb=" N THR C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 4.027A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 4.194A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 508 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 225 through 246 removed outlier: 4.755A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 282 through 283 No H-bonds generated for 'chain 'D' and resid 282 through 283' Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.595A pdb=" N ASP D 315 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.516A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.842A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.622A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 179 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 248 removed outlier: 5.191A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.601A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 391 removed outlier: 4.107A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 419 through 424 removed outlier: 3.969A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 475 removed outlier: 3.550A pdb=" N ALA E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 179 removed outlier: 4.655A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 247 removed outlier: 4.623A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 247 " --> pdb=" O PHE F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 270 removed outlier: 3.836A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 273 No H-bonds generated for 'chain 'F' and resid 271 through 273' Processing helix chain 'F' and resid 284 through 294 removed outlier: 3.551A pdb=" N LEU F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 392 removed outlier: 4.883A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 396 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 45 removed outlier: 4.384A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 removed outlier: 4.197A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 3.648A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 118 Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.799A pdb=" N ASP G 136 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 155 removed outlier: 3.689A pdb=" N SER G 143 " --> pdb=" O THR G 139 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU G 145 " --> pdb=" O GLN G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 159 Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 191 through 197 removed outlier: 3.850A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 276 removed outlier: 3.941A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP G 238 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET G 247 " --> pdb=" O ASN G 243 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.175A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.639A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.491A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.175A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN B 95 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU B 56 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B 93 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.320A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 68 removed outlier: 4.353A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA D 36 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN D 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.434A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.792A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.540A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.309A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.414A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.639A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.162A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 126 through 130 removed outlier: 6.970A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3411 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: 4.21 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7731 1.34 - 1.46: 3828 1.46 - 1.58: 11387 1.58 - 1.69: 15 1.69 - 1.81: 55 Bond restraints: 23016 Sorted by residual: bond pdb=" O4 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 23011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 30188 1.33 - 2.65: 891 2.65 - 3.98: 156 3.98 - 5.31: 41 5.31 - 6.63: 14 Bond angle restraints: 31290 Sorted by residual: angle pdb=" C ALA F 278 " pdb=" CA ALA F 278 " pdb=" CB ALA F 278 " ideal model delta sigma weight residual 116.54 111.24 5.30 1.15e+00 7.56e-01 2.13e+01 angle pdb=" C TYR A 339 " pdb=" N ILE A 340 " pdb=" CA ILE A 340 " ideal model delta sigma weight residual 120.24 122.70 -2.46 6.30e-01 2.52e+00 1.53e+01 angle pdb=" C ILE A 340 " pdb=" CA ILE A 340 " pdb=" CB ILE A 340 " ideal model delta sigma weight residual 114.35 110.88 3.47 1.06e+00 8.90e-01 1.07e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.52 -5.82 1.80e+00 3.09e-01 1.05e+01 angle pdb=" N VAL G 205 " pdb=" CA VAL G 205 " pdb=" C VAL G 205 " ideal model delta sigma weight residual 112.61 108.03 4.58 1.45e+00 4.76e-01 9.98e+00 ... (remaining 31285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13171 17.93 - 35.85: 572 35.85 - 53.78: 133 53.78 - 71.70: 45 71.70 - 89.63: 27 Dihedral angle restraints: 13948 sinusoidal: 5147 harmonic: 8801 Sorted by residual: dihedral pdb=" CA GLY E 220 " pdb=" C GLY E 220 " pdb=" N GLN E 221 " pdb=" CA GLN E 221 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ARG D 274 " pdb=" C ARG D 274 " pdb=" N ILE D 275 " pdb=" CA ILE D 275 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE D 103 " pdb=" C ILE D 103 " pdb=" N ASP D 104 " pdb=" CA ASP D 104 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 13945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3172 0.059 - 0.119: 482 0.119 - 0.178: 81 0.178 - 0.237: 2 0.237 - 0.296: 7 Chirality restraints: 3744 Sorted by residual: chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3741 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 473 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C TYR B 473 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR B 473 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 474 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 406 " 0.120 9.50e-02 1.11e+02 5.44e-02 2.47e+00 pdb=" NE ARG E 406 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 406 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 406 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 406 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 146 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO B 147 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.021 5.00e-02 4.00e+02 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 180 2.64 - 3.20: 21949 3.20 - 3.77: 33996 3.77 - 4.33: 50237 4.33 - 4.90: 82280 Nonbonded interactions: 188642 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb="MG MG A 601 " model vdw 2.070 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 2.070 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR B 178 " pdb="MG MG B 601 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR C 178 " pdb="MG MG C 601 " model vdw 2.079 2.170 ... (remaining 188637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 28 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 315 or (resid 316 through 317 and (name N or n \ ame CA or name C or name O or name CB )) or resid 318 through 356 or (resid 357 \ and (name N or name CA or name C or name O or name CB )) or resid 358 through 39 \ 7 or (resid 398 and (name N or name CA or name C or name O or name CB )) or resi \ d 399 through 410 or (resid 416 through 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 or (resid 424 through 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 447 or (resid 448 thro \ ugh 449 and (name N or name CA or name C or name O or name CB )) or resid 450 or \ (resid 451 through 452 and (name N or name CA or name C or name O or name CB )) \ or resid 453 through 465 or (resid 466 through 467 and (name N or name CA or na \ me C or name O or name CB )) or resid 468 through 489 or (resid 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 through 500 or (resid \ 501 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 600 through 601)) selection = (chain 'B' and ((resid 28 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 80 or (resid 81 and (name N or na \ me CA or name C or name O or name CB )) or resid 82 through 152 or (resid 153 th \ rough 154 and (name N or name CA or name C or name O or name CB )) or resid 155 \ through 182 or (resid 183 and (name N or name CA or name C or name O or name CB \ )) or resid 184 through 329 or (resid 330 and (name N or name CA or name C or na \ me O or name CB )) or resid 331 through 334 or (resid 335 and (name N or name CA \ or name C or name O or name CB )) or resid 336 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 or (resid 363 an \ d (name N or name CA or name C or name O or name CB )) or resid 364 through 382 \ or (resid 383 through 384 and (name N or name CA or name C or name O or name CB \ )) or resid 385 through 399 or (resid 400 through 401 and (name N or name CA or \ name C or name O or name CB )) or resid 402 through 404 or (resid 405 through 42 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 423 through \ 455 or (resid 456 and (name N or name CA or name C or name O or name CB )) or re \ sid 457 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 479 or (resid 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 through 486 or (resid 487 through 488 an \ d (name N or name CA or name C or name O or name CB )) or resid 489 or (resid 49 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 491 through \ 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) or re \ sid 494 through 601)) selection = (chain 'C' and (resid 28 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 152 or (resid 153 thr \ ough 154 and (name N or name CA or name C or name O or name CB )) or resid 155 t \ hrough 315 or (resid 316 through 317 and (name N or name CA or name C or name O \ or name CB )) or resid 318 through 329 or (resid 330 and (name N or name CA or n \ ame C or name O or name CB )) or resid 331 through 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB ) \ ) or resid 364 through 382 or (resid 383 through 384 and (name N or name CA or n \ ame C or name O or name CB )) or resid 385 through 397 or (resid 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 or (resid 400 through \ 401 and (name N or name CA or name C or name O or name CB )) or resid 402 throu \ gh 404 or (resid 405 through 407 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 410 and (name N or name CA or name C or name O or name CB )) \ or (resid 416 through 422 and (name N or name CA or name C or name O or name CB \ )) or (resid 423 through 429 and (name N or name CA or name C or name O or name \ CB )) or resid 430 through 447 or (resid 448 through 449 and (name N or name CA \ or name C or name O or name CB )) or resid 450 or (resid 451 through 452 and (n \ ame N or name CA or name C or name O or name CB )) or resid 453 through 455 or ( \ resid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ through 461 or (resid 462 and (name N or name CA or name C or name O or name CB \ )) or resid 463 through 465 or (resid 466 through 467 and (name N or name CA or \ name C or name O or name CB )) or resid 468 through 479 or (resid 480 and (name \ N or name CA or name C or name O or name CB )) or resid 481 through 487 or (resi \ d 488 and (name N or name CA or name C or name O or name CB )) or resid 489 thro \ ugh 499 or (resid 500 through 509 and (name N or name CA or name C or name O or \ name CB )) or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 400 or (resid 401 a \ nd (name N or name CA or name C or name O or name CB )) or resid 402 through 434 \ or (resid 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 475)) selection = (chain 'E' and (resid 8 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 314 or (resid 315 and (name N or name CA or name C or name O or name C \ B )) or resid 316 through 318 or (resid 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 365 or (resid 366 and (name N or name \ CA or name C or name O or name CB )) or resid 367 through 381 or (resid 382 thro \ ugh 391 and (name N or name CA or name C or name O or name CB )) or (resid 392 t \ hrough 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ through 408 or (resid 409 and (name N or name CA or name C or name O or name CB \ )) or resid 410 through 471 or (resid 472 and (name N or name CA or name C or n \ ame O or name CB )) or resid 473 through 475)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 111 or (r \ esid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 t \ hrough 211 or (resid 212 and (name N or name CA or name C or name O or name CB ) \ ) or resid 213 through 314 or (resid 315 and (name N or name CA or name C or nam \ e O or name CB )) or resid 316 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 365 or (resid 366 and (na \ me N or name CA or name C or name O or name CB )) or resid 367 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 t \ hrough 375 or (resid 376 and (name N or name CA or name C or name O or name CB ) \ ) or resid 377 through 381 or (resid 382 through 391 and (name N or name CA or n \ ame C or name O or name CB )) or resid 392 or (resid 393 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 through 400 or (resid \ 401 and (name N or name CA or name C or name O or name CB )) or resid 402 throu \ gh 408 or (resid 409 and (name N or name CA or name C or name O or name CB )) or \ resid 410 through 434 or (resid 435 and (name N or name CA or name C or name O \ or name CB )) or resid 436 through 463 or (resid 464 and (name N or name CA or n \ ame C or name O or name CB )) or resid 465 through 471 or (resid 472 and (name N \ or name CA or name C or name O or name CB )) or resid 473 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.350 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.002 0.061 23016 Z= 0.125 Angle : 0.587 6.635 31290 Z= 0.326 Chirality : 0.045 0.296 3744 Planarity : 0.004 0.054 4073 Dihedral : 12.530 89.629 8312 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3080 helix: 0.61 (0.14), residues: 1281 sheet: -0.08 (0.22), residues: 509 loop : 0.20 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 406 TYR 0.019 0.001 TYR B 399 PHE 0.012 0.001 PHE C 405 TRP 0.015 0.003 TRP B 258 HIS 0.005 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00249 (23016) covalent geometry : angle 0.58683 (31290) hydrogen bonds : bond 0.13570 ( 1225) hydrogen bonds : angle 7.25286 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.874 Fit side-chains REVERT: A 175 THR cc_start: 0.8821 (p) cc_final: 0.8477 (p) REVERT: A 271 ASP cc_start: 0.8255 (t0) cc_final: 0.7823 (t0) REVERT: A 454 HIS cc_start: 0.6536 (m90) cc_final: 0.6320 (m170) REVERT: B 64 MET cc_start: 0.8268 (ttt) cc_final: 0.7904 (ttm) REVERT: C 271 ASP cc_start: 0.7990 (t0) cc_final: 0.7526 (t0) REVERT: C 335 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: C 357 GLU cc_start: 0.7599 (mp0) cc_final: 0.7396 (mp0) REVERT: D 64 MET cc_start: 0.8601 (mmt) cc_final: 0.8370 (mmp) REVERT: D 127 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7975 (mm-40) REVERT: E 64 MET cc_start: 0.9145 (mmt) cc_final: 0.8876 (mmt) REVERT: E 142 ASP cc_start: 0.6708 (m-30) cc_final: 0.6450 (m-30) REVERT: E 352 ASP cc_start: 0.8249 (m-30) cc_final: 0.8016 (m-30) REVERT: E 368 TYR cc_start: 0.8875 (t80) cc_final: 0.8580 (t80) REVERT: E 449 TYR cc_start: 0.8685 (m-80) cc_final: 0.8424 (m-80) REVERT: F 123 SER cc_start: 0.8842 (p) cc_final: 0.8583 (t) REVERT: F 393 MET cc_start: 0.8024 (mmm) cc_final: 0.7757 (mmm) REVERT: G 30 ARG cc_start: 0.5459 (mtt-85) cc_final: 0.5080 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1726 time to fit residues: 107.3111 Evaluate side-chains 221 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 40.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 454 HIS B 192 ASN B 224 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 GLN E 223 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097137 restraints weight = 30552.806| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.69 r_work: 0.2989 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 23016 Z= 0.327 Angle : 0.700 7.424 31290 Z= 0.366 Chirality : 0.051 0.186 3744 Planarity : 0.005 0.042 4073 Dihedral : 7.127 87.124 3417 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 7.11 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3080 helix: 0.82 (0.15), residues: 1261 sheet: -0.44 (0.22), residues: 526 loop : -0.01 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.037 0.002 TYR B 399 PHE 0.024 0.002 PHE E 457 TRP 0.012 0.002 TRP C 191 HIS 0.008 0.002 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00798 (23016) covalent geometry : angle 0.69971 (31290) hydrogen bonds : bond 0.05106 ( 1225) hydrogen bonds : angle 5.70833 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.9021 (t0) cc_final: 0.8575 (t0) REVERT: B 355 GLU cc_start: 0.8663 (tt0) cc_final: 0.8446 (tt0) REVERT: C 271 ASP cc_start: 0.8814 (t0) cc_final: 0.8498 (t0) REVERT: C 422 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7867 (tpp80) REVERT: C 484 GLU cc_start: 0.8740 (tp30) cc_final: 0.8532 (tt0) REVERT: D 64 MET cc_start: 0.9089 (mmt) cc_final: 0.8855 (mmp) REVERT: D 200 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7937 (mm-30) REVERT: D 256 ASP cc_start: 0.7998 (t0) cc_final: 0.7595 (t0) REVERT: D 375 GLN cc_start: 0.8061 (mt0) cc_final: 0.7759 (mp10) REVERT: D 401 LYS cc_start: 0.6556 (pttt) cc_final: 0.5931 (mttp) REVERT: E 110 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8479 (mttp) REVERT: E 142 ASP cc_start: 0.7431 (m-30) cc_final: 0.7185 (m-30) REVERT: E 368 TYR cc_start: 0.9103 (t80) cc_final: 0.8772 (t80) REVERT: E 375 GLN cc_start: 0.8694 (mt0) cc_final: 0.8464 (mt0) REVERT: E 449 TYR cc_start: 0.9004 (m-80) cc_final: 0.8642 (m-80) REVERT: E 459 MET cc_start: 0.8596 (mmm) cc_final: 0.8360 (tpp) REVERT: F 199 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7240 (mtm110) REVERT: F 393 MET cc_start: 0.8509 (mmm) cc_final: 0.8247 (mmm) REVERT: G 9 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7909 (ttm-80) REVERT: G 30 ARG cc_start: 0.5912 (mtt-85) cc_final: 0.5018 (tpp-160) outliers start: 29 outliers final: 22 residues processed: 260 average time/residue: 0.1685 time to fit residues: 67.0915 Evaluate side-chains 218 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 239 optimal weight: 0.4980 chunk 264 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 283 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 285 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 454 HIS C 418 GLN D 263 GLN E 223 ASN E 385 GLN F 455 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101026 restraints weight = 30409.994| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.73 r_work: 0.2987 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23016 Z= 0.110 Angle : 0.508 7.949 31290 Z= 0.268 Chirality : 0.043 0.148 3744 Planarity : 0.004 0.042 4073 Dihedral : 6.485 80.635 3417 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.39 % Allowed : 8.32 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3080 helix: 1.38 (0.15), residues: 1263 sheet: -0.14 (0.23), residues: 501 loop : 0.10 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 337 TYR 0.022 0.001 TYR A 473 PHE 0.015 0.001 PHE A 359 TRP 0.008 0.001 TRP C 191 HIS 0.003 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00238 (23016) covalent geometry : angle 0.50796 (31290) hydrogen bonds : bond 0.03688 ( 1225) hydrogen bonds : angle 5.13644 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 355 GLU cc_start: 0.7735 (tp30) cc_final: 0.6927 (tt0) REVERT: A 399 TYR cc_start: 0.7361 (t80) cc_final: 0.7056 (t80) REVERT: A 454 HIS cc_start: 0.6530 (m90) cc_final: 0.6097 (m170) REVERT: B 156 ASP cc_start: 0.8178 (t0) cc_final: 0.7903 (t0) REVERT: B 228 MET cc_start: 0.9099 (tpt) cc_final: 0.8856 (tpt) REVERT: B 355 GLU cc_start: 0.8624 (tt0) cc_final: 0.8289 (mt-10) REVERT: C 271 ASP cc_start: 0.8676 (t0) cc_final: 0.8357 (t0) REVERT: D 64 MET cc_start: 0.9095 (mmt) cc_final: 0.8858 (mmp) REVERT: D 256 ASP cc_start: 0.7782 (t0) cc_final: 0.7278 (t0) REVERT: D 401 LYS cc_start: 0.6583 (pttt) cc_final: 0.5908 (mttp) REVERT: E 110 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8431 (mttp) REVERT: E 368 TYR cc_start: 0.9080 (t80) cc_final: 0.8781 (t80) REVERT: E 375 GLN cc_start: 0.8677 (mt0) cc_final: 0.8298 (mt0) REVERT: E 449 TYR cc_start: 0.8865 (m-80) cc_final: 0.8516 (m-80) REVERT: E 459 MET cc_start: 0.8419 (mmm) cc_final: 0.8164 (tpp) REVERT: F 393 MET cc_start: 0.8433 (mmm) cc_final: 0.8179 (mmm) REVERT: G 9 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7863 (ttm-80) REVERT: G 30 ARG cc_start: 0.5911 (mtt-85) cc_final: 0.4978 (tpp-160) outliers start: 31 outliers final: 12 residues processed: 258 average time/residue: 0.1721 time to fit residues: 67.3353 Evaluate side-chains 220 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 296 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 308 GLN E 223 ASN F 172 ASN F 455 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102264 restraints weight = 30245.281| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.71 r_work: 0.3049 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23016 Z= 0.108 Angle : 0.491 7.414 31290 Z= 0.256 Chirality : 0.043 0.156 3744 Planarity : 0.004 0.045 4073 Dihedral : 6.131 78.567 3417 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.39 % Allowed : 9.26 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3080 helix: 1.63 (0.15), residues: 1261 sheet: 0.07 (0.23), residues: 492 loop : 0.16 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.017 0.001 TYR A 473 PHE 0.017 0.001 PHE A 359 TRP 0.007 0.001 TRP C 191 HIS 0.003 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00243 (23016) covalent geometry : angle 0.49084 (31290) hydrogen bonds : bond 0.03339 ( 1225) hydrogen bonds : angle 4.88574 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 355 GLU cc_start: 0.7763 (tp30) cc_final: 0.7146 (tt0) REVERT: A 454 HIS cc_start: 0.6691 (m90) cc_final: 0.6384 (m170) REVERT: B 156 ASP cc_start: 0.8120 (t0) cc_final: 0.7903 (t0) REVERT: B 228 MET cc_start: 0.9058 (tpt) cc_final: 0.8843 (tpt) REVERT: B 355 GLU cc_start: 0.8617 (tt0) cc_final: 0.8269 (mt-10) REVERT: B 363 ILE cc_start: 0.8455 (mt) cc_final: 0.8055 (tp) REVERT: B 385 LEU cc_start: 0.8529 (mt) cc_final: 0.8247 (mt) REVERT: C 64 MET cc_start: 0.8830 (ttp) cc_final: 0.8629 (ttp) REVERT: C 271 ASP cc_start: 0.8640 (t0) cc_final: 0.8130 (t0) REVERT: D 64 MET cc_start: 0.9112 (mmt) cc_final: 0.8866 (mmp) REVERT: D 256 ASP cc_start: 0.7650 (t0) cc_final: 0.6953 (t0) REVERT: D 375 GLN cc_start: 0.8169 (mt0) cc_final: 0.7817 (mp10) REVERT: D 401 LYS cc_start: 0.6769 (pttt) cc_final: 0.6024 (mttp) REVERT: E 203 GLU cc_start: 0.8288 (tp30) cc_final: 0.8072 (tp30) REVERT: E 368 TYR cc_start: 0.9081 (t80) cc_final: 0.8717 (t80) REVERT: E 375 GLN cc_start: 0.8663 (mt0) cc_final: 0.8273 (mt0) REVERT: E 449 TYR cc_start: 0.8884 (m-80) cc_final: 0.8568 (m-80) REVERT: F 172 ASN cc_start: 0.8827 (m-40) cc_final: 0.8590 (m110) REVERT: F 393 MET cc_start: 0.8361 (mmm) cc_final: 0.8095 (mmm) REVERT: F 399 GLN cc_start: 0.7791 (mp10) cc_final: 0.7550 (mp10) REVERT: G 9 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7838 (ttm-80) REVERT: G 30 ARG cc_start: 0.5680 (mtt-85) cc_final: 0.4874 (tpp-160) outliers start: 31 outliers final: 20 residues processed: 260 average time/residue: 0.1569 time to fit residues: 63.7144 Evaluate side-chains 231 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 193 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 122 optimal weight: 0.0270 chunk 124 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN C 418 GLN D 308 GLN E 223 ASN F 455 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097273 restraints weight = 30685.992| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.70 r_work: 0.2905 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23016 Z= 0.245 Angle : 0.579 7.190 31290 Z= 0.302 Chirality : 0.047 0.194 3744 Planarity : 0.004 0.055 4073 Dihedral : 6.321 88.037 3417 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.74 % Allowed : 9.93 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3080 helix: 1.41 (0.15), residues: 1266 sheet: -0.32 (0.23), residues: 530 loop : 0.03 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 190 TYR 0.030 0.002 TYR B 399 PHE 0.019 0.002 PHE B 470 TRP 0.008 0.001 TRP C 191 HIS 0.006 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00593 (23016) covalent geometry : angle 0.57910 (31290) hydrogen bonds : bond 0.04042 ( 1225) hydrogen bonds : angle 5.01215 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 HIS cc_start: 0.6798 (m90) cc_final: 0.6388 (m170) REVERT: B 363 ILE cc_start: 0.8563 (mt) cc_final: 0.8082 (tp) REVERT: D 64 MET cc_start: 0.9130 (mmt) cc_final: 0.8845 (mmp) REVERT: D 189 GLU cc_start: 0.7642 (tp30) cc_final: 0.7361 (tp30) REVERT: D 222 MET cc_start: 0.8293 (mtp) cc_final: 0.7850 (mtt) REVERT: D 256 ASP cc_start: 0.7889 (t0) cc_final: 0.7272 (t0) REVERT: D 334 VAL cc_start: 0.9188 (t) cc_final: 0.8941 (m) REVERT: D 401 LYS cc_start: 0.6835 (pttt) cc_final: 0.6069 (mttp) REVERT: D 465 ASP cc_start: 0.7779 (m-30) cc_final: 0.6872 (t0) REVERT: E 142 ASP cc_start: 0.7227 (m-30) cc_final: 0.7002 (m-30) REVERT: E 368 TYR cc_start: 0.9119 (t80) cc_final: 0.8821 (t80) REVERT: E 375 GLN cc_start: 0.8755 (mt0) cc_final: 0.8374 (mt0) REVERT: E 449 TYR cc_start: 0.9099 (m-80) cc_final: 0.8885 (m-80) REVERT: F 311 TYR cc_start: 0.9029 (t80) cc_final: 0.8736 (t80) REVERT: F 393 MET cc_start: 0.8424 (mmm) cc_final: 0.8145 (mmm) REVERT: G 9 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7817 (ttm-80) REVERT: G 30 ARG cc_start: 0.5809 (mtt-85) cc_final: 0.4901 (tpp-160) outliers start: 39 outliers final: 32 residues processed: 237 average time/residue: 0.1585 time to fit residues: 57.8609 Evaluate side-chains 229 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 194 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 291 optimal weight: 40.0000 chunk 260 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 158 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 196 optimal weight: 0.0670 chunk 223 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN E 223 ASN F 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101978 restraints weight = 30370.189| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.75 r_work: 0.3016 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23016 Z= 0.100 Angle : 0.490 8.932 31290 Z= 0.253 Chirality : 0.043 0.161 3744 Planarity : 0.004 0.049 4073 Dihedral : 5.921 89.203 3417 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 10.87 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.15), residues: 3080 helix: 1.68 (0.15), residues: 1274 sheet: -0.01 (0.24), residues: 491 loop : 0.08 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 190 TYR 0.022 0.001 TYR A 399 PHE 0.012 0.001 PHE A 359 TRP 0.007 0.001 TRP B 191 HIS 0.003 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00222 (23016) covalent geometry : angle 0.48978 (31290) hydrogen bonds : bond 0.03178 ( 1225) hydrogen bonds : angle 4.74812 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8857 (mm) cc_final: 0.8375 (mm) REVERT: A 454 HIS cc_start: 0.6675 (m90) cc_final: 0.6368 (m170) REVERT: B 156 ASP cc_start: 0.8241 (t0) cc_final: 0.7936 (t0) REVERT: B 363 ILE cc_start: 0.8502 (mt) cc_final: 0.8103 (tp) REVERT: C 271 ASP cc_start: 0.8818 (t0) cc_final: 0.8344 (t0) REVERT: D 38 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7850 (mt-10) REVERT: D 64 MET cc_start: 0.9110 (mmt) cc_final: 0.8851 (mmp) REVERT: D 222 MET cc_start: 0.8042 (mtp) cc_final: 0.7732 (mtt) REVERT: D 256 ASP cc_start: 0.7615 (t0) cc_final: 0.7108 (t0) REVERT: D 334 VAL cc_start: 0.9162 (t) cc_final: 0.8937 (m) REVERT: D 381 TYR cc_start: 0.5896 (t80) cc_final: 0.5670 (t80) REVERT: D 401 LYS cc_start: 0.6939 (pttt) cc_final: 0.6237 (mttm) REVERT: E 368 TYR cc_start: 0.9077 (t80) cc_final: 0.8737 (t80) REVERT: E 375 GLN cc_start: 0.8689 (mt0) cc_final: 0.8277 (mt0) REVERT: E 449 TYR cc_start: 0.9028 (m-80) cc_final: 0.8798 (m-80) REVERT: F 208 ASN cc_start: 0.8357 (t0) cc_final: 0.7991 (t0) REVERT: F 393 MET cc_start: 0.8366 (mmm) cc_final: 0.8076 (mmm) REVERT: F 399 GLN cc_start: 0.7754 (mp10) cc_final: 0.7499 (mp10) REVERT: G 9 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: G 30 ARG cc_start: 0.5765 (mtt-85) cc_final: 0.4817 (tpp-160) outliers start: 31 outliers final: 23 residues processed: 235 average time/residue: 0.1593 time to fit residues: 58.4584 Evaluate side-chains 214 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 9 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 181 optimal weight: 30.0000 chunk 117 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 281 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN E 385 GLN F 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098466 restraints weight = 30728.273| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.00 r_work: 0.2910 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23016 Z= 0.222 Angle : 0.561 11.625 31290 Z= 0.289 Chirality : 0.046 0.158 3744 Planarity : 0.004 0.062 4073 Dihedral : 6.032 84.558 3417 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 11.23 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3080 helix: 1.53 (0.15), residues: 1267 sheet: -0.27 (0.23), residues: 517 loop : 0.00 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 190 TYR 0.028 0.001 TYR B 399 PHE 0.018 0.002 PHE B 470 TRP 0.008 0.001 TRP C 191 HIS 0.005 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00536 (23016) covalent geometry : angle 0.56132 (31290) hydrogen bonds : bond 0.03800 ( 1225) hydrogen bonds : angle 4.88382 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 HIS cc_start: 0.6851 (m90) cc_final: 0.6456 (m170) REVERT: B 156 ASP cc_start: 0.8338 (t0) cc_final: 0.7976 (t0) REVERT: B 159 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9051 (m) REVERT: D 38 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 64 MET cc_start: 0.9146 (mmt) cc_final: 0.8867 (mmp) REVERT: D 222 MET cc_start: 0.8179 (mtp) cc_final: 0.7804 (mtt) REVERT: D 256 ASP cc_start: 0.7907 (t0) cc_final: 0.7367 (t0) REVERT: D 334 VAL cc_start: 0.9197 (t) cc_final: 0.8942 (m) REVERT: D 401 LYS cc_start: 0.6857 (pttt) cc_final: 0.6245 (mttm) REVERT: E 368 TYR cc_start: 0.9122 (t80) cc_final: 0.8769 (t80) REVERT: E 375 GLN cc_start: 0.8743 (mt0) cc_final: 0.8341 (mt0) REVERT: F 311 TYR cc_start: 0.9034 (t80) cc_final: 0.8725 (t80) REVERT: G 9 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7773 (ttm-80) REVERT: G 30 ARG cc_start: 0.6021 (mtt-85) cc_final: 0.5008 (tpp-160) outliers start: 42 outliers final: 34 residues processed: 226 average time/residue: 0.1680 time to fit residues: 58.4646 Evaluate side-chains 223 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 248 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 9 optimal weight: 0.1980 chunk 273 optimal weight: 0.2980 chunk 266 optimal weight: 0.0060 chunk 216 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 308 GLN E 385 GLN F 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103684 restraints weight = 30121.082| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.86 r_work: 0.3068 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23016 Z= 0.097 Angle : 0.497 14.393 31290 Z= 0.255 Chirality : 0.043 0.197 3744 Planarity : 0.003 0.056 4073 Dihedral : 5.743 89.726 3417 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 12.04 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 3080 helix: 1.75 (0.15), residues: 1283 sheet: -0.02 (0.24), residues: 491 loop : 0.09 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 190 TYR 0.017 0.001 TYR A 399 PHE 0.010 0.001 PHE F 261 TRP 0.006 0.001 TRP C 191 HIS 0.002 0.000 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00212 (23016) covalent geometry : angle 0.49680 (31290) hydrogen bonds : bond 0.03043 ( 1225) hydrogen bonds : angle 4.64212 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8826 (mm) cc_final: 0.8305 (mm) REVERT: A 454 HIS cc_start: 0.6598 (m90) cc_final: 0.6259 (m170) REVERT: B 156 ASP cc_start: 0.8240 (t0) cc_final: 0.7881 (t0) REVERT: C 271 ASP cc_start: 0.8942 (t0) cc_final: 0.8620 (t0) REVERT: D 64 MET cc_start: 0.9100 (mmt) cc_final: 0.8840 (mmp) REVERT: D 222 MET cc_start: 0.8051 (mtp) cc_final: 0.7790 (mtt) REVERT: D 256 ASP cc_start: 0.7570 (t0) cc_final: 0.7026 (t0) REVERT: D 401 LYS cc_start: 0.6836 (pttt) cc_final: 0.6237 (mttm) REVERT: E 75 LYS cc_start: 0.8474 (tttt) cc_final: 0.8202 (mmtt) REVERT: E 256 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7805 (p0) REVERT: E 368 TYR cc_start: 0.9019 (t80) cc_final: 0.8675 (t80) REVERT: E 375 GLN cc_start: 0.8629 (mt0) cc_final: 0.8187 (mt0) REVERT: F 208 ASN cc_start: 0.8296 (t0) cc_final: 0.7928 (t0) REVERT: F 281 TYR cc_start: 0.9371 (m-80) cc_final: 0.8811 (m-80) REVERT: F 311 TYR cc_start: 0.9015 (t80) cc_final: 0.8717 (t80) REVERT: F 399 GLN cc_start: 0.7756 (mp10) cc_final: 0.7524 (mp10) REVERT: G 9 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: G 30 ARG cc_start: 0.5741 (mtt-85) cc_final: 0.4829 (tpp-160) outliers start: 29 outliers final: 22 residues processed: 234 average time/residue: 0.1664 time to fit residues: 60.0334 Evaluate side-chains 227 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 213 optimal weight: 0.9980 chunk 268 optimal weight: 0.1980 chunk 218 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN E 385 GLN F 367 HIS F 455 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103502 restraints weight = 30257.819| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.72 r_work: 0.3087 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23016 Z= 0.101 Angle : 0.495 13.989 31290 Z= 0.253 Chirality : 0.043 0.193 3744 Planarity : 0.004 0.061 4073 Dihedral : 5.655 89.633 3417 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.30 % Allowed : 11.90 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 3080 helix: 1.80 (0.15), residues: 1281 sheet: 0.08 (0.24), residues: 490 loop : 0.15 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 190 TYR 0.015 0.001 TYR A 399 PHE 0.021 0.001 PHE A 470 TRP 0.007 0.001 TRP C 191 HIS 0.003 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00229 (23016) covalent geometry : angle 0.49465 (31290) hydrogen bonds : bond 0.03026 ( 1225) hydrogen bonds : angle 4.58694 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 454 HIS cc_start: 0.6623 (m90) cc_final: 0.6304 (m170) REVERT: B 124 ASP cc_start: 0.8276 (m-30) cc_final: 0.7865 (p0) REVERT: B 156 ASP cc_start: 0.8185 (t0) cc_final: 0.7849 (t0) REVERT: C 271 ASP cc_start: 0.8882 (t0) cc_final: 0.8527 (t70) REVERT: C 398 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8176 (mt0) REVERT: D 64 MET cc_start: 0.9111 (mmt) cc_final: 0.8823 (mmp) REVERT: D 222 MET cc_start: 0.8039 (mtp) cc_final: 0.7743 (mtt) REVERT: D 256 ASP cc_start: 0.7527 (t0) cc_final: 0.6998 (t0) REVERT: D 401 LYS cc_start: 0.6887 (pttt) cc_final: 0.6288 (mttp) REVERT: D 408 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6822 (mtp85) REVERT: D 440 SER cc_start: 0.7843 (m) cc_final: 0.7549 (t) REVERT: E 75 LYS cc_start: 0.8452 (tttt) cc_final: 0.8217 (mmtt) REVERT: E 256 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7865 (p0) REVERT: E 375 GLN cc_start: 0.8641 (mt0) cc_final: 0.8204 (mt0) REVERT: F 208 ASN cc_start: 0.8326 (t0) cc_final: 0.7989 (t0) REVERT: F 281 TYR cc_start: 0.9399 (m-80) cc_final: 0.8813 (m-80) REVERT: F 297 THR cc_start: 0.8661 (t) cc_final: 0.8303 (p) REVERT: F 311 TYR cc_start: 0.9006 (t80) cc_final: 0.8731 (t80) REVERT: F 399 GLN cc_start: 0.7787 (mp10) cc_final: 0.7540 (mp10) REVERT: G 9 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7804 (ttm-80) REVERT: G 30 ARG cc_start: 0.5794 (mtt-85) cc_final: 0.4838 (tpp-160) REVERT: G 229 GLU cc_start: 0.6284 (tt0) cc_final: 0.5997 (mt-10) outliers start: 29 outliers final: 23 residues processed: 228 average time/residue: 0.1667 time to fit residues: 58.5100 Evaluate side-chains 225 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 40.0000 chunk 263 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 268 optimal weight: 0.3980 chunk 230 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 302 optimal weight: 9.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN F 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103833 restraints weight = 30243.989| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.86 r_work: 0.3089 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23016 Z= 0.100 Angle : 0.495 13.503 31290 Z= 0.253 Chirality : 0.043 0.190 3744 Planarity : 0.004 0.065 4073 Dihedral : 5.650 88.952 3417 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.07 % Allowed : 11.95 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.16), residues: 3080 helix: 1.82 (0.15), residues: 1284 sheet: 0.10 (0.24), residues: 489 loop : 0.14 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 190 TYR 0.015 0.001 TYR A 473 PHE 0.021 0.001 PHE A 470 TRP 0.007 0.001 TRP C 191 HIS 0.002 0.000 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00226 (23016) covalent geometry : angle 0.49491 (31290) hydrogen bonds : bond 0.02964 ( 1225) hydrogen bonds : angle 4.55104 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 HIS cc_start: 0.6608 (m90) cc_final: 0.6273 (m170) REVERT: B 124 ASP cc_start: 0.8314 (m-30) cc_final: 0.7888 (p0) REVERT: B 156 ASP cc_start: 0.8188 (t0) cc_final: 0.7844 (t0) REVERT: C 91 LYS cc_start: 0.8584 (tttt) cc_final: 0.8041 (tptt) REVERT: C 271 ASP cc_start: 0.8881 (t0) cc_final: 0.8590 (t70) REVERT: C 398 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8121 (mt0) REVERT: D 26 GLU cc_start: 0.7145 (mp0) cc_final: 0.6907 (mp0) REVERT: D 64 MET cc_start: 0.9112 (mmt) cc_final: 0.8836 (mmp) REVERT: D 222 MET cc_start: 0.8074 (mtp) cc_final: 0.7779 (mtt) REVERT: D 256 ASP cc_start: 0.7510 (t0) cc_final: 0.6968 (t0) REVERT: D 345 TYR cc_start: 0.7726 (m-10) cc_final: 0.7448 (m-10) REVERT: D 401 LYS cc_start: 0.6855 (pttt) cc_final: 0.6238 (mttp) REVERT: D 440 SER cc_start: 0.7809 (m) cc_final: 0.7505 (t) REVERT: E 75 LYS cc_start: 0.8462 (tttt) cc_final: 0.8189 (mmtt) REVERT: E 256 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7870 (p0) REVERT: E 375 GLN cc_start: 0.8621 (mt0) cc_final: 0.8178 (mt0) REVERT: F 208 ASN cc_start: 0.8272 (t0) cc_final: 0.7933 (t0) REVERT: F 281 TYR cc_start: 0.9400 (m-80) cc_final: 0.8804 (m-80) REVERT: F 297 THR cc_start: 0.8665 (t) cc_final: 0.8318 (p) REVERT: F 311 TYR cc_start: 0.9022 (t80) cc_final: 0.8748 (t80) REVERT: F 399 GLN cc_start: 0.7795 (mp10) cc_final: 0.7530 (mp10) REVERT: G 9 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: G 30 ARG cc_start: 0.5629 (mtt-85) cc_final: 0.4656 (tpp-160) REVERT: G 229 GLU cc_start: 0.6192 (tt0) cc_final: 0.5881 (mt-10) outliers start: 24 outliers final: 22 residues processed: 222 average time/residue: 0.1588 time to fit residues: 54.9511 Evaluate side-chains 226 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103973 restraints weight = 30207.816| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.80 r_work: 0.3078 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23016 Z= 0.147 Angle : 0.519 12.689 31290 Z= 0.267 Chirality : 0.044 0.182 3744 Planarity : 0.004 0.067 4073 Dihedral : 5.757 87.967 3417 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.16 % Allowed : 12.08 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 3080 helix: 1.76 (0.15), residues: 1278 sheet: -0.09 (0.24), residues: 515 loop : 0.14 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 190 TYR 0.017 0.001 TYR B 399 PHE 0.017 0.001 PHE A 470 TRP 0.008 0.001 TRP C 191 HIS 0.004 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00352 (23016) covalent geometry : angle 0.51892 (31290) hydrogen bonds : bond 0.03312 ( 1225) hydrogen bonds : angle 4.64415 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.46 seconds wall clock time: 95 minutes 39.09 seconds (5739.09 seconds total)