Starting phenix.real_space_refine on Sun Feb 18 14:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/02_2024/7px9_13694_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 17 5.49 5 Mg 5 5.21 5 S 67 5.16 5 C 13943 2.51 5 N 3823 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E ARG 494": "NH1" <-> "NH2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "E GLU 559": "OE1" <-> "OE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22194 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3623 Classifications: {'peptide': 463} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain breaks: 3 Chain: "B" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3659 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 22, 'TRANS': 445} Chain breaks: 2 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3542 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3723 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Chain breaks: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 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: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 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} Time building chain proxies: 12.15, per 1000 atoms: 0.55 Number of scatterers: 22194 At special positions: 0 Unit cell: (136.864, 153.972, 127.088, 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 67 16.00 P 17 15.00 Mg 5 11.99 O 4339 8.00 N 3823 7.00 C 13943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 4.2 seconds 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 25 sheets defined 35.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.966A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.648A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.429A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.708A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 544 through 559 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 260 through 273 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 299 through 316 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.613A pdb=" N TYR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 471 through 487 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 510 through 513 Processing helix chain 'B' and resid 516 through 536 Processing helix chain 'B' and resid 544 through 560 removed outlier: 4.103A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 577 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 258 through 273 removed outlier: 4.339A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.651A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 344 through 362 removed outlier: 4.516A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 516 through 536 Processing helix chain 'C' and resid 544 through 554 removed outlier: 3.702A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 577 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 258 through 281 removed outlier: 3.962A pdb=" N LEU D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Proline residue: D 271 - end of helix removed outlier: 5.883A pdb=" N GLU D 276 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 313 removed outlier: 4.035A pdb=" N ALA D 303 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 393 through 405 removed outlier: 4.284A pdb=" N GLY D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 452 Processing helix chain 'D' and resid 461 through 467 removed outlier: 3.716A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 516 through 536 Processing helix chain 'D' and resid 544 through 561 removed outlier: 4.455A pdb=" N ASP D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 removed outlier: 4.506A pdb=" N LYS D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 259 through 273 removed outlier: 4.278A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 299 through 317 removed outlier: 3.508A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 4.151A pdb=" N TYR E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 388 through 400 removed outlier: 4.891A pdb=" N VAL E 393 " --> pdb=" O THR E 390 " (cutoff:3.500A) Proline residue: E 394 - end of helix removed outlier: 3.728A pdb=" N ILE E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.894A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 486 Processing helix chain 'E' and resid 516 through 537 Processing helix chain 'E' and resid 544 through 557 removed outlier: 3.681A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.634A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 275 through 281 Processing helix chain 'F' and resid 300 through 316 Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 344 through 359 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 388 through 399 removed outlier: 5.233A pdb=" N VAL F 393 " --> pdb=" O THR F 390 " (cutoff:3.500A) Proline residue: F 394 - end of helix 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 423 through 426 No H-bonds generated for 'chain 'F' and resid 423 through 426' Processing helix chain 'F' and resid 442 through 452 removed outlier: 3.514A pdb=" N TYR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 467 removed outlier: 4.374A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing helix chain 'F' and resid 510 through 513 Processing helix chain 'F' and resid 516 through 536 Processing helix chain 'F' and resid 544 through 558 removed outlier: 3.723A pdb=" N ASN F 558 " --> pdb=" O GLU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 4.574A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.602A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.814A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 433 through 437 removed outlier: 8.779A pdb=" N VAL A 289 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 411 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU A 291 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A 413 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY A 293 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER A 415 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N PHE A 369 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU A 330 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP A 371 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 332 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 583 through 586 removed outlier: 3.852A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.451A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.551A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B 219 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP B 223 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 433 through 437 removed outlier: 8.146A pdb=" N VAL B 289 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 411 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 291 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B 413 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY B 293 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 366 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 412 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 368 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ALA B 414 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 370 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= I, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= J, first strand: chain 'C' and resid 112 through 117 Processing sheet with id= K, first strand: chain 'C' and resid 183 through 187 removed outlier: 6.102A pdb=" N VAL C 177 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU C 164 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 231 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASP C 223 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 229 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 433 through 437 removed outlier: 8.342A pdb=" N VAL C 289 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 411 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU C 291 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY C 413 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N GLY C 293 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 415 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP C 371 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 332 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 505 through 509 Processing sheet with id= N, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.871A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 183 through 187 removed outlier: 6.055A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 160 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER D 219 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D 231 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP D 223 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA D 229 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 433 through 436 removed outlier: 6.355A pdb=" N VAL D 411 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU D 291 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY D 413 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 506 through 508 removed outlier: 3.781A pdb=" N LEU D 496 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 583 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.574A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.551A pdb=" N GLU E 160 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU E 175 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE E 167 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG E 173 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 433 through 437 removed outlier: 7.886A pdb=" N VAL E 289 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 411 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU E 291 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY E 413 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLY E 293 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER E 415 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 505 through 509 Processing sheet with id= V, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.758A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR F 107 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR F 112 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 183 through 187 removed outlier: 3.809A pdb=" N GLU F 166 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 177 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU F 164 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 231 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP F 223 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA F 229 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 433 through 437 removed outlier: 3.575A pdb=" N GLY F 293 " --> pdb=" O SER F 415 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 506 through 509 786 hydrogen bonds defined for protein. 2256 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: 7.04 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6720 1.33 - 1.45: 2891 1.45 - 1.57: 12807 1.57 - 1.69: 28 1.69 - 1.81: 116 Bond restraints: 22562 Sorted by residual: bond pdb=" C4 ATP F 701 " pdb=" C5 ATP F 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.67e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.65e+01 bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.57e+01 ... (remaining 22557 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.39: 808 107.39 - 114.56: 13380 114.56 - 121.73: 11357 121.73 - 128.91: 4902 128.91 - 136.08: 106 Bond angle restraints: 30553 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 118.55 21.32 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 119.11 20.76 1.00e+00 1.00e+00 4.31e+02 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 119.12 20.75 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 119.89 19.98 1.00e+00 1.00e+00 3.99e+02 ... (remaining 30548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 13488 23.28 - 46.56: 355 46.56 - 69.85: 53 69.85 - 93.13: 19 93.13 - 116.41: 2 Dihedral angle restraints: 13917 sinusoidal: 5805 harmonic: 8112 Sorted by residual: dihedral pdb=" CA ARG D 439 " pdb=" C ARG D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta harmonic sigma weight residual -180.00 -78.26 -101.74 0 5.00e+00 4.00e-02 4.14e+02 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 56.41 -116.41 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" CA ASN D 563 " pdb=" C ASN D 563 " pdb=" N THR D 564 " pdb=" CA THR D 564 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 13914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2492 0.037 - 0.074: 648 0.074 - 0.111: 287 0.111 - 0.149: 48 0.149 - 0.186: 3 Chirality restraints: 3478 Sorted by residual: chirality pdb=" CA ILE D 437 " pdb=" N ILE D 437 " pdb=" C ILE D 437 " pdb=" CB ILE D 437 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS D 297 " pdb=" N CYS D 297 " pdb=" C CYS D 297 " pdb=" CB CYS D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA MET D 486 " pdb=" N MET D 486 " pdb=" C MET D 486 " pdb=" CB MET D 486 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 3475 not shown) Planarity restraints: 3969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 334 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.55e+00 pdb=" N PRO F 335 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 335 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 335 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 561 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO D 562 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 562 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 562 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 247 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.019 5.00e-02 4.00e+02 ... (remaining 3966 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 228 2.58 - 3.16: 18536 3.16 - 3.74: 34567 3.74 - 4.32: 46360 4.32 - 4.90: 77520 Nonbonded interactions: 177211 Sorted by model distance: nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 2.005 2.170 nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.047 2.170 nonbonded pdb=" O2B ATP C 701 " pdb="MG MG C 702 " model vdw 2.054 2.170 nonbonded pdb=" O1B ATP F 701 " pdb="MG MG F 702 " model vdw 2.076 2.170 nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 2.123 2.170 ... (remaining 177206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 97 through 377 or resid 390 through 587)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587)) selection = (chain 'D' and resid 97 through 587) selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 10.470 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 59.970 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.003 0.082 22562 Z= 0.224 Angle : 0.676 21.322 30553 Z= 0.503 Chirality : 0.041 0.186 3478 Planarity : 0.003 0.040 3969 Dihedral : 11.058 116.411 8681 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 5.32 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2779 helix: 2.19 (0.18), residues: 949 sheet: 0.55 (0.23), residues: 549 loop : 0.32 (0.19), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 570 HIS 0.002 0.000 HIS C 460 PHE 0.008 0.001 PHE E 353 TYR 0.008 0.001 TYR A 449 ARG 0.003 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 2.748 Fit side-chains revert: symmetry clash REVERT: A 310 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6588 (mm) REVERT: A 492 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.6975 (t0) REVERT: B 172 HIS cc_start: 0.6917 (t70) cc_final: 0.6574 (t70) REVERT: C 281 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: C 496 LEU cc_start: 0.6591 (tp) cc_final: 0.6118 (tp) REVERT: C 536 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: C 570 TRP cc_start: 0.5759 (m-90) cc_final: 0.3921 (m-90) REVERT: D 420 MET cc_start: 0.5305 (ttt) cc_final: 0.4950 (tpp) REVERT: D 486 MET cc_start: 0.5812 (tmm) cc_final: 0.5465 (tmm) REVERT: E 314 MET cc_start: 0.8026 (mmm) cc_final: 0.7803 (mmm) REVERT: E 520 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7247 (tm-30) REVERT: F 244 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: F 330 LEU cc_start: 0.8913 (mp) cc_final: 0.8705 (mp) REVERT: F 407 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6425 (mm-30) outliers start: 45 outliers final: 14 residues processed: 290 average time/residue: 0.3731 time to fit residues: 164.9176 Evaluate side-chains 141 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 0.0040 chunk 217 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22562 Z= 0.275 Angle : 0.570 8.027 30553 Z= 0.292 Chirality : 0.043 0.162 3478 Planarity : 0.004 0.072 3969 Dihedral : 8.744 110.249 3280 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.81 % Allowed : 8.47 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2779 helix: 1.89 (0.18), residues: 960 sheet: 0.39 (0.23), residues: 552 loop : 0.25 (0.19), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 570 HIS 0.003 0.001 HIS B 348 PHE 0.027 0.002 PHE A 155 TYR 0.020 0.001 TYR A 328 ARG 0.007 0.000 ARG E 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 118 time to evaluate : 2.858 Fit side-chains REVERT: A 310 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6704 (mm) REVERT: A 491 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: B 172 HIS cc_start: 0.6971 (t70) cc_final: 0.6607 (t70) REVERT: C 122 MET cc_start: 0.6827 (mpp) cc_final: 0.6617 (mpp) REVERT: C 160 GLU cc_start: 0.7065 (pm20) cc_final: 0.6615 (pm20) REVERT: C 281 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: C 570 TRP cc_start: 0.6637 (m-90) cc_final: 0.4543 (m-90) REVERT: D 167 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6338 (tp) REVERT: D 244 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5603 (pp20) REVERT: D 420 MET cc_start: 0.5317 (ttt) cc_final: 0.5100 (tpp) REVERT: D 486 MET cc_start: 0.6662 (tmm) cc_final: 0.6295 (tmm) REVERT: E 314 MET cc_start: 0.8017 (mmm) cc_final: 0.7761 (mmm) REVERT: E 508 MET cc_start: 0.8071 (mtp) cc_final: 0.7639 (mtp) REVERT: F 244 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5989 (pp20) outliers start: 67 outliers final: 36 residues processed: 177 average time/residue: 0.2938 time to fit residues: 86.5098 Evaluate side-chains 150 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN E 493 ASN E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22562 Z= 0.391 Angle : 0.646 8.211 30553 Z= 0.337 Chirality : 0.046 0.214 3478 Planarity : 0.005 0.070 3969 Dihedral : 8.761 106.728 3276 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 3.35 % Allowed : 9.52 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2779 helix: 1.41 (0.17), residues: 956 sheet: -0.08 (0.22), residues: 545 loop : -0.09 (0.19), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 187 HIS 0.005 0.001 HIS A 348 PHE 0.027 0.002 PHE C 377 TYR 0.017 0.002 TYR E 583 ARG 0.004 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 117 time to evaluate : 2.590 Fit side-chains REVERT: A 310 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6839 (mm) REVERT: A 328 TYR cc_start: 0.7422 (t80) cc_final: 0.7190 (t80) REVERT: A 491 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 172 HIS cc_start: 0.7034 (t70) cc_final: 0.6757 (t70) REVERT: B 352 ILE cc_start: 0.8665 (mt) cc_final: 0.8401 (mm) REVERT: C 160 GLU cc_start: 0.7266 (pm20) cc_final: 0.6815 (pm20) REVERT: C 281 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: D 167 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5891 (tp) REVERT: D 486 MET cc_start: 0.6447 (tmm) cc_final: 0.6002 (tmm) REVERT: E 508 MET cc_start: 0.8167 (mtp) cc_final: 0.7711 (mtp) REVERT: F 244 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5900 (pp20) outliers start: 80 outliers final: 54 residues processed: 188 average time/residue: 0.3132 time to fit residues: 96.6969 Evaluate side-chains 164 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 105 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 253 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22562 Z= 0.222 Angle : 0.540 6.554 30553 Z= 0.279 Chirality : 0.043 0.180 3478 Planarity : 0.004 0.062 3969 Dihedral : 8.570 109.221 3276 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.25 % Rotamer: Outliers : 2.85 % Allowed : 11.28 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2779 helix: 1.61 (0.17), residues: 951 sheet: -0.10 (0.22), residues: 540 loop : -0.03 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 187 HIS 0.003 0.001 HIS A 460 PHE 0.025 0.002 PHE A 377 TYR 0.012 0.001 TYR F 500 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 116 time to evaluate : 2.696 Fit side-chains REVERT: A 310 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6740 (mm) REVERT: A 330 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6446 (tp) REVERT: A 491 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: B 172 HIS cc_start: 0.6955 (t70) cc_final: 0.6687 (t70) REVERT: B 352 ILE cc_start: 0.8678 (mt) cc_final: 0.8434 (mt) REVERT: C 122 MET cc_start: 0.6625 (mpp) cc_final: 0.6418 (mpp) REVERT: C 160 GLU cc_start: 0.7228 (pm20) cc_final: 0.6779 (pm20) REVERT: C 281 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: D 122 MET cc_start: 0.7106 (mmm) cc_final: 0.6808 (mmm) REVERT: D 167 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6087 (tp) REVERT: D 420 MET cc_start: 0.4940 (tpp) cc_final: 0.4592 (tpp) REVERT: D 486 MET cc_start: 0.6554 (tmm) cc_final: 0.6269 (tmm) REVERT: D 497 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: E 508 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: F 244 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6065 (pp20) REVERT: F 277 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8913 (mm) REVERT: F 420 MET cc_start: 0.7950 (mmt) cc_final: 0.7639 (mmt) outliers start: 68 outliers final: 46 residues processed: 175 average time/residue: 0.2988 time to fit residues: 86.5571 Evaluate side-chains 163 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 229 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22562 Z= 0.311 Angle : 0.588 7.017 30553 Z= 0.306 Chirality : 0.044 0.197 3478 Planarity : 0.005 0.061 3969 Dihedral : 8.639 106.565 3276 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.19 % Allowed : 12.45 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2779 helix: 1.40 (0.17), residues: 955 sheet: -0.27 (0.22), residues: 544 loop : -0.20 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 187 HIS 0.004 0.001 HIS A 460 PHE 0.024 0.002 PHE A 377 TYR 0.015 0.002 TYR E 583 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 113 time to evaluate : 2.754 Fit side-chains REVERT: A 110 ASP cc_start: 0.7904 (t70) cc_final: 0.7657 (t70) REVERT: A 310 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6824 (mm) REVERT: A 328 TYR cc_start: 0.7091 (t80) cc_final: 0.6562 (t80) REVERT: A 330 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6402 (tp) REVERT: A 491 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 172 HIS cc_start: 0.7027 (t70) cc_final: 0.6766 (t70) REVERT: B 352 ILE cc_start: 0.8723 (mt) cc_final: 0.8404 (mm) REVERT: C 160 GLU cc_start: 0.7281 (pm20) cc_final: 0.6850 (pm20) REVERT: D 122 MET cc_start: 0.7039 (mmm) cc_final: 0.6768 (mmm) REVERT: D 167 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6179 (tp) REVERT: D 486 MET cc_start: 0.6579 (tmm) cc_final: 0.6302 (tmm) REVERT: F 244 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6154 (pp20) REVERT: F 277 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8940 (mm) outliers start: 76 outliers final: 56 residues processed: 179 average time/residue: 0.3065 time to fit residues: 90.1494 Evaluate side-chains 164 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 102 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN C 514 ASN D 348 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22562 Z= 0.292 Angle : 0.576 7.436 30553 Z= 0.300 Chirality : 0.044 0.193 3478 Planarity : 0.005 0.061 3969 Dihedral : 8.580 105.520 3274 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 3.35 % Allowed : 13.46 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2779 helix: 1.40 (0.17), residues: 952 sheet: -0.32 (0.22), residues: 538 loop : -0.27 (0.19), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 187 HIS 0.003 0.001 HIS A 460 PHE 0.024 0.002 PHE A 377 TYR 0.013 0.001 TYR E 583 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 109 time to evaluate : 2.593 Fit side-chains REVERT: A 110 ASP cc_start: 0.7935 (t70) cc_final: 0.7689 (t70) REVERT: A 310 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6852 (mm) REVERT: A 328 TYR cc_start: 0.7192 (t80) cc_final: 0.6528 (t80) REVERT: A 330 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6713 (tp) REVERT: A 430 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6617 (mpp80) REVERT: A 491 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: B 172 HIS cc_start: 0.7120 (t70) cc_final: 0.6835 (t70) REVERT: B 352 ILE cc_start: 0.8702 (mt) cc_final: 0.8462 (mt) REVERT: B 373 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (ptp) REVERT: C 160 GLU cc_start: 0.7298 (pm20) cc_final: 0.6871 (pm20) REVERT: D 122 MET cc_start: 0.7278 (mmm) cc_final: 0.6955 (mmm) REVERT: D 167 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6201 (tp) REVERT: D 486 MET cc_start: 0.6588 (tmm) cc_final: 0.6297 (tmm) REVERT: F 244 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6210 (pp20) REVERT: F 277 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8842 (mm) outliers start: 80 outliers final: 55 residues processed: 180 average time/residue: 0.3107 time to fit residues: 91.8938 Evaluate side-chains 166 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 103 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 163 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22562 Z= 0.357 Angle : 0.629 11.162 30553 Z= 0.328 Chirality : 0.045 0.194 3478 Planarity : 0.005 0.062 3969 Dihedral : 8.736 99.201 3274 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.61 % Allowed : 14.05 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2779 helix: 1.24 (0.17), residues: 956 sheet: -0.47 (0.22), residues: 566 loop : -0.38 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 187 HIS 0.004 0.001 HIS A 274 PHE 0.024 0.002 PHE A 377 TYR 0.016 0.002 TYR E 583 ARG 0.003 0.001 ARG F 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 106 time to evaluate : 2.711 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.7961 (t70) cc_final: 0.7718 (t70) REVERT: A 240 ASP cc_start: 0.3580 (OUTLIER) cc_final: 0.2884 (m-30) REVERT: A 310 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6768 (mm) REVERT: A 328 TYR cc_start: 0.7204 (t80) cc_final: 0.6432 (t80) REVERT: A 330 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6785 (tp) REVERT: A 430 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6608 (mpp80) REVERT: A 491 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: B 172 HIS cc_start: 0.6991 (t70) cc_final: 0.6714 (t70) REVERT: B 352 ILE cc_start: 0.8669 (mt) cc_final: 0.8431 (mt) REVERT: B 463 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6590 (t0) REVERT: D 122 MET cc_start: 0.7387 (mmm) cc_final: 0.7012 (mmm) REVERT: D 167 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6228 (tp) REVERT: D 486 MET cc_start: 0.6515 (tmm) cc_final: 0.6283 (tmm) REVERT: E 149 VAL cc_start: 0.8745 (t) cc_final: 0.8465 (m) REVERT: E 567 PRO cc_start: 0.6619 (Cg_exo) cc_final: 0.6301 (Cg_endo) REVERT: F 244 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6072 (pp20) REVERT: F 277 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (mm) outliers start: 86 outliers final: 63 residues processed: 183 average time/residue: 0.3084 time to fit residues: 93.5168 Evaluate side-chains 174 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 102 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22562 Z= 0.346 Angle : 0.619 8.683 30553 Z= 0.323 Chirality : 0.045 0.205 3478 Planarity : 0.005 0.066 3969 Dihedral : 8.686 94.934 3272 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 3.31 % Allowed : 14.26 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2779 helix: 1.20 (0.17), residues: 951 sheet: -0.52 (0.22), residues: 548 loop : -0.45 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 187 HIS 0.004 0.001 HIS A 274 PHE 0.025 0.002 PHE A 377 TYR 0.019 0.002 TYR E 583 ARG 0.004 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 108 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.7973 (t70) cc_final: 0.7728 (t70) REVERT: A 240 ASP cc_start: 0.3316 (OUTLIER) cc_final: 0.2677 (m-30) REVERT: A 328 TYR cc_start: 0.7234 (t80) cc_final: 0.6716 (t80) REVERT: A 430 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6525 (mpp80) REVERT: A 491 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: B 352 ILE cc_start: 0.8611 (mt) cc_final: 0.8366 (mt) REVERT: B 463 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6718 (t0) REVERT: D 122 MET cc_start: 0.7334 (mmm) cc_final: 0.6884 (mmm) REVERT: D 167 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6229 (tp) REVERT: D 486 MET cc_start: 0.6498 (tmm) cc_final: 0.6256 (tmm) REVERT: E 314 MET cc_start: 0.7539 (mmm) cc_final: 0.7175 (mmp) REVERT: E 373 MET cc_start: 0.4270 (ttt) cc_final: 0.3964 (ttt) REVERT: E 478 MET cc_start: 0.8428 (mtm) cc_final: 0.7935 (ptp) REVERT: E 582 VAL cc_start: 0.7659 (p) cc_final: 0.7436 (t) REVERT: F 277 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8847 (mm) outliers start: 79 outliers final: 64 residues processed: 179 average time/residue: 0.2958 time to fit residues: 87.2735 Evaluate side-chains 175 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 105 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 354 GLN Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 225 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 248 optimal weight: 0.0070 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22562 Z= 0.163 Angle : 0.529 8.441 30553 Z= 0.271 Chirality : 0.042 0.161 3478 Planarity : 0.004 0.064 3969 Dihedral : 8.198 96.772 3267 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 2.10 % Allowed : 15.60 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2779 helix: 1.59 (0.17), residues: 953 sheet: -0.35 (0.22), residues: 563 loop : -0.15 (0.19), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 187 HIS 0.002 0.001 HIS F 323 PHE 0.025 0.001 PHE A 377 TYR 0.011 0.001 TYR B 292 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 120 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.7926 (t70) cc_final: 0.7667 (t70) REVERT: A 328 TYR cc_start: 0.7006 (t80) cc_final: 0.6601 (t80) REVERT: A 354 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8211 (pp30) REVERT: A 430 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6554 (mpp80) REVERT: B 352 ILE cc_start: 0.8684 (mt) cc_final: 0.8455 (mt) REVERT: B 463 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6541 (t0) REVERT: D 122 MET cc_start: 0.7269 (mmm) cc_final: 0.6957 (mmm) REVERT: D 486 MET cc_start: 0.6447 (tmm) cc_final: 0.6177 (tmm) REVERT: E 478 MET cc_start: 0.8395 (mtm) cc_final: 0.8066 (ptp) REVERT: E 508 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7660 (mtp) REVERT: E 582 VAL cc_start: 0.7542 (p) cc_final: 0.7314 (t) REVERT: F 277 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8879 (mm) outliers start: 50 outliers final: 39 residues processed: 165 average time/residue: 0.3189 time to fit residues: 86.5880 Evaluate side-chains 152 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.0670 chunk 264 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 0.0030 overall best weight: 3.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22562 Z= 0.332 Angle : 0.614 10.738 30553 Z= 0.318 Chirality : 0.045 0.204 3478 Planarity : 0.005 0.062 3969 Dihedral : 8.478 91.217 3267 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.43 % Allowed : 15.68 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2779 helix: 1.42 (0.17), residues: 946 sheet: -0.53 (0.22), residues: 562 loop : -0.31 (0.19), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 187 HIS 0.003 0.001 HIS A 274 PHE 0.024 0.002 PHE A 377 TYR 0.015 0.002 TYR E 583 ARG 0.004 0.000 ARG F 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 105 time to evaluate : 2.547 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.7940 (t70) cc_final: 0.7683 (t70) REVERT: A 328 TYR cc_start: 0.7139 (t80) cc_final: 0.6673 (t80) REVERT: A 491 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 352 ILE cc_start: 0.8629 (mt) cc_final: 0.8381 (mt) REVERT: B 463 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6966 (t0) REVERT: D 122 MET cc_start: 0.7090 (mmm) cc_final: 0.6764 (mmm) REVERT: D 486 MET cc_start: 0.6386 (tmm) cc_final: 0.6156 (tmm) REVERT: E 314 MET cc_start: 0.7536 (mmm) cc_final: 0.7155 (mmp) REVERT: E 478 MET cc_start: 0.8399 (mtm) cc_final: 0.8033 (ptp) REVERT: E 582 VAL cc_start: 0.7608 (p) cc_final: 0.7398 (t) REVERT: F 277 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8850 (mm) outliers start: 58 outliers final: 48 residues processed: 156 average time/residue: 0.3124 time to fit residues: 79.6333 Evaluate side-chains 154 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 103 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 220 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.085077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068625 restraints weight = 80134.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070180 restraints weight = 46050.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071061 restraints weight = 30272.258| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22562 Z= 0.155 Angle : 0.529 10.509 30553 Z= 0.270 Chirality : 0.042 0.189 3478 Planarity : 0.004 0.061 3969 Dihedral : 8.177 95.496 3267 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 2.05 % Allowed : 15.97 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2779 helix: 1.62 (0.17), residues: 953 sheet: -0.36 (0.22), residues: 551 loop : -0.12 (0.19), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 187 HIS 0.002 0.001 HIS A 274 PHE 0.025 0.001 PHE A 377 TYR 0.012 0.001 TYR B 292 ARG 0.006 0.000 ARG E 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.84 seconds wall clock time: 64 minutes 16.15 seconds (3856.15 seconds total)