Starting phenix.real_space_refine on Thu Mar 5 12:42:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_13694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_13694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_13694_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_13694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7px9_13694/03_2026/7px9_13694.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.01, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 100 helices and 16 sheets defined 40.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.671A pdb=" N PHE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.625A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.648A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.606A pdb=" N LEU A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 346 through 362 Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.708A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 488 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 515 through 538 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.561A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.364A pdb=" N THR A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 317 Processing helix chain 'B' and resid 343 through 359 removed outlier: 3.553A pdb=" N LYS B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 402 Processing helix chain 'B' and resid 441 through 453 removed outlier: 3.613A pdb=" N TYR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 removed outlier: 4.126A pdb=" N GLU B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 removed outlier: 3.545A pdb=" N CYS B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'B' and resid 515 through 537 Processing helix chain 'B' and resid 543 through 559 removed outlier: 3.598A pdb=" N LEU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 578 removed outlier: 4.102A pdb=" N TRP B 570 " --> pdb=" O ASN B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.704A pdb=" N GLU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 274 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 274 through 282 Processing helix chain 'C' and resid 298 through 314 removed outlier: 3.663A pdb=" N ILE C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.892A pdb=" N ARG C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 391 Processing helix chain 'C' and resid 392 through 401 removed outlier: 3.531A pdb=" N LEU C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 470 through 487 Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 515 through 537 Processing helix chain 'C' and resid 543 through 555 removed outlier: 3.755A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 257 through 274 removed outlier: 3.962A pdb=" N LEU D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 298 through 314 removed outlier: 4.035A pdb=" N ALA D 303 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.578A pdb=" N ARG D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 442 through 453 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.716A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 487 Processing helix chain 'D' and resid 515 through 537 Processing helix chain 'D' and resid 543 through 559 removed outlier: 3.551A pdb=" N LEU D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 578 removed outlier: 4.506A pdb=" N LYS D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.519A pdb=" N VAL E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 243' Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 258 through 274 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 274 through 281 Processing helix chain 'E' and resid 298 through 318 removed outlier: 3.508A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 327 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.833A pdb=" N ARG E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 401 Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.894A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 487 Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 515 through 538 Processing helix chain 'E' and resid 543 through 558 removed outlier: 3.934A pdb=" N LEU E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 578 removed outlier: 4.159A pdb=" N ILE E 573 " --> pdb=" O ASP E 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 235 through 243 removed outlier: 3.567A pdb=" N GLU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) 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) removed outlier: 3.761A pdb=" N LEU F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 269 Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.541A pdb=" N TYR F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.600A pdb=" N TYR F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 338 removed outlier: 3.961A pdb=" N LEU F 337 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 360 Processing helix chain 'F' and resid 372 through 376 removed outlier: 3.593A pdb=" N SER F 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 400 Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 422 through 427 removed outlier: 3.571A pdb=" N LEU F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 removed outlier: 3.514A pdb=" N TYR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 4.374A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 487 Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 511 through 514 Processing helix chain 'F' and resid 515 through 537 Processing helix chain 'F' and resid 543 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 569 through 578 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=AA1, first strand: chain 'A' and resid 120 through 125 removed outlier: 7.124A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 6.059A pdb=" N LEU A 164 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 177 " --> pdb=" O LEU A 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 188 current: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'B' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 188 current: chain 'B' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 228 through 233 current: chain 'C' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 188 current: chain 'C' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 228 through 233 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 188 current: chain 'D' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 228 through 233 current: chain 'E' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 188 current: chain 'E' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 228 through 232 current: chain 'F' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 188 current: chain 'F' and resid 228 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.824A pdb=" N ASP A 371 " --> pdb=" O ILE A 332 " (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: 6.523A pdb=" N VAL A 289 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 415 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 291 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.852A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.451A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 120 through 125 current: chain 'B' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 151 through 152 current: chain 'E' and resid 112 through 117 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.635A pdb=" N LEU B 330 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 371 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 332 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 107 removed outlier: 6.731A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 120 through 125 current: chain 'C' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 152 current: chain 'D' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 120 through 125 current: chain 'D' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 151 through 152 current: chain 'F' and resid 112 through 117 Processing sheet with id=AA9, first strand: chain 'C' and resid 328 through 332 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) removed outlier: 6.425A pdb=" N GLY C 288 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 435 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 290 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 505 through 509 Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 333 removed outlier: 6.944A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 366 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 412 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 368 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA D 414 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE D 370 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY D 288 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE D 435 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 290 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.405A pdb=" N LEU E 330 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP E 371 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 289 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER E 415 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 291 " --> pdb=" O SER E 415 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 288 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE E 435 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU E 290 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 505 through 509 Processing sheet with id=AB6, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.889A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (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) Processing sheet with id=AB7, first strand: chain 'F' and resid 506 through 509 858 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.63 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: 0.00 - 4.26: 30455 4.26 - 8.53: 83 8.53 - 12.79: 5 12.79 - 17.06: 2 17.06 - 21.32: 8 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: 220 2.58 - 3.16: 18511 3.16 - 3.74: 34499 3.74 - 4.32: 46222 4.32 - 4.90: 77471 Nonbonded interactions: 176923 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 176918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- 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= 0.258 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 : 3.71 % Favored : 96.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (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 ARG 0.003 0.000 ARG E 378 TYR 0.008 0.001 TYR A 449 PHE 0.008 0.001 PHE E 353 TRP 0.009 0.001 TRP C 570 HIS 0.002 0.000 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00338 (22562) covalent geometry : angle 0.67580 (30553) hydrogen bonds : bond 0.13944 ( 858) hydrogen bonds : angle 5.11451 ( 2460) *********************** 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 to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.845 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: 0.6976 (t0) REVERT: B 172 HIS cc_start: 0.6917 (t70) cc_final: 0.6573 (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: 0.6117 (tp) REVERT: C 536 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: C 570 TRP cc_start: 0.5759 (m-90) cc_final: 0.3922 (m-90) REVERT: D 420 MET cc_start: 0.5305 (ttt) cc_final: 0.4949 (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: 0.7808 (mmm) REVERT: F 244 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5745 (pp20) REVERT: F 330 LEU cc_start: 0.8913 (mp) cc_final: 0.8703 (mp) REVERT: F 407 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6444 (mm-30) outliers start: 45 outliers final: 14 residues processed: 290 average time/residue: 0.1643 time to fit residues: 72.4543 Evaluate side-chains 140 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN D 416 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN F 521 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.087548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071214 restraints weight = 80339.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072513 restraints weight = 46512.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073559 restraints weight = 30185.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073768 restraints weight = 25184.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073797 restraints weight = 22881.993| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1235 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= 0.148 Angle : 0.559 8.263 30553 Z= 0.289 Chirality : 0.043 0.153 3478 Planarity : 0.004 0.070 3969 Dihedral : 8.700 116.753 3280 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.14 % Allowed : 8.09 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2779 helix: 1.95 (0.17), residues: 979 sheet: 0.44 (0.23), residues: 557 loop : 0.36 (0.20), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 572 TYR 0.018 0.001 TYR A 328 PHE 0.026 0.002 PHE C 272 TRP 0.014 0.001 TRP C 570 HIS 0.004 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00345 (22562) covalent geometry : angle 0.55941 (30553) hydrogen bonds : bond 0.03795 ( 858) hydrogen bonds : angle 4.43388 ( 2460) *********************** 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 182 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: B 172 HIS cc_start: 0.7050 (t70) cc_final: 0.6654 (t70) REVERT: C 160 GLU cc_start: 0.7138 (pm20) cc_final: 0.6810 (pm20) REVERT: C 281 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: C 536 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: C 570 TRP cc_start: 0.6418 (m-90) cc_final: 0.4118 (t-100) REVERT: D 167 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6366 (tp) REVERT: D 420 MET cc_start: 0.5304 (ttt) cc_final: 0.5086 (tpp) REVERT: D 486 MET cc_start: 0.6796 (tmm) cc_final: 0.6458 (tmm) REVERT: E 508 MET cc_start: 0.8044 (mtp) cc_final: 0.7613 (mtp) REVERT: F 244 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5817 (pp20) outliers start: 51 outliers final: 31 residues processed: 175 average time/residue: 0.1423 time to fit residues: 40.2375 Evaluate side-chains 148 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 551 ILE 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 345 THR 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 167 ILE 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 G residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 213 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069348 restraints weight = 80791.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070945 restraints weight = 46856.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071773 restraints weight = 29921.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071986 restraints weight = 25536.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072006 restraints weight = 23679.980| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22562 Z= 0.167 Angle : 0.563 7.174 30553 Z= 0.291 Chirality : 0.043 0.162 3478 Planarity : 0.004 0.063 3969 Dihedral : 8.647 117.014 3276 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.98 % Allowed : 8.51 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2779 helix: 1.77 (0.17), residues: 983 sheet: 0.28 (0.23), residues: 558 loop : 0.27 (0.20), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 572 TYR 0.012 0.001 TYR E 583 PHE 0.021 0.002 PHE C 377 TRP 0.009 0.001 TRP C 570 HIS 0.004 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00382 (22562) covalent geometry : angle 0.56265 (30553) hydrogen bonds : bond 0.03582 ( 858) hydrogen bonds : angle 4.34805 ( 2460) *********************** 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 192 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 121 time to evaluate : 0.974 Fit side-chains REVERT: B 172 HIS cc_start: 0.7117 (t70) cc_final: 0.6699 (t70) REVERT: B 463 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6331 (t0) REVERT: C 160 GLU cc_start: 0.7522 (pm20) cc_final: 0.7203 (pm20) REVERT: C 281 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 570 TRP cc_start: 0.6792 (m-90) cc_final: 0.4382 (m-90) REVERT: D 167 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6140 (tp) REVERT: D 420 MET cc_start: 0.5760 (ttt) cc_final: 0.5415 (tpp) REVERT: D 486 MET cc_start: 0.6697 (tmm) cc_final: 0.6277 (tmm) REVERT: E 228 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: E 508 MET cc_start: 0.8075 (mtp) cc_final: 0.7654 (mtp) REVERT: F 244 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5954 (pp20) outliers start: 71 outliers final: 33 residues processed: 183 average time/residue: 0.1379 time to fit residues: 41.3748 Evaluate side-chains 148 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL 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 A residue 518 MET Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR 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 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR 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 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 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 459 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 160 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** E 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068800 restraints weight = 80880.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070029 restraints weight = 46678.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070751 restraints weight = 31600.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071150 restraints weight = 26765.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071181 restraints weight = 24229.899| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.004 0.049 22562 Z= 0.171 Angle : 0.570 7.385 30553 Z= 0.295 Chirality : 0.044 0.174 3478 Planarity : 0.004 0.059 3969 Dihedral : 8.700 115.439 3275 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.81 % Allowed : 9.48 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2779 helix: 1.62 (0.17), residues: 985 sheet: 0.08 (0.23), residues: 539 loop : 0.12 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 572 TYR 0.013 0.001 TYR E 583 PHE 0.027 0.002 PHE A 377 TRP 0.017 0.002 TRP F 187 HIS 0.004 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00400 (22562) covalent geometry : angle 0.57046 (30553) hydrogen bonds : bond 0.03547 ( 858) hydrogen bonds : angle 4.35150 ( 2460) *********************** 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 183 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 116 time to evaluate : 0.633 Fit side-chains REVERT: A 430 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6783 (mpp80) REVERT: B 172 HIS cc_start: 0.7097 (t70) cc_final: 0.6781 (t70) REVERT: B 463 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6641 (t0) REVERT: C 122 MET cc_start: 0.6533 (mpp) cc_final: 0.6317 (mpp) REVERT: C 182 GLU cc_start: 0.7983 (tt0) cc_final: 0.7707 (pm20) REVERT: C 281 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: C 570 TRP cc_start: 0.6724 (m-90) cc_final: 0.4399 (m-90) REVERT: D 122 MET cc_start: 0.7265 (mmm) cc_final: 0.6989 (mmm) REVERT: D 420 MET cc_start: 0.5652 (ttt) cc_final: 0.5270 (tpp) REVERT: D 486 MET cc_start: 0.6822 (tmm) cc_final: 0.6389 (tmm) REVERT: D 497 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: E 420 MET cc_start: 0.7914 (mtp) cc_final: 0.7658 (mtm) REVERT: E 508 MET cc_start: 0.8148 (mtp) cc_final: 0.7759 (mtp) REVERT: F 244 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5936 (pp20) outliers start: 67 outliers final: 42 residues processed: 175 average time/residue: 0.1325 time to fit residues: 38.4437 Evaluate side-chains 156 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 242 VAL 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 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 244 GLU 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 536 GLU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR 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 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 577 LYS 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 497 GLU 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 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 459 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 275 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 156 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.8764 ------------------------------------------------------------------------------- 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 546 HIS D 348 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066644 restraints weight = 80620.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068070 restraints weight = 46939.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068733 restraints weight = 31271.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069173 restraints weight = 26611.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069175 restraints weight = 24275.240| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22562 Z= 0.258 Angle : 0.660 8.095 30553 Z= 0.345 Chirality : 0.046 0.193 3478 Planarity : 0.005 0.061 3969 Dihedral : 9.049 110.325 3275 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.85 % Allowed : 11.19 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2779 helix: 1.31 (0.17), residues: 973 sheet: -0.19 (0.22), residues: 531 loop : -0.22 (0.19), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 494 TYR 0.019 0.002 TYR E 583 PHE 0.026 0.002 PHE C 377 TRP 0.016 0.002 TRP E 570 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00601 (22562) covalent geometry : angle 0.65951 (30553) hydrogen bonds : bond 0.04249 ( 858) hydrogen bonds : angle 4.64169 ( 2460) *********************** 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 177 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 109 time to evaluate : 0.848 Fit side-chains REVERT: A 110 ASP cc_start: 0.7942 (t70) cc_final: 0.7710 (t70) REVERT: A 430 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6515 (mpp80) REVERT: B 172 HIS cc_start: 0.7165 (t70) cc_final: 0.6883 (t70) REVERT: B 352 ILE cc_start: 0.8704 (mt) cc_final: 0.8428 (mm) REVERT: B 463 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6751 (t0) REVERT: C 281 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: D 122 MET cc_start: 0.7313 (mmm) cc_final: 0.7040 (mmm) REVERT: D 420 MET cc_start: 0.5320 (ttt) cc_final: 0.5050 (tpp) REVERT: D 486 MET cc_start: 0.6617 (tmm) cc_final: 0.6349 (tmm) REVERT: E 508 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: E 567 PRO cc_start: 0.6597 (Cg_exo) cc_final: 0.6345 (Cg_endo) REVERT: F 244 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6006 (pp20) outliers start: 68 outliers final: 45 residues processed: 168 average time/residue: 0.1297 time to fit residues: 36.4241 Evaluate side-chains 151 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU 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 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 222 VAL Chi-restraints excluded: chain B residue 244 GLU 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 386 SER Chi-restraints excluded: chain B residue 463 ASP 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 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 499 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 577 LYS 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 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 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 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 459 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 196 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 28 optimal weight: 0.0050 chunk 222 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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** E 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068517 restraints weight = 79876.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069844 restraints weight = 45955.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070631 restraints weight = 30750.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070890 restraints weight = 26142.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070968 restraints weight = 24508.989| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22562 Z= 0.124 Angle : 0.547 9.832 30553 Z= 0.282 Chirality : 0.043 0.166 3478 Planarity : 0.004 0.055 3969 Dihedral : 8.664 114.435 3274 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.22 % Allowed : 12.33 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2779 helix: 1.49 (0.17), residues: 982 sheet: -0.14 (0.23), residues: 529 loop : -0.02 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 427 TYR 0.013 0.001 TYR C 452 PHE 0.026 0.001 PHE A 377 TRP 0.015 0.001 TRP F 187 HIS 0.007 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00287 (22562) covalent geometry : angle 0.54734 (30553) hydrogen bonds : bond 0.03263 ( 858) hydrogen bonds : angle 4.27200 ( 2460) *********************** 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 169 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.931 Fit side-chains REVERT: A 110 ASP cc_start: 0.7979 (t70) cc_final: 0.7745 (t70) REVERT: A 354 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8218 (pp30) REVERT: A 430 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6288 (mpp80) REVERT: B 172 HIS cc_start: 0.7074 (t70) cc_final: 0.6776 (t70) REVERT: B 463 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6746 (t0) REVERT: C 122 MET cc_start: 0.6534 (mpp) cc_final: 0.6326 (mpp) REVERT: C 182 GLU cc_start: 0.7896 (tt0) cc_final: 0.7646 (pm20) REVERT: C 281 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: C 570 TRP cc_start: 0.6666 (m-90) cc_final: 0.4468 (m-90) REVERT: D 122 MET cc_start: 0.7559 (mmm) cc_final: 0.7133 (mmm) REVERT: D 420 MET cc_start: 0.5634 (ttt) cc_final: 0.5245 (tpp) REVERT: D 486 MET cc_start: 0.6682 (tmm) cc_final: 0.6467 (tmm) REVERT: E 373 MET cc_start: 0.4311 (ttt) cc_final: 0.4073 (ttt) REVERT: E 508 MET cc_start: 0.8060 (mtp) cc_final: 0.7608 (mtp) REVERT: E 567 PRO cc_start: 0.6131 (Cg_exo) cc_final: 0.5923 (Cg_endo) REVERT: F 244 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6090 (pp20) outliers start: 53 outliers final: 38 residues processed: 160 average time/residue: 0.1311 time to fit residues: 35.0947 Evaluate side-chains 146 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL 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 A residue 518 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 331 ASN 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 386 SER Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 565 THR 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 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 577 LYS 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 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 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 244 GLU Chi-restraints excluded: chain F residue 332 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 121 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** C 514 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS G 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.082835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066144 restraints weight = 81138.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067943 restraints weight = 46866.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068376 restraints weight = 30299.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068593 restraints weight = 27466.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068648 restraints weight = 26756.657| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22562 Z= 0.250 Angle : 0.662 9.813 30553 Z= 0.344 Chirality : 0.046 0.202 3478 Planarity : 0.005 0.062 3969 Dihedral : 9.024 109.100 3274 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.56 % Allowed : 12.96 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2779 helix: 1.22 (0.17), residues: 973 sheet: -0.32 (0.22), residues: 536 loop : -0.29 (0.19), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 494 TYR 0.018 0.002 TYR E 583 PHE 0.026 0.002 PHE C 377 TRP 0.014 0.002 TRP F 187 HIS 0.005 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00585 (22562) covalent geometry : angle 0.66230 (30553) hydrogen bonds : bond 0.04275 ( 858) hydrogen bonds : angle 4.64246 ( 2460) *********************** 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 164 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 103 time to evaluate : 0.900 Fit side-chains REVERT: A 110 ASP cc_start: 0.8008 (t70) cc_final: 0.7783 (t70) REVERT: A 328 TYR cc_start: 0.7435 (t80) cc_final: 0.6706 (t80) REVERT: A 430 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6543 (mpp80) REVERT: B 172 HIS cc_start: 0.7209 (t70) cc_final: 0.6919 (t70) REVERT: B 352 ILE cc_start: 0.8666 (mt) cc_final: 0.8395 (mm) REVERT: B 463 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6725 (t0) REVERT: C 281 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: D 122 MET cc_start: 0.7392 (mmm) cc_final: 0.6993 (mmm) REVERT: D 486 MET cc_start: 0.6659 (tmm) cc_final: 0.6431 (tmm) REVERT: E 420 MET cc_start: 0.8047 (mtp) cc_final: 0.7822 (mtm) REVERT: E 478 MET cc_start: 0.8597 (mtm) cc_final: 0.8083 (ptp) REVERT: E 518 MET cc_start: 0.8794 (ttm) cc_final: 0.8468 (ttm) REVERT: E 567 PRO cc_start: 0.6531 (Cg_exo) cc_final: 0.6313 (Cg_endo) REVERT: F 244 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6260 (pp20) outliers start: 61 outliers final: 42 residues processed: 155 average time/residue: 0.1354 time to fit residues: 35.3938 Evaluate side-chains 148 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU 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 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 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 331 ASN 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 386 SER Chi-restraints excluded: chain B residue 463 ASP 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 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 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 577 LYS 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 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 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 244 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 51 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 173 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 563 ASN ** D 460 HIS ** 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 = 0.3637 r_free = 0.3637 target = 0.085353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068812 restraints weight = 79768.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070307 restraints weight = 45959.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071201 restraints weight = 29735.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071408 restraints weight = 26290.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071467 restraints weight = 23132.231| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2779 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= 0.106 Angle : 0.542 10.163 30553 Z= 0.278 Chirality : 0.043 0.158 3478 Planarity : 0.004 0.062 3969 Dihedral : 8.556 111.878 3274 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.68 % Allowed : 13.92 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2779 helix: 1.52 (0.17), residues: 978 sheet: -0.19 (0.22), residues: 549 loop : -0.04 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 427 TYR 0.010 0.001 TYR C 452 PHE 0.026 0.001 PHE A 377 TRP 0.020 0.001 TRP F 187 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00240 (22562) covalent geometry : angle 0.54215 (30553) hydrogen bonds : bond 0.03069 ( 858) hydrogen bonds : angle 4.19617 ( 2460) *********************** 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 153 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.896 Fit side-chains REVERT: A 110 ASP cc_start: 0.7952 (t70) cc_final: 0.7713 (t70) REVERT: A 354 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8146 (pp30) REVERT: A 430 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6364 (mpp80) REVERT: B 172 HIS cc_start: 0.6791 (t70) cc_final: 0.6491 (t70) REVERT: B 463 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6783 (t0) REVERT: C 101 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: C 281 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: C 570 TRP cc_start: 0.6401 (m-90) cc_final: 0.4241 (m-90) REVERT: D 122 MET cc_start: 0.7373 (mmm) cc_final: 0.7015 (mmm) REVERT: D 514 ASN cc_start: 0.7674 (t0) cc_final: 0.7267 (t0) REVERT: E 478 MET cc_start: 0.8520 (mtm) cc_final: 0.8144 (ptp) REVERT: E 518 MET cc_start: 0.8654 (ttm) cc_final: 0.8341 (ttm) REVERT: E 567 PRO cc_start: 0.6116 (Cg_exo) cc_final: 0.5873 (Cg_endo) outliers start: 40 outliers final: 31 residues processed: 149 average time/residue: 0.1435 time to fit residues: 35.2582 Evaluate side-chains 141 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain C residue 101 TYR 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 499 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 577 LYS 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 E residue 246 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 132 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 460 HIS ** 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 = 0.3631 r_free = 0.3631 target = 0.085055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068448 restraints weight = 80305.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069891 restraints weight = 47387.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070673 restraints weight = 31077.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070959 restraints weight = 26918.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071024 restraints weight = 24811.796| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22562 Z= 0.124 Angle : 0.548 10.431 30553 Z= 0.280 Chirality : 0.043 0.171 3478 Planarity : 0.004 0.058 3969 Dihedral : 8.439 109.063 3271 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 14.09 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2779 helix: 1.59 (0.17), residues: 979 sheet: -0.14 (0.22), residues: 549 loop : -0.03 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.012 0.001 TYR C 452 PHE 0.026 0.001 PHE A 377 TRP 0.022 0.002 TRP F 187 HIS 0.002 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00290 (22562) covalent geometry : angle 0.54846 (30553) hydrogen bonds : bond 0.03128 ( 858) hydrogen bonds : angle 4.14400 ( 2460) *********************** 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 150 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.879 Fit side-chains REVERT: A 110 ASP cc_start: 0.7955 (t70) cc_final: 0.7716 (t70) REVERT: A 328 TYR cc_start: 0.7597 (t80) cc_final: 0.6893 (t80) REVERT: A 354 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8150 (pp30) REVERT: A 430 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6534 (mpp80) REVERT: B 172 HIS cc_start: 0.6822 (t70) cc_final: 0.6510 (t70) REVERT: B 463 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7004 (t0) REVERT: C 101 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: C 281 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: C 570 TRP cc_start: 0.6471 (m-90) cc_final: 0.4236 (m-90) REVERT: D 122 MET cc_start: 0.7408 (mmm) cc_final: 0.7040 (mmm) REVERT: D 420 MET cc_start: 0.5017 (ttt) cc_final: 0.4507 (tpp) REVERT: D 486 MET cc_start: 0.5695 (tmm) cc_final: 0.5468 (tmm) REVERT: E 478 MET cc_start: 0.8545 (mtm) cc_final: 0.8218 (ptp) REVERT: E 518 MET cc_start: 0.8693 (ttm) cc_final: 0.8381 (ttm) REVERT: E 567 PRO cc_start: 0.6073 (Cg_exo) cc_final: 0.5829 (Cg_endo) outliers start: 43 outliers final: 34 residues processed: 147 average time/residue: 0.1309 time to fit residues: 32.0594 Evaluate side-chains 143 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 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 386 SER Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain C residue 101 TYR 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 499 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 577 LYS 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 E residue 246 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 244 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 225 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** D 460 HIS ** 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 = 0.3598 r_free = 0.3598 target = 0.083542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067233 restraints weight = 80765.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068258 restraints weight = 46535.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069302 restraints weight = 32206.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069421 restraints weight = 27084.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069497 restraints weight = 25036.604| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3025 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= 0.192 Angle : 0.609 10.579 30553 Z= 0.314 Chirality : 0.045 0.202 3478 Planarity : 0.005 0.068 3969 Dihedral : 8.739 107.810 3271 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.84 % Allowed : 14.13 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2779 helix: 1.45 (0.17), residues: 972 sheet: -0.32 (0.22), residues: 549 loop : -0.18 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 485 TYR 0.017 0.002 TYR C 452 PHE 0.024 0.002 PHE A 377 TRP 0.025 0.002 TRP F 187 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00451 (22562) covalent geometry : angle 0.60884 (30553) hydrogen bonds : bond 0.03759 ( 858) hydrogen bonds : angle 4.38644 ( 2460) ********************** 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 149 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.853 Fit side-chains REVERT: A 110 ASP cc_start: 0.7968 (t70) cc_final: 0.7733 (t70) REVERT: A 328 TYR cc_start: 0.7389 (t80) cc_final: 0.6731 (t80) REVERT: A 354 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8222 (pp30) REVERT: A 430 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6393 (mpp80) REVERT: B 463 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6918 (t0) REVERT: C 101 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6922 (m-10) REVERT: C 281 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: C 570 TRP cc_start: 0.6482 (m-90) cc_final: 0.4250 (m-90) REVERT: D 122 MET cc_start: 0.7522 (mmm) cc_final: 0.7214 (mmm) REVERT: D 486 MET cc_start: 0.5553 (tmm) cc_final: 0.5343 (tmm) REVERT: E 478 MET cc_start: 0.8567 (mtm) cc_final: 0.8205 (ptp) REVERT: E 518 MET cc_start: 0.8735 (ttm) cc_final: 0.8437 (ttm) outliers start: 44 outliers final: 35 residues processed: 145 average time/residue: 0.1357 time to fit residues: 32.7444 Evaluate side-chains 143 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 ILE Chi-restraints excluded: chain B residue 331 ASN 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 386 SER Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain C residue 101 TYR 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 499 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 577 LYS 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 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 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 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 169 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 109 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.0030 chunk 175 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- 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 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.084656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067979 restraints weight = 80283.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069581 restraints weight = 47382.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070238 restraints weight = 30329.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070471 restraints weight = 26917.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070499 restraints weight = 25117.266| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22562 Z= 0.128 Angle : 0.558 9.745 30553 Z= 0.286 Chirality : 0.043 0.195 3478 Planarity : 0.004 0.068 3969 Dihedral : 8.550 107.837 3271 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.84 % Allowed : 14.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2779 helix: 1.53 (0.17), residues: 978 sheet: -0.23 (0.22), residues: 544 loop : -0.12 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 427 TYR 0.011 0.001 TYR C 452 PHE 0.025 0.001 PHE A 377 TRP 0.025 0.002 TRP F 187 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00299 (22562) covalent geometry : angle 0.55752 (30553) hydrogen bonds : bond 0.03212 ( 858) hydrogen bonds : angle 4.19973 ( 2460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.85 seconds wall clock time: 49 minutes 58.09 seconds (2998.09 seconds total)