Starting phenix.real_space_refine on Mon May 19 23:12:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekl_28206/05_2025/8ekl_28206.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 12061 2.51 5 N 3157 2.21 5 O 4067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19334 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "G" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.67, per 1000 atoms: 0.60 Number of scatterers: 19334 At special positions: 0 Unit cell: (139.573, 139.573, 124.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4067 8.00 N 3157 7.00 C 12061 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: 4.68 Conformation dependent library (CDL) restraints added in 2.7 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4634 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 22.0% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.771A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 4.506A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.560A pdb=" N ASP A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.019A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.906A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 512 removed outlier: 4.489A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.893A pdb=" N ASP B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.567A pdb=" N GLY C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.919A pdb=" N LYS C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 512 removed outlier: 4.549A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 594 removed outlier: 3.730A pdb=" N ASP C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.508A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.542A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.957A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 503 through 512 removed outlier: 4.492A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 590 removed outlier: 3.787A pdb=" N ASP D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 4.066A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 471 removed outlier: 3.875A pdb=" N LYS E 469 " --> pdb=" O ASP E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 512 removed outlier: 4.554A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 594 removed outlier: 3.807A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER E 591 " --> pdb=" O LYS E 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 592 " --> pdb=" O ILE E 588 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.796A pdb=" N GLU F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 233 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.023A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 471 removed outlier: 3.625A pdb=" N LYS F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 512 removed outlier: 4.594A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 590 removed outlier: 3.834A pdb=" N ASP F 590 " --> pdb=" O ASN F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.705A pdb=" N GLU G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.515A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 471 removed outlier: 3.780A pdb=" N LYS G 469 " --> pdb=" O ASP G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 512 removed outlier: 4.593A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 590 removed outlier: 3.843A pdb=" N ASP G 590 " --> pdb=" O ASN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 311 removed outlier: 6.664A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.979A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 372 through 382 removed outlier: 3.621A pdb=" N SER D 380 " --> pdb=" O HIS D 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 374 through 382 current: chain 'C' and resid 313 through 322 removed outlier: 3.527A pdb=" N LYS C 321 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 374 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 321 " --> pdb=" O TRP G 375 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP G 375 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 374 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 320 " --> pdb=" O SER G 374 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 380 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 374 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 320 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 321 " --> pdb=" O TRP E 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 375 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 374 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 320 " --> pdb=" O SER E 374 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 321 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 375 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.792A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.556A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.938A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.677A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 311 removed outlier: 6.666A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.546A pdb=" N TYR C 439 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.758A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 524 through 531 removed outlier: 3.809A pdb=" N GLU C 524 " --> pdb=" O THR C 521 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.719A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS D 405 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN D 486 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 531 removed outlier: 3.825A pdb=" N GLU D 524 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AD3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'E' and resid 301 through 311 removed outlier: 6.712A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.012A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.778A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AD8, first strand: chain 'E' and resid 524 through 531 removed outlier: 3.822A pdb=" N GLU E 524 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AE1, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE2, first strand: chain 'F' and resid 300 through 311 removed outlier: 5.811A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.523A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.690A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AE6, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.296A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AE8, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'G' and resid 301 through 311 removed outlier: 6.876A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.972A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.823A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS G 405 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN G 486 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF4, first strand: chain 'G' and resid 526 through 531 Processing sheet with id=AF5, first strand: chain 'G' and resid 558 through 559 592 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6419 1.34 - 1.46: 3530 1.46 - 1.57: 9616 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 19628 Sorted by residual: bond pdb=" CB ASP E 471 " pdb=" CG ASP E 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" CB ASP G 471 " pdb=" CG ASP G 471 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB ASP F 471 " pdb=" CG ASP F 471 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 ... (remaining 19623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 26171 1.48 - 2.95: 362 2.95 - 4.43: 46 4.43 - 5.91: 17 5.91 - 7.39: 4 Bond angle restraints: 26600 Sorted by residual: angle pdb=" CA GLU A 522 " pdb=" CB GLU A 522 " pdb=" CG GLU A 522 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.72e+00 angle pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 angle pdb=" C GLU G 522 " pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " ideal model delta sigma weight residual 109.53 114.32 -4.79 1.65e+00 3.67e-01 8.42e+00 angle pdb=" C ARG G 290 " pdb=" N ASP G 291 " pdb=" CA ASP G 291 " ideal model delta sigma weight residual 120.97 113.58 7.39 2.84e+00 1.24e-01 6.76e+00 angle pdb=" C GLU A 522 " pdb=" CA GLU A 522 " pdb=" CB GLU A 522 " ideal model delta sigma weight residual 109.53 113.77 -4.24 1.65e+00 3.67e-01 6.61e+00 ... (remaining 26595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10050 17.97 - 35.95: 1396 35.95 - 53.92: 442 53.92 - 71.89: 68 71.89 - 89.87: 35 Dihedral angle restraints: 11991 sinusoidal: 4760 harmonic: 7231 Sorted by residual: dihedral pdb=" CA ASN G 223 " pdb=" C ASN G 223 " pdb=" N ASP G 224 " pdb=" CA ASP G 224 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASN C 223 " pdb=" C ASN C 223 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN A 223 " pdb=" C ASN A 223 " pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1752 0.028 - 0.057: 784 0.057 - 0.085: 255 0.085 - 0.113: 183 0.113 - 0.141: 50 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE G 460 " pdb=" N ILE G 460 " pdb=" C ILE G 460 " pdb=" CB ILE G 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE D 460 " pdb=" N ILE D 460 " pdb=" C ILE D 460 " pdb=" CB ILE D 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 3021 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 269 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO B 270 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 269 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 270 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 522 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C GLU A 522 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU A 522 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN A 523 " -0.007 2.00e-02 2.50e+03 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 455 2.67 - 3.23: 16720 3.23 - 3.79: 27800 3.79 - 4.34: 40059 4.34 - 4.90: 68324 Nonbonded interactions: 153358 Sorted by model distance: nonbonded pdb=" OE1 GLU G 522 " pdb=" ND2 ASN G 523 " model vdw 2.117 3.120 nonbonded pdb=" OD1 ASP C 222 " pdb="CA CA C 901 " model vdw 2.183 2.510 nonbonded pdb=" OE1 GLU A 522 " pdb=" ND2 ASN A 523 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASP E 222 " pdb="CA CA E 901 " model vdw 2.194 2.510 nonbonded pdb=" OD1 ASP A 222 " pdb="CA CA A 901 " model vdw 2.197 2.510 ... (remaining 153353 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.940 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 0.030 19628 Z= 0.116 Angle : 0.471 7.386 26600 Z= 0.256 Chirality : 0.043 0.141 3024 Planarity : 0.003 0.037 3472 Dihedral : 18.449 89.867 7357 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.18 % Allowed : 35.07 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2457 helix: -1.18 (0.25), residues: 385 sheet: 0.09 (0.21), residues: 630 loop : -0.66 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.013 0.001 PHE D 281 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.22551 ( 587) hydrogen bonds : angle 8.46102 ( 1464) covalent geometry : bond 0.00265 (19628) covalent geometry : angle 0.47089 (26600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 2.189 Fit side-chains REVERT: D 313 GLU cc_start: 0.8574 (pm20) cc_final: 0.8254 (pm20) outliers start: 4 outliers final: 3 residues processed: 219 average time/residue: 0.2614 time to fit residues: 93.2685 Evaluate side-chains 220 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain G residue 377 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 431 ASN D 431 ASN E 431 ASN F 431 ASN G 431 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096167 restraints weight = 27626.686| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.18 r_work: 0.2969 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19628 Z= 0.222 Angle : 0.558 7.695 26600 Z= 0.299 Chirality : 0.046 0.152 3024 Planarity : 0.004 0.045 3472 Dihedral : 4.623 33.151 2651 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.73 % Allowed : 32.07 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2457 helix: -1.36 (0.23), residues: 406 sheet: 0.17 (0.21), residues: 616 loop : -0.83 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.002 0.001 HIS F 314 PHE 0.025 0.002 PHE C 281 TYR 0.013 0.001 TYR B 439 ARG 0.002 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 587) hydrogen bonds : angle 5.64661 ( 1464) covalent geometry : bond 0.00545 (19628) covalent geometry : angle 0.55845 (26600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: C 380 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8329 (t) REVERT: D 223 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: D 380 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8000 (t) REVERT: F 458 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.6934 (ttt-90) outliers start: 81 outliers final: 47 residues processed: 276 average time/residue: 0.2644 time to fit residues: 118.7137 Evaluate side-chains 254 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 112 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 243 optimal weight: 0.0010 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN C 252 GLN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100843 restraints weight = 27061.693| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.15 r_work: 0.3073 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19628 Z= 0.098 Angle : 0.462 6.675 26600 Z= 0.249 Chirality : 0.043 0.143 3024 Planarity : 0.004 0.041 3472 Dihedral : 4.233 22.070 2647 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 32.12 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2457 helix: -1.27 (0.22), residues: 441 sheet: 0.45 (0.21), residues: 567 loop : -0.80 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.014 0.001 PHE G 281 TYR 0.017 0.001 TYR C 396 ARG 0.002 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02772 ( 587) hydrogen bonds : angle 5.13022 ( 1464) covalent geometry : bond 0.00234 (19628) covalent geometry : angle 0.46157 (26600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8576 (pm20) cc_final: 0.8306 (pt0) REVERT: A 379 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 612 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (tt) REVERT: C 252 GLN cc_start: 0.8223 (mm110) cc_final: 0.8004 (mm-40) REVERT: C 380 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8346 (t) REVERT: C 524 GLU cc_start: 0.7529 (tp30) cc_final: 0.7287 (tp30) REVERT: D 313 GLU cc_start: 0.8632 (pm20) cc_final: 0.8192 (pm20) REVERT: D 376 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7251 (m-40) REVERT: D 380 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8020 (t) REVERT: D 589 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7601 (ttpp) REVERT: F 458 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.6986 (ttt-90) REVERT: F 482 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8757 (pt0) REVERT: G 467 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8360 (tp) outliers start: 62 outliers final: 31 residues processed: 278 average time/residue: 0.2667 time to fit residues: 119.0220 Evaluate side-chains 254 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 480 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 140 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 46 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN E 425 GLN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099853 restraints weight = 27560.296| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.18 r_work: 0.3001 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19628 Z= 0.095 Angle : 0.447 6.673 26600 Z= 0.241 Chirality : 0.043 0.142 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.090 20.848 2647 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.06 % Allowed : 30.88 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2457 helix: -1.14 (0.23), residues: 441 sheet: 0.43 (0.21), residues: 602 loop : -0.70 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.014 0.001 PHE C 281 TYR 0.016 0.001 TYR C 396 ARG 0.001 0.000 ARG F 528 Details of bonding type rmsd hydrogen bonds : bond 0.02391 ( 587) hydrogen bonds : angle 4.84838 ( 1464) covalent geometry : bond 0.00227 (19628) covalent geometry : angle 0.44728 (26600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 223 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 491 ASN cc_start: 0.7780 (p0) cc_final: 0.7564 (p0) REVERT: B 482 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8961 (pt0) REVERT: B 491 ASN cc_start: 0.7503 (p0) cc_final: 0.7251 (p0) REVERT: B 612 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 380 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8376 (t) REVERT: C 524 GLU cc_start: 0.7509 (tp30) cc_final: 0.7282 (tp30) REVERT: D 313 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: D 380 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8019 (t) REVERT: D 589 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7428 (ttpp) REVERT: E 589 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7359 (ttpp) REVERT: F 458 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7015 (ttt-90) REVERT: G 467 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8302 (tp) REVERT: G 474 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7553 (tttt) outliers start: 88 outliers final: 46 residues processed: 299 average time/residue: 0.2819 time to fit residues: 134.9875 Evaluate side-chains 274 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 70 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 0.0570 chunk 242 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 231 optimal weight: 0.4980 chunk 209 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 overall best weight: 2.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN C 567 ASN D 376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098285 restraints weight = 27751.316| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.19 r_work: 0.2979 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19628 Z= 0.142 Angle : 0.482 7.003 26600 Z= 0.259 Chirality : 0.044 0.140 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.228 22.256 2647 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.92 % Allowed : 31.43 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2457 helix: -1.11 (0.23), residues: 434 sheet: 0.53 (0.21), residues: 567 loop : -0.71 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 503 HIS 0.001 0.000 HIS F 314 PHE 0.019 0.002 PHE F 281 TYR 0.014 0.001 TYR C 396 ARG 0.001 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 587) hydrogen bonds : angle 4.81628 ( 1464) covalent geometry : bond 0.00349 (19628) covalent geometry : angle 0.48213 (26600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 217 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7782 (tt) REVERT: B 612 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8362 (tt) REVERT: C 380 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8361 (t) REVERT: C 524 GLU cc_start: 0.7540 (tp30) cc_final: 0.7327 (tp30) REVERT: D 380 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7967 (t) REVERT: D 589 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7649 (ttpp) REVERT: E 482 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: E 589 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7359 (ttpp) REVERT: F 458 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7009 (ttt-90) REVERT: G 467 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8303 (tp) REVERT: G 474 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7598 (tttt) outliers start: 85 outliers final: 60 residues processed: 292 average time/residue: 0.2657 time to fit residues: 124.5276 Evaluate side-chains 280 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 210 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 217 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 229 optimal weight: 0.5980 chunk 230 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN C 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099664 restraints weight = 27647.534| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.19 r_work: 0.2991 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19628 Z= 0.097 Angle : 0.453 6.819 26600 Z= 0.244 Chirality : 0.043 0.140 3024 Planarity : 0.004 0.038 3472 Dihedral : 4.103 21.687 2647 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.01 % Allowed : 31.52 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2457 helix: -1.08 (0.23), residues: 441 sheet: 0.46 (0.21), residues: 602 loop : -0.66 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.014 0.001 PHE C 281 TYR 0.014 0.001 TYR C 396 ARG 0.002 0.000 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.02316 ( 587) hydrogen bonds : angle 4.73268 ( 1464) covalent geometry : bond 0.00231 (19628) covalent geometry : angle 0.45341 (26600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 220 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 491 ASN cc_start: 0.7800 (p0) cc_final: 0.7558 (p0) REVERT: B 612 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (tt) REVERT: C 380 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8336 (t) REVERT: C 524 GLU cc_start: 0.7497 (tp30) cc_final: 0.7283 (tp30) REVERT: D 313 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: D 380 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7992 (t) REVERT: D 458 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (tmt-80) REVERT: D 589 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (ttpp) REVERT: E 482 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8839 (pt0) REVERT: E 589 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7351 (ttpp) REVERT: F 458 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7003 (ttt-90) REVERT: G 467 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8382 (tp) REVERT: G 474 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (tttt) outliers start: 87 outliers final: 57 residues processed: 296 average time/residue: 0.2724 time to fit residues: 128.2268 Evaluate side-chains 285 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 75 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN C 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095745 restraints weight = 27581.679| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.18 r_work: 0.2934 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19628 Z= 0.244 Angle : 0.566 7.745 26600 Z= 0.301 Chirality : 0.047 0.143 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.619 25.268 2647 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.38 % Allowed : 31.29 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2457 helix: -1.21 (0.22), residues: 427 sheet: 0.24 (0.21), residues: 616 loop : -0.77 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 503 HIS 0.002 0.001 HIS F 314 PHE 0.031 0.003 PHE F 281 TYR 0.013 0.002 TYR B 439 ARG 0.002 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 587) hydrogen bonds : angle 4.89746 ( 1464) covalent geometry : bond 0.00600 (19628) covalent geometry : angle 0.56566 (26600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 207 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 411 ASN cc_start: 0.8535 (m-40) cc_final: 0.8321 (m110) REVERT: B 237 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 482 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8955 (pt0) REVERT: C 380 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8363 (t) REVERT: D 376 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6798 (t0) REVERT: D 380 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7972 (t) REVERT: D 458 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8615 (tmt-80) REVERT: D 589 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (ttpp) REVERT: E 589 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7527 (ttpp) REVERT: F 458 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.6943 (ttt-90) REVERT: G 467 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8384 (tp) outliers start: 95 outliers final: 65 residues processed: 294 average time/residue: 0.2820 time to fit residues: 132.0202 Evaluate side-chains 281 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 205 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 57 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN C 567 ASN D 376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097270 restraints weight = 27700.678| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.18 r_work: 0.2959 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19628 Z= 0.154 Angle : 0.506 7.969 26600 Z= 0.271 Chirality : 0.045 0.141 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.455 24.879 2647 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.82 % Allowed : 31.71 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2457 helix: -1.25 (0.22), residues: 441 sheet: 0.43 (0.21), residues: 602 loop : -0.85 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 503 HIS 0.001 0.000 HIS F 314 PHE 0.020 0.002 PHE C 281 TYR 0.012 0.001 TYR C 396 ARG 0.001 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.02748 ( 587) hydrogen bonds : angle 4.82958 ( 1464) covalent geometry : bond 0.00379 (19628) covalent geometry : angle 0.50571 (26600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 211 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 524 GLU cc_start: 0.7948 (tp30) cc_final: 0.7663 (tp30) REVERT: B 482 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8903 (pt0) REVERT: C 380 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8355 (t) REVERT: D 380 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7962 (t) REVERT: D 458 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8604 (tmt-80) REVERT: D 589 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7622 (ttpp) REVERT: E 589 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7397 (ttpp) REVERT: F 458 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.6993 (ttt-90) REVERT: G 467 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 83 outliers final: 66 residues processed: 283 average time/residue: 0.2720 time to fit residues: 122.1358 Evaluate side-chains 281 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 214 optimal weight: 0.0010 chunk 135 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.097877 restraints weight = 27536.437| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.17 r_work: 0.2970 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19628 Z= 0.138 Angle : 0.490 7.521 26600 Z= 0.263 Chirality : 0.044 0.141 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.360 24.328 2647 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.87 % Allowed : 31.80 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2457 helix: -1.19 (0.22), residues: 441 sheet: 0.31 (0.21), residues: 616 loop : -0.74 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 503 HIS 0.001 0.000 HIS F 314 PHE 0.018 0.002 PHE C 281 TYR 0.012 0.001 TYR C 396 ARG 0.001 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.02580 ( 587) hydrogen bonds : angle 4.74896 ( 1464) covalent geometry : bond 0.00339 (19628) covalent geometry : angle 0.49022 (26600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 212 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 458 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7961 (tmt-80) REVERT: A 524 GLU cc_start: 0.7921 (tp30) cc_final: 0.7632 (tp30) REVERT: B 482 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8852 (pt0) REVERT: C 380 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8360 (t) REVERT: D 380 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7970 (t) REVERT: D 458 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8611 (tmt-80) REVERT: D 589 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7615 (ttpp) REVERT: E 482 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8872 (pt0) REVERT: E 589 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7379 (ttpp) REVERT: F 458 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.6934 (ttt-90) REVERT: G 467 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8367 (tp) outliers start: 84 outliers final: 71 residues processed: 285 average time/residue: 0.2811 time to fit residues: 126.5834 Evaluate side-chains 290 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 208 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 132 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN G 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098709 restraints weight = 27475.980| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.17 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19628 Z= 0.118 Angle : 0.474 7.361 26600 Z= 0.255 Chirality : 0.044 0.140 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.236 23.264 2647 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.92 % Allowed : 31.84 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2457 helix: -1.11 (0.23), residues: 441 sheet: 0.53 (0.21), residues: 602 loop : -0.76 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 PHE 0.015 0.002 PHE C 281 TYR 0.014 0.001 TYR E 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02383 ( 587) hydrogen bonds : angle 4.68243 ( 1464) covalent geometry : bond 0.00286 (19628) covalent geometry : angle 0.47432 (26600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 213 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 458 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8026 (tmt-80) REVERT: A 524 GLU cc_start: 0.7964 (tp30) cc_final: 0.7665 (tp30) REVERT: B 237 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8390 (mm) REVERT: B 482 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8867 (pt0) REVERT: B 612 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8349 (tt) REVERT: C 380 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8334 (t) REVERT: C 539 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7843 (mt-10) REVERT: D 380 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.8010 (t) REVERT: D 458 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8584 (tmt-80) REVERT: D 589 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7621 (ttpp) REVERT: E 482 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8871 (pt0) REVERT: E 589 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7383 (ttpp) REVERT: F 458 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7003 (ttt-90) REVERT: G 467 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8358 (tp) REVERT: G 474 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7598 (tttt) outliers start: 85 outliers final: 66 residues processed: 288 average time/residue: 0.3008 time to fit residues: 137.1211 Evaluate side-chains 290 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100290 restraints weight = 27546.876| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.18 r_work: 0.3007 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19628 Z= 0.092 Angle : 0.451 6.945 26600 Z= 0.243 Chirality : 0.043 0.141 3024 Planarity : 0.004 0.042 3472 Dihedral : 4.039 21.418 2647 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.59 % Allowed : 31.98 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2457 helix: -1.03 (0.24), residues: 420 sheet: 0.49 (0.21), residues: 602 loop : -0.59 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 PHE 0.011 0.001 PHE C 281 TYR 0.016 0.001 TYR E 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02084 ( 587) hydrogen bonds : angle 4.58463 ( 1464) covalent geometry : bond 0.00220 (19628) covalent geometry : angle 0.45140 (26600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9497.70 seconds wall clock time: 165 minutes 14.48 seconds (9914.48 seconds total)