Starting phenix.real_space_refine on Mon Jun 16 22:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekl_28206/06_2025/8ekl_28206.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekl_28206/06_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_28206/06_2025/8ekl_28206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekl_28206/06_2025/8ekl_28206.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekl_28206/06_2025/8ekl_28206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekl_28206/06_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-5710/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: 13.39, per 1000 atoms: 0.69 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: 4.62 Conformation dependent library (CDL) restraints added in 2.4 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: 2.84 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: 6.80 Time building geometry restraints manager: 5.51 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.010 Find NCS groups from input model: 0.920 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.890 ------------------------------------------------------------------------------- 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 : 2.341 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: 0.2913 time to fit residues: 104.3672 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 : 2.443 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096111 restraints weight = 27642.914| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.18 r_work: 0.2968 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0688 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 : 0.559 7.719 26600 Z= 0.299 Chirality : 0.046 0.152 3024 Planarity : 0.004 0.045 3472 Dihedral : 4.626 33.150 2651 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.64 % Allowed : 32.17 % 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: -1.37 (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 0.04017 ( 587) hydrogen bonds : angle 5.64166 ( 1464) covalent geometry : bond 0.00545 (19628) covalent geometry : angle 0.55863 (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 288 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 209 time to evaluate : 2.157 Fit side-chains revert: symmetry clash REVERT: C 380 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8331 (t) REVERT: D 223 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: D 380 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8002 (t) REVERT: F 458 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.6936 (ttt-90) outliers start: 79 outliers final: 46 residues processed: 274 average time/residue: 0.2724 time to fit residues: 121.1679 Evaluate side-chains 253 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 176 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.123373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099031 restraints weight = 27149.828| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.14 r_work: 0.3050 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19628 Z= 0.146 Angle : 0.497 7.103 26600 Z= 0.267 Chirality : 0.044 0.142 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.435 23.658 2647 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.87 % Allowed : 31.47 % 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: -1.01 (0.16), residues: 2457 helix: -1.33 (0.22), residues: 434 sheet: 0.23 (0.21), residues: 616 loop : -0.83 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.019 0.002 PHE G 281 TYR 0.016 0.001 TYR C 396 ARG 0.001 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 587) hydrogen bonds : angle 5.20053 ( 1464) covalent geometry : bond 0.00359 (19628) covalent geometry : angle 0.49680 (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 300 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 216 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7764 (tt) REVERT: B 612 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 380 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8345 (t) REVERT: C 524 GLU cc_start: 0.7572 (tp30) cc_final: 0.7323 (tp30) REVERT: D 313 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: D 376 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7251 (m-40) REVERT: D 380 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 589 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7633 (ttpp) REVERT: F 458 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.6913 (ttt-90) REVERT: F 482 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8790 (pt0) REVERT: G 467 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8387 (tp) outliers start: 84 outliers final: 48 residues processed: 290 average time/residue: 0.2717 time to fit residues: 126.5070 Evaluate side-chains 270 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 484 SER 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 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 LEU 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 B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU 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 429 ILE 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 280 SER Chi-restraints excluded: chain D residue 281 PHE 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 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 314 HIS 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 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 377 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 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: 2.9990 chunk 18 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 55 optimal weight: 0.0470 chunk 46 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.124275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099974 restraints weight = 27337.620| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.15 r_work: 0.3047 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19628 Z= 0.116 Angle : 0.471 6.931 26600 Z= 0.254 Chirality : 0.044 0.142 3024 Planarity : 0.004 0.041 3472 Dihedral : 4.300 22.793 2647 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.24 % Allowed : 31.11 % 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: -0.90 (0.16), residues: 2457 helix: -1.22 (0.23), residues: 434 sheet: 0.44 (0.21), residues: 602 loop : -0.82 (0.16), residues: 1421 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 0.016 0.002 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 0.02645 ( 587) hydrogen bonds : angle 4.95585 ( 1464) covalent geometry : bond 0.00282 (19628) covalent geometry : angle 0.47101 (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 315 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 223 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7784 (tt) REVERT: B 237 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (mm) REVERT: B 612 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8410 (tt) REVERT: C 380 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8377 (t) REVERT: C 491 ASN cc_start: 0.7653 (p0) cc_final: 0.7360 (p0) REVERT: C 524 GLU cc_start: 0.7542 (tp30) cc_final: 0.7298 (tp30) REVERT: D 313 GLU cc_start: 0.8667 (pm20) cc_final: 0.8320 (pt0) REVERT: D 376 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: D 380 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.8009 (t) REVERT: D 589 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7495 (ttpp) REVERT: F 458 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.6979 (ttt-90) REVERT: F 482 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: G 467 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8368 (tp) outliers start: 92 outliers final: 59 residues processed: 302 average time/residue: 0.2852 time to fit residues: 138.3553 Evaluate side-chains 283 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 379 LEU 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 323 VAL 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 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 476 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU 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 442 LYS 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 405 LYS 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 F residue 281 PHE 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 377 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 70 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 56 optimal weight: 0.0020 chunk 242 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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 G 411 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099343 restraints weight = 27677.726| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.18 r_work: 0.2998 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0892 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= 0.100 Angle : 0.456 6.796 26600 Z= 0.246 Chirality : 0.043 0.141 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.159 21.676 2647 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.38 % Allowed : 31.15 % 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: -0.80 (0.16), residues: 2457 helix: -1.15 (0.23), residues: 441 sheet: 0.53 (0.21), residues: 567 loop : -0.74 (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 C 281 TYR 0.015 0.001 TYR C 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02377 ( 587) hydrogen bonds : angle 4.79498 ( 1464) covalent geometry : bond 0.00240 (19628) covalent geometry : angle 0.45609 (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 322 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 227 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7780 (tt) REVERT: A 491 ASN cc_start: 0.7789 (p0) cc_final: 0.7562 (p0) REVERT: A 524 GLU cc_start: 0.7940 (tp30) cc_final: 0.7719 (tp30) REVERT: B 612 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (tt) REVERT: C 380 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8341 (t) REVERT: C 491 ASN cc_start: 0.7591 (p0) cc_final: 0.7309 (p0) REVERT: C 524 GLU cc_start: 0.7512 (tp30) cc_final: 0.7294 (tp30) REVERT: D 313 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: D 380 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7992 (t) REVERT: D 458 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8558 (tmt-80) REVERT: D 589 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7475 (ttpp) REVERT: E 482 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: F 458 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7008 (ttt-90) REVERT: G 467 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8373 (tp) REVERT: G 474 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7579 (tttt) outliers start: 95 outliers final: 62 residues processed: 310 average time/residue: 0.2955 time to fit residues: 145.7831 Evaluate side-chains 287 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 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 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL 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 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 323 VAL 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 451 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 241 ILE 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 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 281 PHE Chi-restraints excluded: chain E residue 313 GLU 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 484 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 311 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 217 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 D 376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101022 restraints weight = 27594.721| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.19 r_work: 0.3022 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1035 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= 0.083 Angle : 0.436 6.559 26600 Z= 0.235 Chirality : 0.042 0.140 3024 Planarity : 0.003 0.038 3472 Dihedral : 3.965 20.771 2647 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.82 % Allowed : 31.66 % Favored : 64.52 % 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: -0.66 (0.16), residues: 2457 helix: -1.02 (0.23), residues: 441 sheet: 0.53 (0.21), residues: 602 loop : -0.64 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 375 HIS 0.001 0.000 HIS F 314 PHE 0.011 0.001 PHE C 281 TYR 0.014 0.001 TYR C 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02089 ( 587) hydrogen bonds : angle 4.64797 ( 1464) covalent geometry : bond 0.00194 (19628) covalent geometry : angle 0.43642 (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 306 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 491 ASN cc_start: 0.7710 (p0) cc_final: 0.7502 (p0) REVERT: B 612 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8357 (tt) REVERT: C 380 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8347 (t) REVERT: C 491 ASN cc_start: 0.7460 (p0) cc_final: 0.7228 (p0) REVERT: C 524 GLU cc_start: 0.7490 (tp30) cc_final: 0.7281 (tp30) REVERT: D 313 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: D 380 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.8054 (t) REVERT: D 458 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8518 (tmt-80) REVERT: D 589 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7620 (ttpp) REVERT: E 482 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8834 (pt0) REVERT: F 458 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.6990 (ttt-90) REVERT: G 467 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8308 (tp) REVERT: G 474 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7557 (tttt) outliers start: 83 outliers final: 54 residues processed: 297 average time/residue: 0.3760 time to fit residues: 179.1908 Evaluate side-chains 278 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU 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 480 THR Chi-restraints excluded: chain A residue 484 SER 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 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 259 SER 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 480 THR Chi-restraints excluded: chain D residue 259 SER 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 259 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 313 GLU 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 484 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 313 GLU 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 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 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: 5.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 241 optimal weight: 0.0980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098250 restraints weight = 27436.021| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.16 r_work: 0.2972 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19628 Z= 0.157 Angle : 0.497 8.230 26600 Z= 0.267 Chirality : 0.044 0.214 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.208 22.529 2647 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.42 % Allowed : 31.43 % Favored : 64.15 % 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: -0.76 (0.16), residues: 2457 helix: -1.13 (0.23), residues: 441 sheet: 0.58 (0.21), residues: 602 loop : -0.76 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 PHE 0.021 0.002 PHE D 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 0.02655 ( 587) hydrogen bonds : angle 4.69987 ( 1464) covalent geometry : bond 0.00385 (19628) covalent geometry : angle 0.49663 (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 303 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 207 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 612 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 288 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: C 380 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8372 (t) REVERT: D 380 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7988 (t) REVERT: D 458 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8593 (tmt-80) REVERT: D 589 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7651 (ttpp) REVERT: E 482 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8869 (pt0) REVERT: F 458 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7006 (ttt-90) REVERT: G 467 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8387 (tp) REVERT: G 474 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7646 (tttt) outliers start: 96 outliers final: 67 residues processed: 293 average time/residue: 0.3079 time to fit residues: 143.4533 Evaluate side-chains 284 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 206 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 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 480 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 588 ILE 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 434 SER 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 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 259 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 323 VAL 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 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 377 THR 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 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 484 SER 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 259 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 57 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 173 optimal weight: 0.0050 chunk 199 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.9600 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.121194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097201 restraints weight = 27734.151| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.17 r_work: 0.2958 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19628 Z= 0.175 Angle : 0.520 7.700 26600 Z= 0.279 Chirality : 0.045 0.197 3024 Planarity : 0.004 0.041 3472 Dihedral : 4.397 23.930 2647 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.15 % Allowed : 31.84 % Favored : 64.01 % 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: -0.88 (0.16), residues: 2457 helix: -1.24 (0.22), residues: 441 sheet: 0.49 (0.21), residues: 602 loop : -0.82 (0.16), residues: 1414 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 0.022 0.002 PHE D 281 TYR 0.012 0.001 TYR B 439 ARG 0.002 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 587) hydrogen bonds : angle 4.77361 ( 1464) covalent geometry : bond 0.00432 (19628) covalent geometry : angle 0.51975 (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 293 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 203 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7826 (tt) REVERT: B 237 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8427 (mm) REVERT: B 612 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8351 (tt) REVERT: C 288 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: C 380 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8355 (t) REVERT: D 380 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7978 (t) REVERT: D 458 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8616 (tmt-80) REVERT: D 589 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7636 (ttpp) REVERT: E 482 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8878 (pt0) REVERT: F 458 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.6949 (ttt-90) REVERT: G 467 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8350 (tp) REVERT: G 474 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7608 (tttt) outliers start: 90 outliers final: 70 residues processed: 283 average time/residue: 0.3444 time to fit residues: 157.5428 Evaluate side-chains 285 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 203 time to evaluate : 3.218 ------------------------------------------------------------------------------- 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 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 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 SER 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 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 434 SER 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 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU 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 288 GLU Chi-restraints excluded: chain C residue 323 VAL 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 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 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 484 SER 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 259 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 323 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 191 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.122355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098361 restraints weight = 27498.387| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.17 r_work: 0.2976 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19628 Z= 0.130 Angle : 0.487 7.545 26600 Z= 0.262 Chirality : 0.044 0.178 3024 Planarity : 0.004 0.040 3472 Dihedral : 4.284 23.388 2647 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.06 % Allowed : 31.66 % Favored : 64.29 % 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: -1.15 (0.22), residues: 441 sheet: 0.54 (0.21), residues: 602 loop : -0.77 (0.16), residues: 1414 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 0.016 0.002 PHE D 281 TYR 0.012 0.001 TYR C 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02523 ( 587) hydrogen bonds : angle 4.71330 ( 1464) covalent geometry : bond 0.00316 (19628) covalent geometry : angle 0.48691 (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 298 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (tt) REVERT: A 458 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8020 (tmt-80) REVERT: B 612 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8344 (tt) REVERT: C 288 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: C 380 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8355 (t) REVERT: D 380 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 458 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8610 (tmt-80) REVERT: D 589 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7622 (ttpp) REVERT: E 482 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8871 (pt0) REVERT: F 458 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7008 (ttt-90) REVERT: G 467 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8371 (tp) REVERT: G 474 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (tttt) outliers start: 88 outliers final: 71 residues processed: 286 average time/residue: 0.3288 time to fit residues: 148.4759 Evaluate side-chains 287 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 204 time to evaluate : 2.844 ------------------------------------------------------------------------------- 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 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 484 SER 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 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 434 SER 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 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 288 GLU 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 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 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 484 SER 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 223 ASN Chi-restraints excluded: chain G residue 259 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 323 VAL 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 132 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.121889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097928 restraints weight = 27528.764| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.17 r_work: 0.2968 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19628 Z= 0.144 Angle : 0.498 7.495 26600 Z= 0.267 Chirality : 0.044 0.178 3024 Planarity : 0.004 0.041 3472 Dihedral : 4.309 23.544 2647 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.10 % Allowed : 31.52 % Favored : 64.38 % 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: -0.81 (0.16), residues: 2457 helix: -1.15 (0.22), residues: 441 sheet: 0.52 (0.21), residues: 602 loop : -0.77 (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 0.019 0.002 PHE D 281 TYR 0.018 0.001 TYR E 396 ARG 0.001 0.000 ARG G 458 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 587) hydrogen bonds : angle 4.71461 ( 1464) covalent geometry : bond 0.00353 (19628) covalent geometry : angle 0.49776 (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 295 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 206 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7849 (tt) REVERT: A 458 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8048 (tmt-80) REVERT: B 612 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8347 (tt) REVERT: C 288 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: C 380 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8360 (t) REVERT: C 539 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7861 (mt-10) REVERT: D 380 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8027 (t) REVERT: D 458 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (tmt-80) REVERT: D 589 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7632 (ttpp) REVERT: E 482 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8877 (pt0) REVERT: F 458 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7014 (ttt-90) REVERT: G 467 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8371 (tp) REVERT: G 474 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (tttt) outliers start: 89 outliers final: 74 residues processed: 285 average time/residue: 0.2780 time to fit residues: 125.9523 Evaluate side-chains 290 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 204 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 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 484 SER 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 434 SER 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 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 259 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 288 GLU 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 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 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 484 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 307 LEU 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 259 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 323 VAL 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: 10.0000 chunk 12 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.0020 chunk 131 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 180 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6402 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.125053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101284 restraints weight = 27505.918| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.19 r_work: 0.3027 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1150 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= 0.083 Angle : 0.445 6.915 26600 Z= 0.240 Chirality : 0.042 0.169 3024 Planarity : 0.004 0.040 3472 Dihedral : 3.922 20.248 2647 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.76 % Allowed : 32.86 % Favored : 64.38 % 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: -0.53 (0.16), residues: 2457 helix: -0.93 (0.24), residues: 420 sheet: 0.57 (0.21), residues: 602 loop : -0.53 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 PHE 0.007 0.001 PHE B 487 TYR 0.018 0.001 TYR E 396 ARG 0.001 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.01911 ( 587) hydrogen bonds : angle 4.55325 ( 1464) covalent geometry : bond 0.00191 (19628) covalent geometry : angle 0.44450 (26600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10285.27 seconds wall clock time: 182 minutes 56.57 seconds (10976.57 seconds total)