Starting phenix.real_space_refine on Sun Aug 24 10:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekl_28206/08_2025/8ekl_28206.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekl_28206/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ekl_28206/08_2025/8ekl_28206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekl_28206/08_2025/8ekl_28206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ekl_28206/08_2025/8ekl_28206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekl_28206/08_2025/8ekl_28206.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.60, per 1000 atoms: 0.24 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: 1.50 Conformation dependent library (CDL) restraints added in 766.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 3.91 Time building geometry restraints manager: 2.05 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: 0.01 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.970 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- 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 : 5.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 529 TYR 0.009 0.001 TYR B 439 PHE 0.013 0.001 PHE D 281 TRP 0.005 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00265 (19628) covalent geometry : angle 0.47089 (26600) hydrogen bonds : bond 0.22551 ( 587) hydrogen bonds : angle 8.46102 ( 1464) *********************** 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 : 0.711 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: 0.1258 time to fit residues: 44.8130 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 : 0.769 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 235 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 F 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095720 restraints weight = 27787.036| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.18 r_work: 0.2977 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19628 Z= 0.244 Angle : 0.575 7.798 26600 Z= 0.308 Chirality : 0.047 0.151 3024 Planarity : 0.004 0.046 3472 Dihedral : 4.682 33.075 2651 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.92 % Allowed : 32.17 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.16), residues: 2457 helix: -1.40 (0.23), residues: 406 sheet: 0.14 (0.21), residues: 616 loop : -0.86 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 458 TYR 0.014 0.002 TYR B 439 PHE 0.027 0.002 PHE C 281 TRP 0.006 0.001 TRP B 503 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00600 (19628) covalent geometry : angle 0.57505 (26600) hydrogen bonds : bond 0.04129 ( 587) hydrogen bonds : angle 5.66283 ( 1464) *********************** 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 293 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 208 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: C 380 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8325 (t) REVERT: D 223 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: D 380 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.7996 (t) REVERT: D 524 GLU cc_start: 0.7558 (tp30) cc_final: 0.7341 (tp30) REVERT: D 589 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7639 (ttpp) REVERT: F 458 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.6942 (ttt-90) outliers start: 85 outliers final: 50 residues processed: 278 average time/residue: 0.1225 time to fit residues: 55.9127 Evaluate side-chains 254 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 379 LEU Chi-restraints excluded: chain A residue 428 GLN 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 223 ASN 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 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR 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 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 323 VAL Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 45 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 146 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 E 425 GLN G 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098676 restraints weight = 27477.148| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.15 r_work: 0.3021 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19628 Z= 0.154 Angle : 0.506 7.194 26600 Z= 0.272 Chirality : 0.045 0.143 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.489 24.320 2647 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.78 % Allowed : 31.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.16), residues: 2457 helix: -1.36 (0.22), residues: 434 sheet: 0.20 (0.21), residues: 616 loop : -0.87 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 458 TYR 0.015 0.001 TYR C 396 PHE 0.021 0.002 PHE G 281 TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00380 (19628) covalent geometry : angle 0.50590 (26600) hydrogen bonds : bond 0.03202 ( 587) hydrogen bonds : angle 5.23143 ( 1464) *********************** 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 292 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 612 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8422 (tt) REVERT: C 252 GLN cc_start: 0.8365 (mm110) cc_final: 0.8131 (mm-40) REVERT: C 380 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8346 (t) REVERT: C 524 GLU cc_start: 0.7590 (tp30) cc_final: 0.7342 (tp30) REVERT: D 313 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: D 376 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7250 (m-40) REVERT: D 380 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8003 (t) REVERT: F 458 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.6907 (ttt-90) REVERT: G 467 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8397 (tp) outliers start: 82 outliers final: 50 residues processed: 282 average time/residue: 0.1299 time to fit residues: 59.1016 Evaluate side-chains 262 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 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 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 281 PHE Chi-restraints excluded: chain C residue 380 SER 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 E residue 272 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 281 PHE 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 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR 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 476 ILE 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 231 optimal weight: 0.0980 chunk 166 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.123226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099444 restraints weight = 27601.789| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.18 r_work: 0.2995 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0848 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= 0.093 Angle : 0.451 6.751 26600 Z= 0.244 Chirality : 0.043 0.142 3024 Planarity : 0.004 0.040 3472 Dihedral : 4.192 22.263 2647 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.64 % Allowed : 31.75 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2457 helix: -1.21 (0.22), residues: 441 sheet: 0.48 (0.21), residues: 567 loop : -0.78 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 528 TYR 0.015 0.001 TYR C 396 PHE 0.012 0.001 PHE C 281 TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00218 (19628) covalent geometry : angle 0.45113 (26600) hydrogen bonds : bond 0.02408 ( 587) hydrogen bonds : angle 4.90483 ( 1464) *********************** 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 306 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ASN cc_start: 0.7832 (p0) cc_final: 0.7622 (p0) REVERT: B 612 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8371 (tt) REVERT: C 380 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8388 (t) REVERT: C 491 ASN cc_start: 0.7585 (p0) cc_final: 0.7323 (p0) REVERT: C 524 GLU cc_start: 0.7497 (tp30) cc_final: 0.7287 (tp30) REVERT: D 313 GLU cc_start: 0.8627 (pm20) cc_final: 0.8062 (pm20) REVERT: D 376 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7237 (m-40) REVERT: D 380 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.8029 (t) REVERT: D 589 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7415 (ttpp) REVERT: F 458 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7001 (ttt-90) REVERT: G 467 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8349 (tp) outliers start: 79 outliers final: 44 residues processed: 295 average time/residue: 0.1249 time to fit residues: 59.3649 Evaluate side-chains 268 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 379 LEU 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 434 SER 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 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 451 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 241 ILE 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 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 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 313 GLU 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 480 THR Chi-restraints excluded: chain F residue 484 SER 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 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 61 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 221 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099690 restraints weight = 27568.278| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.18 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19628 Z= 0.101 Angle : 0.454 6.627 26600 Z= 0.244 Chirality : 0.043 0.141 3024 Planarity : 0.004 0.039 3472 Dihedral : 4.112 21.612 2647 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.82 % Allowed : 31.57 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2457 helix: -1.12 (0.23), residues: 441 sheet: 0.58 (0.21), residues: 567 loop : -0.71 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 529 TYR 0.015 0.001 TYR C 396 PHE 0.014 0.001 PHE F 281 TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00241 (19628) covalent geometry : angle 0.45403 (26600) hydrogen bonds : bond 0.02352 ( 587) hydrogen bonds : angle 4.76712 ( 1464) *********************** 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 305 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 222 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ASN cc_start: 0.7754 (p0) cc_final: 0.7534 (p0) REVERT: B 612 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 380 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8373 (t) REVERT: C 491 ASN cc_start: 0.7533 (p0) cc_final: 0.7266 (p0) REVERT: C 524 GLU cc_start: 0.7521 (tp30) cc_final: 0.7300 (tp30) REVERT: D 313 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: D 380 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8001 (t) REVERT: D 458 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8556 (tmt-80) REVERT: E 482 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8831 (pt0) REVERT: F 458 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7012 (ttt-90) REVERT: G 467 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8321 (tp) REVERT: G 474 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7560 (tttt) outliers start: 83 outliers final: 54 residues processed: 295 average time/residue: 0.1233 time to fit residues: 58.9018 Evaluate side-chains 275 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU 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 484 SER Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 434 SER 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 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN C 567 ASN D 376 ASN D 523 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095484 restraints weight = 27501.303| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.13 r_work: 0.2973 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 19628 Z= 0.355 Angle : 0.657 8.457 26600 Z= 0.349 Chirality : 0.051 0.159 3024 Planarity : 0.005 0.048 3472 Dihedral : 4.994 28.096 2647 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.84 % Allowed : 31.29 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.16), residues: 2457 helix: -1.47 (0.22), residues: 427 sheet: 0.04 (0.21), residues: 616 loop : -0.93 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 458 TYR 0.016 0.002 TYR B 439 PHE 0.044 0.003 PHE F 281 TRP 0.007 0.001 TRP B 375 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00877 (19628) covalent geometry : angle 0.65731 (26600) hydrogen bonds : bond 0.04034 ( 587) hydrogen bonds : angle 5.11450 ( 1464) *********************** 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 308 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 203 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: C 380 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8330 (t) REVERT: C 524 GLU cc_start: 0.7727 (tp30) cc_final: 0.7523 (tp30) REVERT: D 380 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7969 (t) REVERT: E 314 HIS cc_start: 0.7676 (m-70) cc_final: 0.7422 (m-70) REVERT: E 458 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8613 (tmt-80) REVERT: F 458 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.6960 (ttt-90) REVERT: G 467 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (tp) outliers start: 105 outliers final: 65 residues processed: 294 average time/residue: 0.1308 time to fit residues: 61.6621 Evaluate side-chains 270 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 314 HIS Chi-restraints excluded: chain A residue 377 THR 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 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 475 GLN 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 573 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 480 THR Chi-restraints excluded: chain C residue 516 SER 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 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE 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 458 ARG Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 615 THR 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 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 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 476 ILE Chi-restraints excluded: chain G residue 480 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 212 optimal weight: 0.0770 chunk 49 optimal weight: 0.0980 chunk 214 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN C 425 GLN C 567 ASN G 411 ASN G 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099958 restraints weight = 27430.590| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.17 r_work: 0.2997 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0977 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 : 0.470 7.543 26600 Z= 0.255 Chirality : 0.043 0.207 3024 Planarity : 0.004 0.040 3472 Dihedral : 4.295 24.506 2647 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 33.55 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2457 helix: -1.20 (0.23), residues: 441 sheet: 0.44 (0.21), residues: 567 loop : -0.78 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 528 TYR 0.014 0.001 TYR C 396 PHE 0.007 0.001 PHE A 487 TRP 0.015 0.001 TRP D 375 HIS 0.001 0.000 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00185 (19628) covalent geometry : angle 0.46992 (26600) hydrogen bonds : bond 0.02215 ( 587) hydrogen bonds : angle 4.81816 ( 1464) *********************** 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 268 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 458 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8016 (tmt-80) REVERT: C 380 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8324 (t) REVERT: C 491 ASN cc_start: 0.7619 (p0) cc_final: 0.7301 (p0) REVERT: D 313 GLU cc_start: 0.8616 (pm20) cc_final: 0.7976 (pm20) REVERT: D 458 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8590 (tmt-80) REVERT: E 482 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: F 458 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.6994 (ttt-90) REVERT: G 467 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8374 (tp) outliers start: 51 outliers final: 33 residues processed: 262 average time/residue: 0.1316 time to fit residues: 55.1390 Evaluate side-chains 251 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG 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 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 377 THR 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 E residue 259 SER Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 313 GLU 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 F residue 545 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 287 THR 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 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 86 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 463 ASN C 567 ASN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098479 restraints weight = 27589.242| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.18 r_work: 0.3020 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0984 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= 0.128 Angle : 0.481 7.255 26600 Z= 0.259 Chirality : 0.044 0.176 3024 Planarity : 0.004 0.042 3472 Dihedral : 4.298 23.826 2647 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.72 % Allowed : 33.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.16), residues: 2457 helix: -1.18 (0.23), residues: 441 sheet: 0.36 (0.21), residues: 616 loop : -0.72 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 529 TYR 0.013 0.001 TYR C 396 PHE 0.017 0.002 PHE F 281 TRP 0.009 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00312 (19628) covalent geometry : angle 0.48149 (26600) hydrogen bonds : bond 0.02457 ( 587) hydrogen bonds : angle 4.73177 ( 1464) *********************** 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 272 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 458 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7971 (tmt-80) REVERT: C 380 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 313 GLU cc_start: 0.8673 (pm20) cc_final: 0.8108 (pm20) REVERT: D 458 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (tmt-80) REVERT: F 458 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7020 (ttt-90) REVERT: G 467 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8364 (tp) outliers start: 59 outliers final: 46 residues processed: 262 average time/residue: 0.1322 time to fit residues: 55.3160 Evaluate side-chains 260 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG 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 272 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 251 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 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 323 VAL 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 E residue 259 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 GLU 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 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 287 THR 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 480 THR Chi-restraints excluded: chain G residue 522 GLU Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 199 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 38 optimal weight: 0.0770 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 243 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 overall best weight: 2.8544 ------------------------------------------------------------------------------- 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 G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097343 restraints weight = 27604.352| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.18 r_work: 0.3001 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0990 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= 0.169 Angle : 0.517 7.621 26600 Z= 0.277 Chirality : 0.045 0.171 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.447 24.848 2647 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.59 % Allowed : 32.49 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2457 helix: -1.16 (0.23), residues: 434 sheet: 0.27 (0.21), residues: 616 loop : -0.75 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 458 TYR 0.016 0.001 TYR E 396 PHE 0.021 0.002 PHE A 281 TRP 0.006 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00415 (19628) covalent geometry : angle 0.51651 (26600) hydrogen bonds : bond 0.02787 ( 587) hydrogen bonds : angle 4.78908 ( 1464) *********************** 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 283 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 458 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8026 (tmt-80) REVERT: B 612 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 380 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 313 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: D 458 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8620 (tmt-80) REVERT: F 458 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7031 (ttt-90) REVERT: G 467 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8380 (tp) REVERT: G 474 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7593 (tttt) outliers start: 78 outliers final: 57 residues processed: 271 average time/residue: 0.1304 time to fit residues: 56.2329 Evaluate side-chains 273 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 371 ASN 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 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 272 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 612 LEU 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 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL 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 E residue 281 PHE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE 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 223 ASN Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 287 THR 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 480 THR Chi-restraints excluded: chain G residue 522 GLU Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN C 567 ASN G 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098835 restraints weight = 27512.367| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.16 r_work: 0.3025 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19628 Z= 0.116 Angle : 0.478 7.364 26600 Z= 0.258 Chirality : 0.044 0.170 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.268 23.653 2647 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.36 % Allowed : 32.76 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.16), residues: 2457 helix: -1.14 (0.23), residues: 441 sheet: 0.54 (0.21), residues: 602 loop : -0.77 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 529 TYR 0.017 0.001 TYR E 396 PHE 0.013 0.001 PHE A 281 TRP 0.005 0.001 TRP D 375 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00281 (19628) covalent geometry : angle 0.47810 (26600) hydrogen bonds : bond 0.02372 ( 587) hydrogen bonds : angle 4.70675 ( 1464) ********************** 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 287 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 458 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7998 (tmt-80) REVERT: B 612 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 380 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8369 (t) REVERT: D 313 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: D 458 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (tmt-80) REVERT: E 482 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: F 458 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7011 (ttt-90) REVERT: G 467 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8379 (tp) REVERT: G 474 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7600 (tttt) outliers start: 73 outliers final: 55 residues processed: 275 average time/residue: 0.1275 time to fit residues: 56.2139 Evaluate side-chains 274 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER 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 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL 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 E residue 281 PHE Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 429 ILE 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 287 THR 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 522 GLU Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 203 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 G 411 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101668 restraints weight = 27468.936| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.17 r_work: 0.3026 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1176 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 : 0.446 7.238 26600 Z= 0.242 Chirality : 0.043 0.259 3024 Planarity : 0.004 0.041 3472 Dihedral : 3.941 20.306 2647 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 2.67 % Allowed : 33.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2457 helix: -0.93 (0.24), residues: 420 sheet: 0.56 (0.21), residues: 602 loop : -0.55 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 529 TYR 0.017 0.001 TYR E 396 PHE 0.007 0.001 PHE A 487 TRP 0.006 0.001 TRP A 375 HIS 0.000 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00189 (19628) covalent geometry : angle 0.44623 (26600) hydrogen bonds : bond 0.01891 ( 587) hydrogen bonds : angle 4.55499 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.24 seconds wall clock time: 80 minutes 17.80 seconds (4817.80 seconds total)