Starting phenix.real_space_refine on Tue Nov 19 10:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekl_28206/11_2024/8ekl_28206.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 12061 2.51 5 N 3157 2.21 5 O 4067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19334 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "G" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2760 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 340} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.43 Number of scatterers: 19334 At special positions: 0 Unit cell: (139.573, 139.573, 124.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4067 8.00 N 3157 7.00 C 12061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4634 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 22.0% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.771A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 4.506A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.560A pdb=" N ASP A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.019A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.906A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 512 removed outlier: 4.489A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.893A pdb=" N ASP B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.567A pdb=" N GLY C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.919A pdb=" N LYS C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 512 removed outlier: 4.549A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 594 removed outlier: 3.730A pdb=" N ASP C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.508A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.542A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.957A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 503 through 512 removed outlier: 4.492A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 512 " --> pdb=" O SER D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 590 removed outlier: 3.787A pdb=" N ASP D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 4.066A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 471 removed outlier: 3.875A pdb=" N LYS E 469 " --> pdb=" O ASP E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 512 removed outlier: 4.554A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 594 removed outlier: 3.807A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER E 591 " --> pdb=" O LYS E 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 592 " --> pdb=" O ILE E 588 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.796A pdb=" N GLU F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 233 " --> pdb=" O SER F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.023A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 471 removed outlier: 3.625A pdb=" N LYS F 469 " --> pdb=" O ASP F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 512 removed outlier: 4.594A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 590 removed outlier: 3.834A pdb=" N ASP F 590 " --> pdb=" O ASN F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.705A pdb=" N GLU G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.515A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 471 removed outlier: 3.780A pdb=" N LYS G 469 " --> pdb=" O ASP G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 512 removed outlier: 4.593A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 590 removed outlier: 3.843A pdb=" N ASP G 590 " --> pdb=" O ASN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 311 removed outlier: 6.664A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.979A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 372 through 382 removed outlier: 3.621A pdb=" N SER D 380 " --> pdb=" O HIS D 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 374 through 382 current: chain 'C' and resid 313 through 322 removed outlier: 3.527A pdb=" N LYS C 321 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 374 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 321 " --> pdb=" O TRP G 375 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP G 375 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 374 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 320 " --> pdb=" O SER G 374 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 380 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 374 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 320 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 321 " --> pdb=" O TRP E 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 375 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 374 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 320 " --> pdb=" O SER E 374 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 321 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 375 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 320 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.792A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.556A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.938A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.677A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 311 removed outlier: 6.666A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.546A pdb=" N TYR C 439 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.758A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 524 through 531 removed outlier: 3.809A pdb=" N GLU C 524 " --> pdb=" O THR C 521 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.696A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.719A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS D 405 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN D 486 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 531 removed outlier: 3.825A pdb=" N GLU D 524 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AD3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'E' and resid 301 through 311 removed outlier: 6.712A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.012A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.778A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AD8, first strand: chain 'E' and resid 524 through 531 removed outlier: 3.822A pdb=" N GLU E 524 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AE1, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE2, first strand: chain 'F' and resid 300 through 311 removed outlier: 5.811A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.523A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.690A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AE6, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.296A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AE8, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'G' and resid 301 through 311 removed outlier: 6.876A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.972A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.823A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS G 405 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN G 486 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF4, first strand: chain 'G' and resid 526 through 531 Processing sheet with id=AF5, first strand: chain 'G' and resid 558 through 559 592 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 5.33 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.140 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.110 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- 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= 0.175 Angle : 0.471 7.386 26600 Z= 0.256 Chirality : 0.043 0.141 3024 Planarity : 0.003 0.037 3472 Dihedral : 18.449 89.867 7357 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.18 % Allowed : 35.07 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2457 helix: -1.18 (0.25), residues: 385 sheet: 0.09 (0.21), residues: 630 loop : -0.66 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 503 HIS 0.003 0.001 HIS D 314 PHE 0.013 0.001 PHE D 281 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 2.467 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: 0.2891 time to fit residues: 103.0942 Evaluate side-chains 220 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain G residue 377 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 431 ASN D 431 ASN E 431 ASN F 431 ASN G 431 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19628 Z= 0.358 Angle : 0.558 7.695 26600 Z= 0.299 Chirality : 0.046 0.152 3024 Planarity : 0.004 0.045 3472 Dihedral : 4.623 33.151 2651 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.73 % Allowed : 32.07 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2457 helix: -1.36 (0.23), residues: 406 sheet: 0.17 (0.21), residues: 616 loop : -0.83 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.002 0.001 HIS F 314 PHE 0.025 0.002 PHE C 281 TYR 0.013 0.001 TYR B 439 ARG 0.002 0.000 ARG G 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: C 380 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8347 (t) REVERT: D 223 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8051 (m-40) REVERT: D 380 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8040 (t) REVERT: F 458 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.6891 (ttt-90) outliers start: 81 outliers final: 47 residues processed: 276 average time/residue: 0.2776 time to fit residues: 124.2011 Evaluate side-chains 254 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 0.0170 chunk 221 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 567 ASN B 567 ASN C 252 GLN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19628 Z= 0.265 Angle : 0.512 7.276 26600 Z= 0.275 Chirality : 0.045 0.143 3024 Planarity : 0.004 0.044 3472 Dihedral : 4.510 24.223 2647 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.01 % Allowed : 31.47 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2457 helix: -1.37 (0.22), residues: 434 sheet: 0.19 (0.21), residues: 616 loop : -0.87 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS F 314 PHE 0.022 0.002 PHE C 281 TYR 0.016 0.001 TYR C 396 ARG 0.002 0.000 ARG A 458 *********************** 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 301 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 214 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 237 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 612 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8393 (tt) REVERT: C 252 GLN cc_start: 0.8261 (mm110) cc_final: 0.8002 (mm-40) REVERT: C 380 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8362 (t) REVERT: D 223 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8073 (m-40) REVERT: D 313 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: D 376 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7273 (m-40) REVERT: D 380 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8032 (t) REVERT: D 589 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: F 458 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.6903 (ttt-90) REVERT: F 482 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8919 (pt0) REVERT: G 467 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8431 (tp) outliers start: 87 outliers final: 53 residues processed: 290 average time/residue: 0.2902 time to fit residues: 134.9558 Evaluate side-chains 270 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 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 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 237 ILE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 476 ILE 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 314 HIS 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 482 GLN 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 220 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 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 411 ASN A 567 ASN B 567 ASN E 425 GLN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19628 Z= 0.205 Angle : 0.483 7.077 26600 Z= 0.260 Chirality : 0.044 0.142 3024 Planarity : 0.004 0.042 3472 Dihedral : 4.382 23.419 2647 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.06 % Allowed : 31.47 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2457 helix: -1.26 (0.22), residues: 434 sheet: 0.26 (0.21), residues: 616 loop : -0.80 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 503 HIS 0.001 0.000 HIS F 314 PHE 0.018 0.002 PHE C 281 TYR 0.016 0.001 TYR C 396 ARG 0.001 0.000 ARG F 528 *********************** 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: 88 poor density : 218 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 612 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8380 (tt) REVERT: C 252 GLN cc_start: 0.8182 (mm110) cc_final: 0.7876 (mm-40) REVERT: C 380 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8388 (t) REVERT: D 313 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: D 376 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7232 (m-40) REVERT: D 380 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (t) REVERT: D 589 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7485 (ttpp) REVERT: F 458 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.6927 (ttt-90) REVERT: F 482 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8899 (pt0) REVERT: G 467 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8436 (tp) outliers start: 88 outliers final: 56 residues processed: 293 average time/residue: 0.3050 time to fit residues: 142.5836 Evaluate side-chains 275 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 476 ILE Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 313 GLU Chi-restraints excluded: chain E residue 405 LYS 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 287 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 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19628 Z= 0.539 Angle : 0.635 8.433 26600 Z= 0.338 Chirality : 0.050 0.155 3024 Planarity : 0.005 0.046 3472 Dihedral : 4.964 27.128 2647 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.48 % Allowed : 30.92 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2457 helix: -1.53 (0.22), residues: 427 sheet: -0.02 (0.21), residues: 616 loop : -0.97 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 503 HIS 0.002 0.001 HIS F 314 PHE 0.039 0.003 PHE F 281 TYR 0.016 0.002 TYR B 439 ARG 0.002 0.000 ARG C 232 *********************** 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 324 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 205 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (tt) REVERT: C 380 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (t) REVERT: D 376 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7232 (m-40) REVERT: D 380 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8021 (t) REVERT: D 442 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9131 (ttmt) REVERT: D 589 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7665 (ttpp) REVERT: F 458 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.6910 (ttt-90) REVERT: F 482 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8953 (pt0) REVERT: G 467 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8440 (tp) outliers start: 119 outliers final: 84 residues processed: 308 average time/residue: 0.2788 time to fit residues: 138.2799 Evaluate side-chains 295 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 202 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 438 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 272 THR 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 428 GLN Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL 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 442 LYS Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain E residue 272 THR 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 575 CYS 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 287 THR Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 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 Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 567 ASN C 252 GLN C 425 GLN G 411 ASN G 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0925 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= 0.152 Angle : 0.471 7.353 26600 Z= 0.254 Chirality : 0.043 0.143 3024 Planarity : 0.004 0.041 3472 Dihedral : 4.366 24.339 2647 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.41 % Allowed : 33.00 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2457 helix: -1.31 (0.22), residues: 441 sheet: 0.31 (0.21), residues: 567 loop : -0.86 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS F 314 PHE 0.011 0.001 PHE D 281 TYR 0.015 0.001 TYR C 396 ARG 0.001 0.000 ARG G 529 *********************** 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 295 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7802 (tt) REVERT: C 380 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8341 (t) REVERT: C 491 ASN cc_start: 0.7699 (p0) cc_final: 0.7404 (p0) REVERT: D 313 GLU cc_start: 0.8597 (pm20) cc_final: 0.8149 (pm20) REVERT: D 376 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: D 380 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8010 (t) REVERT: D 442 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9095 (ttmt) REVERT: D 458 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8589 (tmt-80) REVERT: D 589 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7492 (ttpp) REVERT: E 482 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.9024 (pt0) REVERT: F 458 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.6925 (ttt-90) REVERT: F 482 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8911 (pt0) REVERT: G 467 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8435 (tp) outliers start: 74 outliers final: 45 residues processed: 285 average time/residue: 0.2958 time to fit residues: 133.3092 Evaluate side-chains 270 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 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 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR 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 F residue 223 ASN Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 173 optimal weight: 0.0070 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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 463 ASN C 567 ASN G 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19628 Z= 0.322 Angle : 0.531 7.677 26600 Z= 0.284 Chirality : 0.046 0.143 3024 Planarity : 0.004 0.046 3472 Dihedral : 4.586 25.535 2647 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.56 % Allowed : 32.03 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2457 helix: -1.32 (0.22), residues: 434 sheet: 0.14 (0.21), residues: 616 loop : -0.85 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 503 HIS 0.001 0.000 HIS F 314 PHE 0.026 0.002 PHE F 281 TYR 0.013 0.001 TYR B 439 ARG 0.002 0.000 ARG A 458 *********************** 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 309 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7851 (tt) REVERT: A 458 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8079 (tmt-80) REVERT: C 252 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7788 (mm-40) REVERT: C 380 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8375 (t) REVERT: D 376 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: D 380 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (t) REVERT: D 442 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9119 (ttmt) REVERT: D 458 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8623 (tmt-80) REVERT: F 458 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.6904 (ttt-90) REVERT: F 482 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8933 (pt0) REVERT: G 467 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8447 (tp) outliers start: 99 outliers final: 70 residues processed: 299 average time/residue: 0.2953 time to fit residues: 139.7058 Evaluate side-chains 287 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 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 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR 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 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 573 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR 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 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19628 Z= 0.271 Angle : 0.516 7.912 26600 Z= 0.276 Chirality : 0.045 0.143 3024 Planarity : 0.004 0.045 3472 Dihedral : 4.543 25.512 2647 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.52 % Allowed : 32.12 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2457 helix: -1.29 (0.22), residues: 434 sheet: 0.31 (0.21), residues: 602 loop : -0.90 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 503 HIS 0.001 0.000 HIS F 314 PHE 0.020 0.002 PHE F 281 TYR 0.013 0.001 TYR B 439 ARG 0.001 0.000 ARG C 529 *********************** 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 307 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 209 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 458 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8068 (tmt-80) REVERT: B 612 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8363 (tt) REVERT: C 252 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7771 (mm-40) REVERT: C 380 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8370 (t) REVERT: D 269 ASP cc_start: 0.9080 (p0) cc_final: 0.8875 (p0) REVERT: D 376 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7195 (m-40) REVERT: D 380 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8007 (t) REVERT: D 442 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9103 (ttmt) REVERT: D 458 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8623 (tmt-80) REVERT: E 482 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.9028 (pt0) REVERT: F 458 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.6899 (ttt-90) REVERT: F 482 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8918 (pt0) REVERT: G 467 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8444 (tp) outliers start: 98 outliers final: 75 residues processed: 294 average time/residue: 0.3201 time to fit residues: 148.6888 Evaluate side-chains 293 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 206 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 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 C residue 569 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 442 LYS 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 311 THR Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 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 281 PHE Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN 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 214 optimal weight: 0.0020 chunk 226 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0975 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= 0.187 Angle : 0.478 7.370 26600 Z= 0.257 Chirality : 0.044 0.142 3024 Planarity : 0.004 0.043 3472 Dihedral : 4.323 24.103 2647 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.15 % Allowed : 32.58 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2457 helix: -1.19 (0.23), residues: 434 sheet: 0.41 (0.21), residues: 602 loop : -0.81 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 375 HIS 0.001 0.000 HIS F 314 PHE 0.013 0.001 PHE F 281 TYR 0.014 0.001 TYR E 396 ARG 0.002 0.000 ARG C 529 *********************** 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 304 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 214 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 458 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7970 (tmt-80) REVERT: B 612 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8351 (tt) REVERT: C 380 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8344 (t) REVERT: D 380 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.8026 (t) REVERT: D 442 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (ttmt) REVERT: D 458 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8599 (tmt-80) REVERT: E 482 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9017 (pt0) REVERT: F 458 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.6877 (ttt-90) REVERT: G 467 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8443 (tp) outliers start: 90 outliers final: 64 residues processed: 291 average time/residue: 0.2962 time to fit residues: 136.9739 Evaluate side-chains 286 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 212 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 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 287 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 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 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 380 SER Chi-restraints excluded: chain D residue 442 LYS 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 311 THR Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 434 SER 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 263 GLU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 458 ARG Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 484 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 161 optimal weight: 0.1980 chunk 244 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 D 376 ASN G 265 ASN G 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19628 Z= 0.164 Angle : 0.466 6.962 26600 Z= 0.251 Chirality : 0.043 0.142 3024 Planarity : 0.004 0.042 3472 Dihedral : 4.190 22.850 2647 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.59 % Allowed : 33.09 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2457 helix: -1.09 (0.23), residues: 434 sheet: 0.50 (0.21), residues: 567 loop : -0.71 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 375 HIS 0.001 0.000 HIS F 314 PHE 0.013 0.001 PHE F 281 TYR 0.015 0.001 TYR E 396 ARG 0.001 0.000 ARG C 529 ********************** 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 296 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (tt) REVERT: A 458 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8015 (tmt-80) REVERT: B 612 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (tt) REVERT: C 380 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8344 (t) REVERT: D 380 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8067 (t) REVERT: D 442 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9064 (ttmt) REVERT: D 458 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8618 (tmt-80) REVERT: E 482 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9007 (pt0) REVERT: F 458 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.6962 (ttt-90) REVERT: G 467 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8443 (tp) outliers start: 78 outliers final: 57 residues processed: 285 average time/residue: 0.1913 time to fit residues: 87.0944 Evaluate side-chains 280 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 THR 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 287 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 442 LYS 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 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 311 THR 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 263 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 GLU Chi-restraints excluded: chain F residue 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 287 THR Chi-restraints excluded: chain G residue 313 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 523 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN B 567 ASN C 567 ASN D 376 ASN G 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099096 restraints weight = 27242.280| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.14 r_work: 0.2982 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1005 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: