Starting phenix.real_space_refine on Tue Jun 17 08:20:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.map" model { file = "/net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbf_44419/06_2025/9bbf_44419.cif" } resolution = 3.6 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= 0.006 sd= 0.064 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 38 5.16 5 C 12458 2.51 5 N 3246 2.21 5 O 4124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19880 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2612 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2612 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2612 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2612 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2592 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "F" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2588 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain breaks: 2 Chain: "G" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2612 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "Z" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1626 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} 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: 12.05, per 1000 atoms: 0.61 Number of scatterers: 19880 At special positions: 0 Unit cell: (115.7, 137.15, 132.6, 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 38 16.00 O 4124 8.00 N 3246 7.00 C 12458 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: 5.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 60 sheets defined 24.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 250 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 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.526A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.282A 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 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.633A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.599A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.862A 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 572 through 576 Processing helix chain 'B' and resid 581 through 595 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 253 removed outlier: 3.640A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.971A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.715A pdb=" N ASP C 505 " --> pdb=" O SER C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 595 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.627A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.533A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 3.789A 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 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 502 through 505 removed outlier: 3.570A pdb=" N ASP D 505 " --> pdb=" O SER D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 505' Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 572 through 576 removed outlier: 3.764A pdb=" N VAL D 576 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.779A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN E 252 " --> pdb=" O PHE E 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 253 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.867A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 572 through 576 removed outlier: 3.614A pdb=" N VAL E 576 " --> pdb=" O GLU E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 594 Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.648A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 506 through 513 Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 572 through 576 removed outlier: 3.630A pdb=" N VAL F 576 " --> pdb=" O GLU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 594 removed outlier: 3.684A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.756A 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 463 through 472 Processing helix chain 'G' and resid 506 through 513 Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.882A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 79 removed outlier: 3.639A pdb=" N ALA Z 66 " --> pdb=" O ASP Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 95 removed outlier: 4.418A pdb=" N GLU Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER Z 91 " --> pdb=" O GLU Z 87 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR Z 92 " --> pdb=" O ALA Z 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 104 Processing helix chain 'Z' and resid 120 through 131 Processing helix chain 'Z' and resid 168 through 176 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 300 through 311 removed outlier: 5.322A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 311 removed outlier: 5.322A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.463A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.463A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.349A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 558 through 560 Processing sheet with id=AB2, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB3, first strand: chain 'B' and resid 300 through 311 removed outlier: 5.354A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 300 through 311 removed outlier: 5.354A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AB6, first strand: chain 'B' and resid 417 through 423 removed outlier: 5.218A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 482 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B 411 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR B 480 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 413 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 478 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 491 removed outlier: 3.604A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 497 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 525 through 530 Processing sheet with id=AB9, first strand: chain 'B' and resid 558 through 560 Processing sheet with id=AC1, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 311 removed outlier: 5.514A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 300 through 311 removed outlier: 5.514A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AC5, first strand: chain 'C' and resid 417 through 423 removed outlier: 5.297A pdb=" N THR C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 414 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 420 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN C 482 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN C 411 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR C 480 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 413 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU C 478 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AC7, first strand: chain 'C' and resid 525 through 530 Processing sheet with id=AC8, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC9, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AD1, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.495A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.495A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 389 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 381 through 382 Processing sheet with id=AD4, first strand: chain 'D' and resid 417 through 423 removed outlier: 5.215A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 420 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 417 through 423 removed outlier: 5.215A pdb=" N THR D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 414 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 420 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.631A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 558 through 560 Processing sheet with id=AD8, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD9, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.420A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.420A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 389 " --> pdb=" O ILE E 460 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 381 through 382 Processing sheet with id=AE3, first strand: chain 'E' and resid 417 through 423 removed outlier: 5.239A pdb=" N THR E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 414 " --> pdb=" O THR E 418 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 482 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN E 411 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR E 480 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL E 413 " --> pdb=" O LEU E 478 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU E 478 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 525 through 530 Processing sheet with id=AE5, first strand: chain 'E' and resid 558 through 560 Processing sheet with id=AE6, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AE7, first strand: chain 'F' and resid 300 through 309 removed outlier: 6.964A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 300 through 309 removed outlier: 6.964A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE F 460 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AF1, first strand: chain 'F' and resid 417 through 423 removed outlier: 5.257A pdb=" N THR F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU F 414 " --> pdb=" O THR F 418 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 420 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN F 482 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN F 411 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR F 480 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL F 413 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU F 478 " --> pdb=" O VAL F 413 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 525 through 530 Processing sheet with id=AF3, first strand: chain 'F' and resid 558 through 560 Processing sheet with id=AF4, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AF5, first strand: chain 'G' and resid 300 through 311 removed outlier: 5.495A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 300 through 311 removed outlier: 5.495A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 417 through 423 removed outlier: 6.647A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 417 through 423 removed outlier: 6.647A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AG1, first strand: chain 'G' and resid 525 through 530 Processing sheet with id=AG2, first strand: chain 'G' and resid 558 through 560 Processing sheet with id=AG3, first strand: chain 'Z' and resid 139 through 141 removed outlier: 6.978A pdb=" N LEU Z 205 " --> pdb=" O ALA Z 253 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA Z 255 " --> pdb=" O LEU Z 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS Z 207 " --> pdb=" O ALA Z 255 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 182 through 184 Processing sheet with id=AG5, first strand: chain 'Z' and resid 187 through 189 removed outlier: 3.693A pdb=" N LYS Z 187 " --> pdb=" O ILE Z 229 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE Z 229 " --> pdb=" O LYS Z 187 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR Z 227 " --> pdb=" O ILE Z 189 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 244 through 245 681 hydrogen bonds defined for protein. 1707 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: 7.04 Time building geometry restraints manager: 6.04 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: 6478 1.34 - 1.46: 2737 1.46 - 1.57: 10894 1.57 - 1.69: 2 1.69 - 1.81: 69 Bond restraints: 20180 Sorted by residual: bond pdb=" CG1 ILE Z 243 " pdb=" CD1 ILE Z 243 " ideal model delta sigma weight residual 1.513 1.393 0.120 3.90e-02 6.57e+02 9.43e+00 bond pdb=" CB PRO F 543 " pdb=" CG PRO F 543 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.37e+00 bond pdb=" CG PRO C 538 " pdb=" CD PRO C 538 " ideal model delta sigma weight residual 1.503 1.566 -0.063 3.40e-02 8.65e+02 3.49e+00 bond pdb=" CB ASN D 432 " pdb=" CG ASN D 432 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.30e+00 bond pdb=" CB PRO C 538 " pdb=" CG PRO C 538 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.63e+00 ... (remaining 20175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 26929 2.45 - 4.89: 316 4.89 - 7.34: 42 7.34 - 9.79: 9 9.79 - 12.23: 3 Bond angle restraints: 27299 Sorted by residual: angle pdb=" CA PRO F 543 " pdb=" N PRO F 543 " pdb=" CD PRO F 543 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 angle pdb=" C GLN C 495 " pdb=" CA GLN C 495 " pdb=" CB GLN C 495 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.43e+01 angle pdb=" CB MET Z 216 " pdb=" CG MET Z 216 " pdb=" SD MET Z 216 " ideal model delta sigma weight residual 112.70 100.47 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA LYS Z 65 " pdb=" CB LYS Z 65 " pdb=" CG LYS Z 65 " ideal model delta sigma weight residual 114.10 122.15 -8.05 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CA PRO C 538 " pdb=" N PRO C 538 " pdb=" CD PRO C 538 " ideal model delta sigma weight residual 112.00 106.46 5.54 1.40e+00 5.10e-01 1.56e+01 ... (remaining 27294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10320 17.74 - 35.48: 1545 35.48 - 53.22: 448 53.22 - 70.95: 61 70.95 - 88.69: 25 Dihedral angle restraints: 12399 sinusoidal: 4986 harmonic: 7413 Sorted by residual: dihedral pdb=" CA MET D 403 " pdb=" C MET D 403 " pdb=" N TYR D 404 " pdb=" CA TYR D 404 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA GLY Z 232 " pdb=" C GLY Z 232 " pdb=" N TYR Z 233 " pdb=" CA TYR Z 233 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA TYR B 439 " pdb=" C TYR B 439 " pdb=" N PRO B 440 " pdb=" CA PRO B 440 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 12396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2332 0.054 - 0.107: 624 0.107 - 0.160: 122 0.160 - 0.214: 11 0.214 - 0.267: 1 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CB ILE C 507 " pdb=" CA ILE C 507 " pdb=" CG1 ILE C 507 " pdb=" CG2 ILE C 507 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU Z 217 " pdb=" CB LEU Z 217 " pdb=" CD1 LEU Z 217 " pdb=" CD2 LEU Z 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 302 " pdb=" CA VAL A 302 " pdb=" CG1 VAL A 302 " pdb=" CG2 VAL A 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 3087 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 542 " -0.097 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO F 543 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO F 543 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO F 543 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 542 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO C 543 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 543 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 543 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 542 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO D 543 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 543 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 543 " 0.055 5.00e-02 4.00e+02 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3495 2.77 - 3.30: 18320 3.30 - 3.83: 32967 3.83 - 4.37: 38337 4.37 - 4.90: 68066 Nonbonded interactions: 161185 Sorted by model distance: nonbonded pdb=" O ILE C 510 " pdb=" OG SER C 514 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR D 221 " pdb=" OD2 ASP D 228 " model vdw 2.239 3.040 nonbonded pdb=" OE1 GLN A 425 " pdb=" OG1 THR A 451 " model vdw 2.240 3.040 nonbonded pdb=" OG SER D 264 " pdb=" OD1 ASN D 265 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLN B 425 " pdb=" OG1 THR B 451 " model vdw 2.246 3.040 ... (remaining 161180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) selection = (chain 'B' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) selection = (chain 'C' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) selection = (chain 'D' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) selection = (chain 'E' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) selection = chain 'F' selection = (chain 'G' and (resid 218 through 490 or resid 495 through 615 or resid 901 thro \ ugh 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.370 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.126 20180 Z= 0.180 Angle : 0.705 12.232 27299 Z= 0.382 Chirality : 0.050 0.267 3090 Planarity : 0.006 0.140 3549 Dihedral : 18.122 88.692 7637 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.36 % Allowed : 32.96 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.16), residues: 2497 helix: -1.00 (0.21), residues: 538 sheet: -0.17 (0.21), residues: 607 loop : -1.29 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 245 HIS 0.003 0.001 HIS Z 207 PHE 0.027 0.002 PHE F 580 TYR 0.024 0.001 TYR Z 233 ARG 0.013 0.001 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.15198 ( 636) hydrogen bonds : angle 7.25289 ( 1707) covalent geometry : bond 0.00422 (20180) covalent geometry : angle 0.70515 (27299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 278 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.7471 (pt0) cc_final: 0.7248 (pt0) REVERT: B 575 CYS cc_start: 0.8785 (m) cc_final: 0.8449 (m) REVERT: C 589 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8513 (mtpt) REVERT: E 570 PRO cc_start: 0.7996 (Cg_exo) cc_final: 0.7718 (Cg_endo) REVERT: E 589 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8013 (tppt) REVERT: G 458 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8537 (mtp85) REVERT: G 534 ASN cc_start: 0.6389 (t0) cc_final: 0.6173 (t0) outliers start: 8 outliers final: 5 residues processed: 283 average time/residue: 0.2853 time to fit residues: 128.4126 Evaluate side-chains 266 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 261 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain Z residue 180 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 127 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 427 ASN A 428 GLN A 509 GLN B 432 ASN B 466 GLN C 265 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 252 GLN D 428 GLN D 432 ASN D 602 ASN E 432 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN G 428 GLN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 GLN G 602 ASN Z 162 ASN Z 183 GLN Z 213 ASN Z 221 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126573 restraints weight = 31115.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130618 restraints weight = 16096.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133149 restraints weight = 10661.369| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20180 Z= 0.133 Angle : 0.538 6.715 27299 Z= 0.287 Chirality : 0.045 0.148 3090 Planarity : 0.005 0.080 3549 Dihedral : 5.002 51.689 2720 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.82 % Allowed : 29.59 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.17), residues: 2497 helix: -0.57 (0.22), residues: 530 sheet: -0.27 (0.21), residues: 625 loop : -1.09 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 245 HIS 0.003 0.001 HIS Z 207 PHE 0.017 0.001 PHE C 281 TYR 0.021 0.001 TYR Z 233 ARG 0.006 0.000 ARG Z 76 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 636) hydrogen bonds : angle 5.71817 ( 1707) covalent geometry : bond 0.00310 (20180) covalent geometry : angle 0.53825 (27299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 273 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7618 (mp10) cc_final: 0.7394 (mp10) REVERT: B 575 CYS cc_start: 0.8869 (m) cc_final: 0.8474 (m) REVERT: C 506 TYR cc_start: 0.8267 (m-80) cc_final: 0.7520 (m-80) REVERT: D 469 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8206 (mtpt) REVERT: D 567 ASN cc_start: 0.7139 (t0) cc_final: 0.6870 (t0) REVERT: E 245 TRP cc_start: 0.8009 (t60) cc_final: 0.7682 (t60) REVERT: E 281 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8220 (p90) REVERT: E 589 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8057 (tppt) REVERT: G 449 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8272 (tt) REVERT: G 458 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8533 (mtp85) REVERT: Z 76 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7636 (ttp80) outliers start: 85 outliers final: 43 residues processed: 333 average time/residue: 0.2989 time to fit residues: 158.1217 Evaluate side-chains 292 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 260 ASN Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 225 VAL Chi-restraints excluded: chain Z residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 200 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 72 optimal weight: 0.0980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN D 602 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 GLN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122629 restraints weight = 31048.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126551 restraints weight = 16267.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129034 restraints weight = 10903.737| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20180 Z= 0.173 Angle : 0.551 8.502 27299 Z= 0.293 Chirality : 0.046 0.153 3090 Planarity : 0.004 0.069 3549 Dihedral : 4.791 31.513 2713 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.25 % Allowed : 28.65 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.17), residues: 2497 helix: -0.48 (0.22), residues: 531 sheet: -0.39 (0.21), residues: 628 loop : -1.09 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 245 HIS 0.003 0.001 HIS Z 207 PHE 0.023 0.001 PHE C 281 TYR 0.017 0.001 TYR Z 233 ARG 0.007 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 636) hydrogen bonds : angle 5.49466 ( 1707) covalent geometry : bond 0.00402 (20180) covalent geometry : angle 0.55134 (27299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 270 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7658 (mp10) cc_final: 0.7395 (mp10) REVERT: A 428 GLN cc_start: 0.7674 (mt0) cc_final: 0.7244 (mp10) REVERT: B 575 CYS cc_start: 0.8907 (m) cc_final: 0.8482 (m) REVERT: B 589 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8370 (mmtt) REVERT: B 593 LYS cc_start: 0.8455 (ttpt) cc_final: 0.7658 (tttm) REVERT: C 506 TYR cc_start: 0.8303 (m-80) cc_final: 0.7651 (m-80) REVERT: D 469 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8234 (mtpt) REVERT: D 567 ASN cc_start: 0.7245 (t0) cc_final: 0.6943 (t0) REVERT: E 245 TRP cc_start: 0.8099 (t60) cc_final: 0.7745 (t60) REVERT: E 251 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: E 281 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8363 (p90) REVERT: F 304 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6844 (tpp) REVERT: G 458 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8557 (mtp85) outliers start: 117 outliers final: 72 residues processed: 358 average time/residue: 0.2862 time to fit residues: 163.0378 Evaluate side-chains 329 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 253 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 196 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 225 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 314 HIS ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.156615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124054 restraints weight = 31886.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128042 restraints weight = 16674.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130562 restraints weight = 11158.734| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20180 Z= 0.155 Angle : 0.541 7.636 27299 Z= 0.285 Chirality : 0.045 0.149 3090 Planarity : 0.004 0.067 3549 Dihedral : 4.747 31.223 2713 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.39 % Allowed : 28.69 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.17), residues: 2497 helix: -0.35 (0.22), residues: 526 sheet: -0.39 (0.21), residues: 626 loop : -1.09 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 249 PHE 0.021 0.001 PHE C 281 TYR 0.014 0.001 TYR Z 233 ARG 0.007 0.000 ARG Z 76 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 636) hydrogen bonds : angle 5.32797 ( 1707) covalent geometry : bond 0.00361 (20180) covalent geometry : angle 0.54086 (27299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 260 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7686 (mp10) cc_final: 0.7438 (mp10) REVERT: A 385 GLU cc_start: 0.8617 (tp30) cc_final: 0.8339 (tp30) REVERT: A 428 GLN cc_start: 0.7917 (mt0) cc_final: 0.7580 (mp10) REVERT: B 575 CYS cc_start: 0.8918 (m) cc_final: 0.8460 (m) REVERT: B 589 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8375 (mmtt) REVERT: B 593 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7671 (tttm) REVERT: C 506 TYR cc_start: 0.8340 (m-80) cc_final: 0.7619 (m-80) REVERT: D 469 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8206 (mtpt) REVERT: D 567 ASN cc_start: 0.7340 (t0) cc_final: 0.7047 (t0) REVERT: E 251 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: E 281 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8321 (p90) REVERT: E 589 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8185 (tppt) REVERT: F 304 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.6860 (tpp) REVERT: G 449 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8210 (tt) REVERT: G 458 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8546 (mtp85) REVERT: Z 145 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7319 (tt0) outliers start: 120 outliers final: 83 residues processed: 356 average time/residue: 0.2813 time to fit residues: 158.8405 Evaluate side-chains 342 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 225 VAL Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 392 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119554 restraints weight = 32213.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123411 restraints weight = 17204.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125853 restraints weight = 11659.688| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20180 Z= 0.247 Angle : 0.620 7.777 27299 Z= 0.328 Chirality : 0.048 0.156 3090 Planarity : 0.005 0.065 3549 Dihedral : 5.017 36.788 2713 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 6.74 % Allowed : 27.80 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.16), residues: 2497 helix: -0.53 (0.22), residues: 528 sheet: -0.70 (0.21), residues: 617 loop : -1.23 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 245 HIS 0.004 0.001 HIS Z 207 PHE 0.033 0.002 PHE C 281 TYR 0.017 0.002 TYR G 254 ARG 0.008 0.001 ARG Z 76 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 636) hydrogen bonds : angle 5.43924 ( 1707) covalent geometry : bond 0.00576 (20180) covalent geometry : angle 0.61963 (27299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 270 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7765 (mp10) cc_final: 0.7352 (mp10) REVERT: A 403 MET cc_start: 0.8618 (ttt) cc_final: 0.8415 (ttt) REVERT: B 305 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 575 CYS cc_start: 0.8912 (m) cc_final: 0.8453 (m) REVERT: B 589 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8393 (mmtt) REVERT: C 506 TYR cc_start: 0.8445 (m-80) cc_final: 0.7863 (m-80) REVERT: C 537 ASP cc_start: 0.8201 (t0) cc_final: 0.7923 (t0) REVERT: C 568 ASP cc_start: 0.8334 (m-30) cc_final: 0.7997 (m-30) REVERT: D 469 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8159 (mtpt) REVERT: D 567 ASN cc_start: 0.7483 (t0) cc_final: 0.7165 (t0) REVERT: E 251 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: E 589 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8324 (tptp) REVERT: F 304 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.6836 (tpp) REVERT: F 609 MET cc_start: 0.6896 (mtp) cc_final: 0.6690 (mtp) REVERT: G 449 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8322 (tt) REVERT: G 458 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8625 (mtp85) REVERT: Z 62 ASP cc_start: 0.8091 (m-30) cc_final: 0.7716 (m-30) REVERT: Z 145 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7477 (tt0) outliers start: 150 outliers final: 102 residues processed: 393 average time/residue: 0.2939 time to fit residues: 183.0510 Evaluate side-chains 357 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 249 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 455 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 257 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 106 optimal weight: 0.9990 chunk 244 optimal weight: 0.0870 chunk 124 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125407 restraints weight = 31608.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129501 restraints weight = 16600.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132082 restraints weight = 11075.434| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20180 Z= 0.107 Angle : 0.537 9.688 27299 Z= 0.280 Chirality : 0.045 0.159 3090 Planarity : 0.004 0.058 3549 Dihedral : 4.712 32.640 2713 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.27 % Allowed : 30.04 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.17), residues: 2497 helix: -0.18 (0.23), residues: 526 sheet: -0.46 (0.21), residues: 621 loop : -1.05 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 245 HIS 0.002 0.001 HIS Z 249 PHE 0.014 0.001 PHE C 281 TYR 0.018 0.001 TYR E 404 ARG 0.011 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.02647 ( 636) hydrogen bonds : angle 5.17639 ( 1707) covalent geometry : bond 0.00250 (20180) covalent geometry : angle 0.53697 (27299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 283 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7796 (mp10) cc_final: 0.7524 (mp10) REVERT: B 575 CYS cc_start: 0.8913 (m) cc_final: 0.8461 (m) REVERT: C 506 TYR cc_start: 0.8407 (m-80) cc_final: 0.7742 (m-80) REVERT: C 537 ASP cc_start: 0.8190 (t0) cc_final: 0.7873 (t0) REVERT: D 464 TYR cc_start: 0.8319 (t80) cc_final: 0.8060 (t80) REVERT: D 469 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8125 (mtpt) REVERT: D 567 ASN cc_start: 0.7448 (t0) cc_final: 0.7122 (t0) REVERT: E 281 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8309 (p90) REVERT: E 589 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8285 (tptp) REVERT: F 304 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6870 (tpp) REVERT: F 535 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4956 (mm) REVERT: G 449 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8167 (tt) REVERT: G 458 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8582 (mtp85) REVERT: Z 62 ASP cc_start: 0.7983 (m-30) cc_final: 0.7656 (m-30) REVERT: Z 145 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: Z 177 GLN cc_start: 0.7501 (tp40) cc_final: 0.7287 (mm-40) outliers start: 95 outliers final: 69 residues processed: 361 average time/residue: 0.3018 time to fit residues: 172.3862 Evaluate side-chains 338 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 490 LYS Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 225 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117268 restraints weight = 31453.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120988 restraints weight = 16640.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123378 restraints weight = 11279.619| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20180 Z= 0.276 Angle : 0.650 9.142 27299 Z= 0.343 Chirality : 0.049 0.157 3090 Planarity : 0.005 0.061 3549 Dihedral : 5.042 37.595 2713 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.15 % Allowed : 28.69 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.16), residues: 2497 helix: -0.50 (0.22), residues: 527 sheet: -0.73 (0.22), residues: 602 loop : -1.24 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 245 HIS 0.004 0.001 HIS Z 207 PHE 0.033 0.002 PHE C 281 TYR 0.017 0.002 TYR E 404 ARG 0.015 0.001 ARG Z 71 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 636) hydrogen bonds : angle 5.38064 ( 1707) covalent geometry : bond 0.00644 (20180) covalent geometry : angle 0.64953 (27299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 258 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: B 561 ASP cc_start: 0.7460 (t0) cc_final: 0.7231 (t0) REVERT: B 575 CYS cc_start: 0.8920 (m) cc_final: 0.8460 (m) REVERT: C 304 MET cc_start: 0.9110 (tpp) cc_final: 0.8847 (ttm) REVERT: C 506 TYR cc_start: 0.8493 (m-80) cc_final: 0.7927 (m-80) REVERT: C 537 ASP cc_start: 0.8316 (t0) cc_final: 0.7988 (t0) REVERT: C 568 ASP cc_start: 0.8381 (m-30) cc_final: 0.8027 (m-30) REVERT: D 469 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8148 (mtpt) REVERT: D 567 ASN cc_start: 0.7565 (t0) cc_final: 0.7227 (t0) REVERT: E 251 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: E 475 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: E 589 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8302 (tptp) REVERT: F 304 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6836 (tpp) REVERT: F 535 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5007 (mm) REVERT: G 449 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8320 (tt) REVERT: G 458 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8624 (mtp85) REVERT: Z 62 ASP cc_start: 0.8127 (m-30) cc_final: 0.7677 (m-30) REVERT: Z 71 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8072 (mmt-90) REVERT: Z 145 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: Z 177 GLN cc_start: 0.7540 (tp40) cc_final: 0.7296 (mm-40) outliers start: 137 outliers final: 98 residues processed: 369 average time/residue: 0.2847 time to fit residues: 167.3676 Evaluate side-chains 353 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 246 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 455 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 71 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 189 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117955 restraints weight = 31586.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121742 restraints weight = 16650.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124144 restraints weight = 11250.160| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20180 Z= 0.224 Angle : 0.619 9.010 27299 Z= 0.325 Chirality : 0.048 0.178 3090 Planarity : 0.005 0.061 3549 Dihedral : 5.037 35.174 2713 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.79 % Allowed : 29.05 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.16), residues: 2497 helix: -0.49 (0.22), residues: 527 sheet: -0.85 (0.21), residues: 602 loop : -1.19 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 245 HIS 0.003 0.001 HIS Z 207 PHE 0.025 0.002 PHE C 281 TYR 0.018 0.001 TYR B 230 ARG 0.013 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 636) hydrogen bonds : angle 5.38619 ( 1707) covalent geometry : bond 0.00525 (20180) covalent geometry : angle 0.61870 (27299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 259 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 ASP cc_start: 0.7477 (t0) cc_final: 0.7249 (t0) REVERT: B 575 CYS cc_start: 0.8920 (m) cc_final: 0.8430 (m) REVERT: C 304 MET cc_start: 0.9081 (tpp) cc_final: 0.8877 (ttm) REVERT: C 506 TYR cc_start: 0.8516 (m-80) cc_final: 0.7957 (m-80) REVERT: C 537 ASP cc_start: 0.8340 (t0) cc_final: 0.8050 (t0) REVERT: C 568 ASP cc_start: 0.8375 (m-30) cc_final: 0.8005 (m-30) REVERT: D 469 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8191 (mtpt) REVERT: D 567 ASN cc_start: 0.7585 (t0) cc_final: 0.7259 (t0) REVERT: E 475 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: E 589 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8291 (tptp) REVERT: F 304 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6854 (tpp) REVERT: F 429 ILE cc_start: 0.8826 (mt) cc_final: 0.8368 (pt) REVERT: F 535 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4952 (mm) REVERT: G 449 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8326 (tt) REVERT: G 458 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8632 (mtp85) REVERT: Z 62 ASP cc_start: 0.8147 (m-30) cc_final: 0.7723 (m-30) REVERT: Z 145 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: Z 177 GLN cc_start: 0.7524 (tp40) cc_final: 0.7297 (mm-40) outliers start: 129 outliers final: 103 residues processed: 361 average time/residue: 0.2896 time to fit residues: 165.0748 Evaluate side-chains 361 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 252 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 257 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119559 restraints weight = 31205.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123366 restraints weight = 16442.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125792 restraints weight = 11107.895| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20180 Z= 0.169 Angle : 0.584 8.091 27299 Z= 0.306 Chirality : 0.046 0.154 3090 Planarity : 0.004 0.059 3549 Dihedral : 4.932 33.164 2713 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.25 % Allowed : 29.95 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.17), residues: 2497 helix: -0.35 (0.22), residues: 527 sheet: -0.79 (0.22), residues: 607 loop : -1.16 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 245 HIS 0.002 0.001 HIS Z 207 PHE 0.021 0.001 PHE B 281 TYR 0.017 0.001 TYR B 230 ARG 0.013 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 636) hydrogen bonds : angle 5.28859 ( 1707) covalent geometry : bond 0.00399 (20180) covalent geometry : angle 0.58405 (27299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 265 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 CYS cc_start: 0.8928 (m) cc_final: 0.8438 (m) REVERT: C 506 TYR cc_start: 0.8493 (m-80) cc_final: 0.7852 (m-80) REVERT: C 537 ASP cc_start: 0.8377 (t0) cc_final: 0.8076 (t0) REVERT: C 568 ASP cc_start: 0.8353 (m-30) cc_final: 0.7978 (m-30) REVERT: D 469 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8177 (mtpt) REVERT: D 567 ASN cc_start: 0.7542 (t0) cc_final: 0.7191 (t0) REVERT: E 475 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: E 589 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8275 (tptp) REVERT: F 304 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.6870 (tpp) REVERT: F 429 ILE cc_start: 0.8802 (mt) cc_final: 0.8316 (pt) REVERT: F 535 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.5008 (mm) REVERT: G 449 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8261 (tt) REVERT: G 458 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8618 (mtp85) REVERT: Z 62 ASP cc_start: 0.8120 (m-30) cc_final: 0.7694 (m-30) REVERT: Z 145 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: Z 177 GLN cc_start: 0.7545 (tp40) cc_final: 0.7321 (mm-40) outliers start: 117 outliers final: 98 residues processed: 354 average time/residue: 0.2810 time to fit residues: 158.2825 Evaluate side-chains 360 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 256 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 455 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 490 LYS Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122462 restraints weight = 31928.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126387 restraints weight = 16913.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128887 restraints weight = 11371.721| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20180 Z= 0.149 Angle : 0.577 9.279 27299 Z= 0.302 Chirality : 0.046 0.149 3090 Planarity : 0.004 0.059 3549 Dihedral : 4.834 32.190 2713 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.49 % Allowed : 30.89 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.17), residues: 2497 helix: -0.28 (0.23), residues: 528 sheet: -0.73 (0.21), residues: 616 loop : -1.14 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 245 HIS 0.003 0.001 HIS Z 207 PHE 0.018 0.001 PHE B 281 TYR 0.016 0.001 TYR B 230 ARG 0.013 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 636) hydrogen bonds : angle 5.19839 ( 1707) covalent geometry : bond 0.00353 (20180) covalent geometry : angle 0.57678 (27299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 265 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 CYS cc_start: 0.8926 (m) cc_final: 0.8423 (m) REVERT: C 432 ASN cc_start: 0.7626 (p0) cc_final: 0.7352 (p0) REVERT: C 506 TYR cc_start: 0.8447 (m-80) cc_final: 0.7820 (m-80) REVERT: C 537 ASP cc_start: 0.8333 (t0) cc_final: 0.8055 (t0) REVERT: C 568 ASP cc_start: 0.8322 (m-30) cc_final: 0.7952 (m-30) REVERT: D 469 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8154 (mtpt) REVERT: D 511 ASP cc_start: 0.8740 (m-30) cc_final: 0.8434 (m-30) REVERT: D 567 ASN cc_start: 0.7512 (t0) cc_final: 0.7164 (t0) REVERT: E 475 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: E 589 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8280 (tptp) REVERT: F 304 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6865 (tpp) REVERT: F 535 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4993 (mm) REVERT: G 449 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8253 (tt) REVERT: G 458 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8608 (mtp85) REVERT: Z 62 ASP cc_start: 0.8078 (m-30) cc_final: 0.7701 (m-30) REVERT: Z 145 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: Z 177 GLN cc_start: 0.7526 (tp40) cc_final: 0.7312 (mm-40) REVERT: Z 199 GLU cc_start: 0.7730 (tp30) cc_final: 0.7528 (tp30) outliers start: 100 outliers final: 89 residues processed: 340 average time/residue: 0.2947 time to fit residues: 159.8275 Evaluate side-chains 353 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 258 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 475 GLN Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 490 LYS Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 109 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.154678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122288 restraints weight = 31967.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126184 restraints weight = 16863.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128656 restraints weight = 11368.401| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20180 Z= 0.157 Angle : 0.576 8.094 27299 Z= 0.302 Chirality : 0.046 0.147 3090 Planarity : 0.004 0.059 3549 Dihedral : 4.805 32.101 2713 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.07 % Allowed : 30.18 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.17), residues: 2497 helix: -0.26 (0.23), residues: 528 sheet: -0.65 (0.21), residues: 611 loop : -1.12 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 245 HIS 0.003 0.001 HIS Z 207 PHE 0.020 0.001 PHE C 281 TYR 0.015 0.001 TYR B 230 ARG 0.013 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 636) hydrogen bonds : angle 5.16531 ( 1707) covalent geometry : bond 0.00370 (20180) covalent geometry : angle 0.57587 (27299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6649.35 seconds wall clock time: 116 minutes 31.12 seconds (6991.12 seconds total)