Starting phenix.real_space_refine on Thu Sep 18 19:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbf_44419/09_2025/9bbf_44419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbf_44419/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bbf_44419/09_2025/9bbf_44419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbf_44419/09_2025/9bbf_44419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bbf_44419/09_2025/9bbf_44419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbf_44419/09_2025/9bbf_44419.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.08, per 1000 atoms: 0.26 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: 1.75 Conformation dependent library (CDL) restraints added in 858.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 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: 3.55 Time building geometry restraints manager: 2.36 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 902)) selection = (chain 'B' and (resid 218 through 490 or resid 495 through 902)) selection = (chain 'C' and (resid 218 through 490 or resid 495 through 902)) selection = (chain 'D' and (resid 218 through 490 or resid 495 through 902)) selection = (chain 'E' and (resid 218 through 490 or resid 495 through 902)) selection = chain 'F' selection = (chain 'G' and (resid 218 through 490 or resid 495 through 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- 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 : 9.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (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 ARG 0.013 0.001 ARG B 528 TYR 0.024 0.001 TYR Z 233 PHE 0.027 0.002 PHE F 580 TRP 0.045 0.002 TRP C 245 HIS 0.003 0.001 HIS Z 207 Details of bonding type rmsd covalent geometry : bond 0.00422 (20180) covalent geometry : angle 0.70515 (27299) hydrogen bonds : bond 0.15198 ( 636) hydrogen bonds : angle 7.25289 ( 1707) *********************** 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 : 0.923 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: 0.8535 (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: 0.1393 time to fit residues: 63.0888 Evaluate side-chains 267 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 216 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 428 GLN A 509 GLN B 432 ASN B 466 GLN C 265 ASN C 428 GLN C 432 ASN C 454 GLN C 463 ASN D 252 GLN D 428 GLN D 432 ASN D 602 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3919 r_free = 0.3919 target = 0.153006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121107 restraints weight = 31134.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125028 restraints weight = 16372.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127502 restraints weight = 11011.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129025 restraints weight = 8707.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129811 restraints weight = 7594.283| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20180 Z= 0.208 Angle : 0.594 6.945 27299 Z= 0.317 Chirality : 0.047 0.151 3090 Planarity : 0.005 0.086 3549 Dihedral : 5.177 52.466 2720 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.89 % Allowed : 28.87 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.16), residues: 2497 helix: -0.72 (0.22), residues: 530 sheet: -0.49 (0.21), residues: 613 loop : -1.14 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 76 TYR 0.025 0.001 TYR Z 233 PHE 0.027 0.002 PHE C 281 TRP 0.012 0.001 TRP C 245 HIS 0.004 0.001 HIS Z 207 Details of bonding type rmsd covalent geometry : bond 0.00483 (20180) covalent geometry : angle 0.59426 (27299) hydrogen bonds : bond 0.03487 ( 636) hydrogen bonds : angle 5.79962 ( 1707) *********************** 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 380 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 271 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7673 (mp10) cc_final: 0.7308 (mp10) REVERT: B 575 CYS cc_start: 0.8861 (m) cc_final: 0.8465 (m) REVERT: B 593 LYS cc_start: 0.8457 (ttpt) cc_final: 0.7654 (tttm) REVERT: C 506 TYR cc_start: 0.8368 (m-80) cc_final: 0.7628 (m-80) REVERT: C 537 ASP cc_start: 0.8048 (t0) cc_final: 0.7746 (t0) REVERT: D 469 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8200 (mtpt) REVERT: D 567 ASN cc_start: 0.7246 (t0) cc_final: 0.6975 (t0) REVERT: E 245 TRP cc_start: 0.8109 (t60) cc_final: 0.7807 (t60) REVERT: E 251 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: E 589 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8086 (tppt) REVERT: F 304 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6777 (tpp) REVERT: G 449 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8275 (tt) REVERT: G 458 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8603 (mtp85) REVERT: G 534 ASN cc_start: 0.6345 (t0) cc_final: 0.6117 (t0) outliers start: 109 outliers final: 62 residues processed: 351 average time/residue: 0.1339 time to fit residues: 74.8954 Evaluate side-chains 319 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain A residue 412 LEU 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 281 PHE 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 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 421 THR 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 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 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 546 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 251 GLU 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 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 535 LEU 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 453 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 603 VAL 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 G residue 531 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG 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 17 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 72 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 D 432 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN ** 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 = 0.3970 r_free = 0.3970 target = 0.158464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127003 restraints weight = 31258.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131077 restraints weight = 16102.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133629 restraints weight = 10613.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135193 restraints weight = 8273.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136152 restraints weight = 7156.485| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20180 Z= 0.103 Angle : 0.515 8.567 27299 Z= 0.273 Chirality : 0.044 0.147 3090 Planarity : 0.004 0.067 3549 Dihedral : 4.714 30.075 2713 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.36 % Allowed : 29.50 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2497 helix: -0.39 (0.22), residues: 531 sheet: -0.27 (0.21), residues: 621 loop : -1.07 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 528 TYR 0.014 0.001 TYR Z 233 PHE 0.014 0.001 PHE C 281 TRP 0.022 0.001 TRP B 245 HIS 0.003 0.001 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00238 (20180) covalent geometry : angle 0.51457 (27299) hydrogen bonds : bond 0.02826 ( 636) hydrogen bonds : angle 5.46539 ( 1707) *********************** 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: 97 poor density : 290 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7724 (mp10) cc_final: 0.7517 (mp10) REVERT: A 589 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8204 (mmtm) REVERT: B 575 CYS cc_start: 0.8860 (m) cc_final: 0.8402 (m) REVERT: C 506 TYR cc_start: 0.8274 (m-80) cc_final: 0.7550 (m-80) REVERT: D 567 ASN cc_start: 0.7234 (t0) cc_final: 0.6937 (t0) REVERT: E 245 TRP cc_start: 0.8009 (t60) cc_final: 0.7701 (t60) REVERT: E 281 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8239 (p90) REVERT: E 570 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7776 (Cg_endo) REVERT: E 589 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8106 (tppt) REVERT: F 304 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6790 (tpp) REVERT: F 429 ILE cc_start: 0.8604 (mt) cc_final: 0.8398 (mt) REVERT: G 458 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8494 (mtp85) outliers start: 97 outliers final: 55 residues processed: 364 average time/residue: 0.1331 time to fit residues: 77.3912 Evaluate side-chains 313 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 288 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL 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 605 LEU Chi-restraints excluded: chain C residue 288 GLU 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 447 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 489 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 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 219 LEU 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 453 ASP 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 569 ILE 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 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 243 VAL 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 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 Z residue 55 ARG Chi-restraints excluded: chain Z residue 208 LEU Chi-restraints excluded: chain Z residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 196 optimal weight: 9.9990 chunk 130 optimal weight: 0.0060 chunk 150 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 536 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126155 restraints weight = 31429.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130170 restraints weight = 16221.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132709 restraints weight = 10719.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134263 restraints weight = 8365.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135143 restraints weight = 7228.873| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20180 Z= 0.121 Angle : 0.524 7.731 27299 Z= 0.274 Chirality : 0.045 0.147 3090 Planarity : 0.004 0.060 3549 Dihedral : 4.621 31.117 2713 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.12 % Allowed : 28.51 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2497 helix: -0.22 (0.23), residues: 528 sheet: -0.23 (0.21), residues: 619 loop : -1.05 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 76 TYR 0.013 0.001 TYR F 506 PHE 0.015 0.001 PHE B 281 TRP 0.011 0.001 TRP B 245 HIS 0.003 0.001 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00281 (20180) covalent geometry : angle 0.52371 (27299) hydrogen bonds : bond 0.02709 ( 636) hydrogen bonds : angle 5.25336 ( 1707) *********************** 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 379 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 265 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7676 (mp10) cc_final: 0.7475 (mp10) REVERT: A 604 LYS cc_start: 0.8159 (tttm) cc_final: 0.7959 (tptm) REVERT: B 575 CYS cc_start: 0.8865 (m) cc_final: 0.8383 (m) REVERT: B 593 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7618 (tttm) REVERT: C 506 TYR cc_start: 0.8281 (m-80) cc_final: 0.7540 (m-80) REVERT: D 567 ASN cc_start: 0.7303 (t0) cc_final: 0.7006 (t0) REVERT: E 245 TRP cc_start: 0.8047 (t60) cc_final: 0.7709 (t60) REVERT: E 281 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8189 (p90) REVERT: E 570 PRO cc_start: 0.8021 (Cg_exo) cc_final: 0.7788 (Cg_endo) REVERT: F 429 ILE cc_start: 0.8627 (mt) cc_final: 0.8400 (mt) REVERT: G 449 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8158 (tt) REVERT: G 458 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8499 (mtp85) REVERT: G 536 GLN cc_start: 0.5751 (OUTLIER) cc_final: 0.5489 (mp10) REVERT: Z 145 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 114 outliers final: 68 residues processed: 351 average time/residue: 0.1375 time to fit residues: 76.5208 Evaluate side-chains 323 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 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 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 429 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 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 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 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 569 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP 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 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 480 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 490 LYS Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 536 GLN 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 208 LEU Chi-restraints excluded: chain Z residue 225 VAL Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 69 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 117 optimal weight: 0.1980 chunk 110 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 392 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122919 restraints weight = 31911.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126869 restraints weight = 16890.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129346 restraints weight = 11396.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130911 restraints weight = 9027.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131828 restraints weight = 7850.864| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20180 Z= 0.187 Angle : 0.570 7.547 27299 Z= 0.300 Chirality : 0.046 0.154 3090 Planarity : 0.004 0.060 3549 Dihedral : 4.740 32.312 2713 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.70 % Allowed : 28.11 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2497 helix: -0.33 (0.22), residues: 528 sheet: -0.41 (0.21), residues: 615 loop : -1.08 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 76 TYR 0.013 0.001 TYR F 404 PHE 0.022 0.002 PHE C 281 TRP 0.027 0.002 TRP B 245 HIS 0.002 0.001 HIS Z 207 Details of bonding type rmsd covalent geometry : bond 0.00434 (20180) covalent geometry : angle 0.57015 (27299) hydrogen bonds : bond 0.02998 ( 636) hydrogen bonds : angle 5.22843 ( 1707) *********************** 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 393 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 266 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: B 305 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: B 575 CYS cc_start: 0.8905 (m) cc_final: 0.8425 (m) REVERT: B 589 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8377 (mmtt) REVERT: B 593 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7620 (tttm) REVERT: C 506 TYR cc_start: 0.8321 (m-80) cc_final: 0.7612 (m-80) REVERT: D 567 ASN cc_start: 0.7401 (t0) cc_final: 0.7096 (t0) REVERT: E 251 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: F 304 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.6824 (tpp) REVERT: F 535 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.5019 (mm) REVERT: G 449 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8223 (tt) REVERT: G 458 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8573 (mtp85) REVERT: Z 62 ASP cc_start: 0.7974 (m-30) cc_final: 0.7635 (m-30) REVERT: Z 145 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: Z 177 GLN cc_start: 0.7591 (tp40) cc_final: 0.7373 (mm-40) outliers start: 127 outliers final: 91 residues processed: 365 average time/residue: 0.1379 time to fit residues: 80.6943 Evaluate side-chains 353 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 255 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 460 ILE Chi-restraints excluded: chain A residue 499 GLU 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 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 535 LEU 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 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 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 259 SER 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 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 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 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 507 ILE Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 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 478 LEU Chi-restraints excluded: chain F residue 480 THR 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 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 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 G residue 609 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.3939 r_free = 0.3939 target = 0.155924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123254 restraints weight = 31692.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127196 restraints weight = 16750.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129711 restraints weight = 11284.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131247 restraints weight = 8908.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132178 restraints weight = 7758.664| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20180 Z= 0.161 Angle : 0.554 9.221 27299 Z= 0.291 Chirality : 0.046 0.150 3090 Planarity : 0.004 0.059 3549 Dihedral : 4.715 31.390 2713 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.43 % Allowed : 28.74 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.17), residues: 2497 helix: -0.26 (0.22), residues: 526 sheet: -0.49 (0.21), residues: 622 loop : -1.06 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 76 TYR 0.011 0.001 TYR G 254 PHE 0.019 0.001 PHE C 281 TRP 0.014 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00376 (20180) covalent geometry : angle 0.55438 (27299) hydrogen bonds : bond 0.02871 ( 636) hydrogen bonds : angle 5.19987 ( 1707) *********************** 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 383 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 262 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 TRP cc_start: 0.8118 (t60) cc_final: 0.7842 (t60) REVERT: B 575 CYS cc_start: 0.8918 (m) cc_final: 0.8442 (m) REVERT: B 589 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8418 (mmtt) REVERT: B 593 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7635 (tttm) REVERT: C 304 MET cc_start: 0.9051 (tpp) cc_final: 0.8841 (ttm) REVERT: C 432 ASN cc_start: 0.7661 (p0) cc_final: 0.7416 (p0) REVERT: C 506 TYR cc_start: 0.8350 (m-80) cc_final: 0.7641 (m-80) REVERT: C 537 ASP cc_start: 0.8087 (t0) cc_final: 0.7832 (t0) REVERT: D 567 ASN cc_start: 0.7443 (t0) cc_final: 0.7106 (t0) REVERT: F 304 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.6806 (tpp) REVERT: F 535 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.5021 (mm) REVERT: G 449 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8235 (tt) REVERT: G 458 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8568 (mtp85) REVERT: Z 62 ASP cc_start: 0.7994 (m-30) cc_final: 0.7680 (m-30) REVERT: Z 145 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7366 (tt0) outliers start: 121 outliers final: 92 residues processed: 355 average time/residue: 0.1367 time to fit residues: 78.1447 Evaluate side-chains 347 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 251 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 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 429 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 571 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 259 SER 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 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 E residue 219 LEU 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 453 ASP 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 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 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 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 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 225 VAL Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 151 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 428 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122771 restraints weight = 31794.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126715 restraints weight = 16789.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129220 restraints weight = 11323.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130745 restraints weight = 8953.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131579 restraints weight = 7809.900| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20180 Z= 0.164 Angle : 0.560 10.249 27299 Z= 0.293 Chirality : 0.046 0.148 3090 Planarity : 0.004 0.058 3549 Dihedral : 4.726 32.210 2713 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.97 % Allowed : 28.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.17), residues: 2497 helix: -0.31 (0.22), residues: 528 sheet: -0.52 (0.22), residues: 592 loop : -1.04 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 76 TYR 0.017 0.001 TYR G 254 PHE 0.020 0.001 PHE C 281 TRP 0.011 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 207 Details of bonding type rmsd covalent geometry : bond 0.00385 (20180) covalent geometry : angle 0.55964 (27299) hydrogen bonds : bond 0.02862 ( 636) hydrogen bonds : angle 5.16925 ( 1707) *********************** 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 397 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 264 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLN cc_start: 0.7789 (mt0) cc_final: 0.7431 (mp10) REVERT: A 604 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8063 (tptm) REVERT: B 245 TRP cc_start: 0.8145 (t60) cc_final: 0.7909 (t60) REVERT: B 305 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: B 575 CYS cc_start: 0.8898 (m) cc_final: 0.8432 (m) REVERT: B 589 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8408 (mmtt) REVERT: C 506 TYR cc_start: 0.8376 (m-80) cc_final: 0.7673 (m-80) REVERT: C 537 ASP cc_start: 0.8145 (t0) cc_final: 0.7879 (t0) REVERT: C 568 ASP cc_start: 0.8240 (m-30) cc_final: 0.7898 (m-30) REVERT: D 567 ASN cc_start: 0.7474 (t0) cc_final: 0.7128 (t0) REVERT: E 251 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: F 304 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.6795 (tpp) REVERT: F 535 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.5029 (mm) REVERT: G 449 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8223 (tt) REVERT: G 458 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8582 (mtp85) REVERT: Z 62 ASP cc_start: 0.8014 (m-30) cc_final: 0.7688 (m-30) REVERT: Z 71 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8277 (mmt-90) REVERT: Z 145 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7332 (tt0) outliers start: 133 outliers final: 96 residues processed: 368 average time/residue: 0.1350 time to fit residues: 79.9368 Evaluate side-chains 359 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 256 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 258 VAL 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 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 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 604 LYS 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 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 260 ASN 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 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 259 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE 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 E residue 251 GLU 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 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 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 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 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 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 Chi-restraints excluded: chain Z residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 174 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** 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 = 0.3984 r_free = 0.3984 target = 0.159847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127350 restraints weight = 31639.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131508 restraints weight = 16551.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134119 restraints weight = 11015.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135716 restraints weight = 8637.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136621 restraints weight = 7485.050| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20180 Z= 0.105 Angle : 0.530 9.557 27299 Z= 0.277 Chirality : 0.045 0.165 3090 Planarity : 0.004 0.055 3549 Dihedral : 4.576 34.942 2713 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.86 % Allowed : 30.85 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.17), residues: 2497 helix: -0.09 (0.23), residues: 527 sheet: -0.31 (0.23), residues: 561 loop : -0.97 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 528 TYR 0.017 0.001 TYR G 254 PHE 0.010 0.001 PHE E 281 TRP 0.043 0.002 TRP C 245 HIS 0.002 0.000 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00243 (20180) covalent geometry : angle 0.53048 (27299) hydrogen bonds : bond 0.02505 ( 636) hydrogen bonds : angle 5.00635 ( 1707) *********************** 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 373 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 287 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8602 (tp30) cc_final: 0.8389 (tp30) REVERT: B 245 TRP cc_start: 0.8135 (t60) cc_final: 0.7892 (t60) REVERT: B 314 HIS cc_start: 0.5385 (OUTLIER) cc_final: 0.4525 (m-70) REVERT: B 575 CYS cc_start: 0.8879 (m) cc_final: 0.8419 (m) REVERT: C 506 TYR cc_start: 0.8320 (m-80) cc_final: 0.7538 (m-80) REVERT: C 537 ASP cc_start: 0.8168 (t0) cc_final: 0.7899 (t0) REVERT: D 265 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8151 (m110) REVERT: D 507 ILE cc_start: 0.8382 (pt) cc_final: 0.7865 (pt) REVERT: D 511 ASP cc_start: 0.8723 (m-30) cc_final: 0.8420 (m-30) REVERT: D 567 ASN cc_start: 0.7403 (t0) cc_final: 0.7064 (t0) REVERT: F 304 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.6786 (tpp) REVERT: F 535 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4991 (mm) REVERT: G 449 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8180 (tt) REVERT: G 458 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8516 (mtp85) REVERT: Z 62 ASP cc_start: 0.7934 (m-30) cc_final: 0.7393 (m-30) REVERT: Z 145 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7284 (tt0) outliers start: 86 outliers final: 62 residues processed: 356 average time/residue: 0.1372 time to fit residues: 78.4030 Evaluate side-chains 328 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 258 VAL Chi-restraints excluded: chain A residue 389 ILE 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 241 ILE Chi-restraints excluded: chain B residue 314 HIS 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 558 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR 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 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 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 287 THR 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 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 309 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 428 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 172 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 229 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** 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 = 0.3958 r_free = 0.3958 target = 0.157596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125223 restraints weight = 31543.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129188 restraints weight = 16701.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131729 restraints weight = 11222.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133302 restraints weight = 8848.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134163 restraints weight = 7695.491| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20180 Z= 0.135 Angle : 0.559 9.443 27299 Z= 0.293 Chirality : 0.045 0.179 3090 Planarity : 0.004 0.085 3549 Dihedral : 4.553 34.690 2711 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.95 % Allowed : 31.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2497 helix: -0.12 (0.23), residues: 526 sheet: -0.31 (0.22), residues: 581 loop : -0.94 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 76 TYR 0.016 0.001 TYR G 254 PHE 0.017 0.001 PHE B 281 TRP 0.031 0.001 TRP C 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00317 (20180) covalent geometry : angle 0.55882 (27299) hydrogen bonds : bond 0.02678 ( 636) hydrogen bonds : angle 4.96005 ( 1707) *********************** 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 351 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 263 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 CYS cc_start: 0.8893 (m) cc_final: 0.8419 (m) REVERT: B 593 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7632 (tttm) REVERT: C 506 TYR cc_start: 0.8290 (m-80) cc_final: 0.7534 (m-80) REVERT: C 537 ASP cc_start: 0.8208 (t0) cc_final: 0.7928 (t0) REVERT: C 568 ASP cc_start: 0.8189 (m-30) cc_final: 0.7855 (m-30) REVERT: D 265 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8266 (m110) REVERT: D 567 ASN cc_start: 0.7390 (t0) cc_final: 0.7034 (t0) REVERT: E 589 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8182 (tppt) REVERT: F 288 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: F 304 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6761 (tpp) REVERT: F 429 ILE cc_start: 0.8647 (mt) cc_final: 0.8292 (pt) REVERT: F 452 MET cc_start: 0.7498 (ptp) cc_final: 0.7220 (ptt) REVERT: F 535 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4966 (mm) REVERT: G 449 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8195 (tt) REVERT: G 458 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8542 (mtp85) REVERT: Z 145 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7373 (tt0) outliers start: 88 outliers final: 75 residues processed: 330 average time/residue: 0.1376 time to fit residues: 72.7313 Evaluate side-chains 338 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 257 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 258 VAL 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 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 241 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 437 ASP Chi-restraints excluded: chain B residue 460 ILE 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 281 PHE Chi-restraints excluded: chain C residue 287 THR 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 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 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 287 THR 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 467 LEU 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 603 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP 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 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 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 89 LEU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 162 ASN Chi-restraints excluded: chain Z residue 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126842 restraints weight = 30815.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130598 restraints weight = 16613.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133028 restraints weight = 11278.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134524 restraints weight = 8917.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135358 restraints weight = 7744.675| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20180 Z= 0.106 Angle : 0.554 9.643 27299 Z= 0.288 Chirality : 0.045 0.163 3090 Planarity : 0.004 0.053 3549 Dihedral : 4.496 35.334 2711 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.82 % Allowed : 31.48 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.17), residues: 2497 helix: -0.03 (0.23), residues: 526 sheet: -0.20 (0.22), residues: 580 loop : -0.88 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 528 TYR 0.017 0.001 TYR G 254 PHE 0.010 0.001 PHE B 281 TRP 0.044 0.002 TRP B 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00248 (20180) covalent geometry : angle 0.55408 (27299) hydrogen bonds : bond 0.02501 ( 636) hydrogen bonds : angle 4.89766 ( 1707) ********************** 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 353 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 268 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 575 CYS cc_start: 0.8855 (m) cc_final: 0.8372 (m) REVERT: B 593 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7619 (tttm) REVERT: C 506 TYR cc_start: 0.8277 (m-80) cc_final: 0.7503 (m-80) REVERT: C 537 ASP cc_start: 0.8151 (t0) cc_final: 0.7890 (t0) REVERT: C 549 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7736 (tt0) REVERT: C 568 ASP cc_start: 0.8138 (m-30) cc_final: 0.7808 (m-30) REVERT: D 265 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (m110) REVERT: D 432 ASN cc_start: 0.7969 (m-40) cc_final: 0.7621 (m-40) REVERT: D 567 ASN cc_start: 0.7355 (t0) cc_final: 0.6995 (t0) REVERT: E 589 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8180 (tppt) REVERT: F 288 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: F 304 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6766 (tpp) REVERT: F 429 ILE cc_start: 0.8638 (mt) cc_final: 0.8289 (pt) REVERT: F 452 MET cc_start: 0.7493 (ptp) cc_final: 0.7251 (ptt) REVERT: F 535 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4956 (mm) REVERT: G 449 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8169 (tt) REVERT: G 458 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8516 (mtp85) REVERT: Z 145 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7248 (tt0) outliers start: 85 outliers final: 71 residues processed: 333 average time/residue: 0.1413 time to fit residues: 74.9182 Evaluate side-chains 336 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 258 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 241 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 460 ILE 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 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 455 PHE 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 259 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 287 THR 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 467 LEU 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 603 VAL Chi-restraints excluded: chain E residue 309 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 288 GLU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 404 TYR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP 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 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 89 LEU 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 25 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 224 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127372 restraints weight = 31321.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131409 restraints weight = 16262.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133983 restraints weight = 10800.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135582 restraints weight = 8429.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136550 restraints weight = 7279.383| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20180 Z= 0.109 Angle : 0.555 10.366 27299 Z= 0.287 Chirality : 0.045 0.160 3090 Planarity : 0.004 0.056 3549 Dihedral : 4.457 35.668 2711 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.86 % Allowed : 31.48 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2497 helix: 0.02 (0.23), residues: 526 sheet: -0.18 (0.22), residues: 580 loop : -0.85 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 528 TYR 0.016 0.001 TYR G 254 PHE 0.012 0.001 PHE B 281 TRP 0.034 0.002 TRP B 245 HIS 0.002 0.000 HIS Z 249 Details of bonding type rmsd covalent geometry : bond 0.00258 (20180) covalent geometry : angle 0.55494 (27299) hydrogen bonds : bond 0.02513 ( 636) hydrogen bonds : angle 4.83022 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3706.10 seconds wall clock time: 65 minutes 9.99 seconds (3909.99 seconds total)