Starting phenix.real_space_refine on Sat Jul 4 08:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbf_44419/07_2026/9bbf_44419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbf_44419/07_2026/9bbf_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_44419/07_2026/9bbf_44419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbf_44419/07_2026/9bbf_44419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bbf_44419/07_2026/9bbf_44419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbf_44419/07_2026/9bbf_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 4.60, per 1000 atoms: 0.23 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: 1.76 Conformation dependent library (CDL) restraints added in 852.6 milliseconds 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: 0.45 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: 3.52 Time building geometry restraints manager: 2.35 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 18.820 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 are 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/Z covalent geometry : bond 0.00422 / 0.18 (20180) covalent geometry : angle 0.70515 / 0.38 (27299) hydrogen bonds : bond 0.15198 / 9.79 ( 636) hydrogen bonds : angle 7.25289 / 5.06 ( 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 : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.7471 (pt0) cc_final: 0.7248 (pt0) REVERT: B 575 CYS cc_start: 0.8785 (m) cc_final: 0.8449 (m) REVERT: C 589 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8513 (mtpt) REVERT: E 570 PRO cc_start: 0.7996 (Cg_exo) cc_final: 0.7718 (Cg_endo) REVERT: E 589 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8013 (tppt) REVERT: G 458 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8537 (mtp85) REVERT: G 534 ASN cc_start: 0.6389 (t0) cc_final: 0.6173 (t0) outliers start: 8 outliers final: 5 residues processed: 283 average time/residue: 0.1316 time to fit residues: 59.8461 Evaluate side-chains 266 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 261 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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... 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 223 ASN ** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122939 restraints weight = 31444.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126815 restraints weight = 16429.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129338 restraints weight = 11023.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130829 restraints weight = 8693.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131729 restraints weight = 7592.544| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20180 Z= 0.209 Angle : 0.598 6.738 27299 Z= 0.320 Chirality : 0.047 0.151 3090 Planarity : 0.005 0.086 3549 Dihedral : 5.189 52.275 2720 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.12 % Allowed : 28.74 % 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 are not related in a simple way. whole: -1.41 (0.16), residues: 2497 helix: -0.78 (0.21), residues: 531 sheet: -0.49 (0.21), residues: 623 loop : -1.17 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 528 TYR 0.026 0.001 TYR Z 233 PHE 0.028 0.002 PHE C 281 TRP 0.013 0.002 TRP C 245 HIS 0.004 0.001 HIS Z 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (20180) covalent geometry : angle 0.59792 / 0.32 (27299) hydrogen bonds : bond 0.03521 / 2.23 ( 636) hydrogen bonds : angle 5.82196 / 4.06 ( 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 382 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 268 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7680 (mp10) cc_final: 0.7235 (mp10) REVERT: B 575 CYS cc_start: 0.8847 (m) cc_final: 0.8442 (m) REVERT: B 593 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7644 (tttm) REVERT: C 506 TYR cc_start: 0.8360 (m-80) cc_final: 0.7632 (m-80) REVERT: D 469 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8205 (mtpt) REVERT: D 567 ASN cc_start: 0.7231 (t0) cc_final: 0.6962 (t0) REVERT: E 245 TRP cc_start: 0.8060 (t60) cc_final: 0.7778 (t60) REVERT: E 251 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: E 589 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8096 (tppt) REVERT: F 304 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.6761 (tpp) REVERT: G 449 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8282 (tt) REVERT: G 458 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8607 (mtp85) REVERT: G 534 ASN cc_start: 0.6362 (t0) cc_final: 0.6142 (t0) outliers start: 114 outliers final: 66 residues processed: 351 average time/residue: 0.1361 time to fit residues: 76.3292 Evaluate side-chains 320 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 250 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 304 MET 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 225 ASN 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 231 GLU 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 Chi-restraints excluded: chain Z residue 257 VAL 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: 0.9990 chunk 68 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124404 restraints weight = 31245.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128404 restraints weight = 16167.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130929 restraints weight = 10747.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132471 restraints weight = 8422.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133403 restraints weight = 7316.979| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20180 Z= 0.140 Angle : 0.538 8.656 27299 Z= 0.286 Chirality : 0.045 0.150 3090 Planarity : 0.005 0.070 3549 Dihedral : 4.828 30.655 2713 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.98 % Allowed : 29.19 % 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 are not related in a simple way. whole: -1.24 (0.17), residues: 2497 helix: -0.51 (0.22), residues: 531 sheet: -0.41 (0.21), residues: 626 loop : -1.11 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 528 TYR 0.015 0.001 TYR Z 233 PHE 0.019 0.001 PHE C 281 TRP 0.022 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (20180) covalent geometry : angle 0.53762 / 0.29 (27299) hydrogen bonds : bond 0.03024 / 1.93 ( 636) hydrogen bonds : angle 5.52900 / 3.85 ( 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 390 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 279 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7658 (mp10) cc_final: 0.7217 (mp10) REVERT: A 589 LYS cc_start: 0.8404 (mmtm) cc_final: 0.8174 (mmtm) REVERT: B 575 CYS cc_start: 0.8883 (m) cc_final: 0.8437 (m) REVERT: B 593 LYS cc_start: 0.8438 (ttpt) cc_final: 0.7617 (tttm) REVERT: C 506 TYR cc_start: 0.8318 (m-80) cc_final: 0.7668 (m-80) REVERT: D 469 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8212 (mtpt) REVERT: D 567 ASN cc_start: 0.7299 (t0) cc_final: 0.6986 (t0) REVERT: E 245 TRP cc_start: 0.8065 (t60) cc_final: 0.7711 (t60) REVERT: E 281 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (p90) REVERT: E 570 PRO cc_start: 0.8061 (Cg_exo) cc_final: 0.7834 (Cg_endo) REVERT: F 304 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.6777 (tpp) REVERT: G 458 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8549 (mtp85) REVERT: G 536 GLN cc_start: 0.5901 (OUTLIER) cc_final: 0.5678 (mp10) REVERT: Z 145 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7247 (tt0) outliers start: 111 outliers final: 69 residues processed: 363 average time/residue: 0.1252 time to fit residues: 72.8768 Evaluate side-chains 328 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 429 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 260 ASN 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 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 281 PHE 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 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 D residue 225 ASN 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 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 542 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 260 ASN Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 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 304 MET 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 243 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 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 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 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 196 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 150 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 ASN A 428 GLN B 314 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126611 restraints weight = 31082.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130469 restraints weight = 15946.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132964 restraints weight = 10544.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134487 restraints weight = 8229.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135387 restraints weight = 7113.496| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20180 Z= 0.145 Angle : 0.538 7.948 27299 Z= 0.282 Chirality : 0.045 0.154 3090 Planarity : 0.004 0.063 3549 Dihedral : 4.760 31.394 2713 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.93 % Allowed : 28.15 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2497 helix: -0.37 (0.22), residues: 528 sheet: -0.39 (0.21), residues: 620 loop : -1.09 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 76 TYR 0.014 0.001 TYR Z 233 PHE 0.021 0.001 PHE C 281 TRP 0.011 0.001 TRP B 245 HIS 0.003 0.001 HIS Z 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (20180) covalent geometry : angle 0.53797 / 0.28 (27299) hydrogen bonds : bond 0.02884 / 1.83 ( 636) hydrogen bonds : angle 5.29254 / 3.68 ( 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 399 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 267 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7684 (mp10) cc_final: 0.7459 (mp10) REVERT: A 499 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: A 589 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8148 (mmtm) REVERT: B 245 TRP cc_start: 0.8090 (t60) cc_final: 0.7829 (t60) REVERT: B 575 CYS cc_start: 0.8883 (m) cc_final: 0.8421 (m) REVERT: B 593 LYS cc_start: 0.8465 (ttpt) cc_final: 0.7635 (tttm) REVERT: C 506 TYR cc_start: 0.8336 (m-80) cc_final: 0.7523 (m-80) REVERT: D 469 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8152 (mtpt) REVERT: D 567 ASN cc_start: 0.7371 (t0) cc_final: 0.7087 (t0) REVERT: E 281 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8324 (p90) REVERT: E 589 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8236 (tppt) REVERT: F 304 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.6809 (tpp) REVERT: G 449 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8209 (tt) REVERT: G 458 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8562 (mtp85) REVERT: Z 76 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7648 (ttp80) REVERT: Z 145 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: Z 177 GLN cc_start: 0.7561 (tp40) cc_final: 0.7324 (mm-40) outliers start: 132 outliers final: 88 residues processed: 372 average time/residue: 0.1265 time to fit residues: 75.7768 Evaluate side-chains 350 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 256 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE 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 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 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 260 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 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 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 542 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 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 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 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: 2.9990 chunk 195 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN B 314 HIS ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN E 428 GLN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 GLN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 GLN G 534 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119232 restraints weight = 32000.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123038 restraints weight = 17011.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125468 restraints weight = 11527.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126961 restraints weight = 9144.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127837 restraints weight = 7991.666| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.006 0.048 20180 Z= 0.259 Angle : 0.630 8.003 27299 Z= 0.333 Chirality : 0.049 0.157 3090 Planarity : 0.005 0.064 3549 Dihedral : 5.015 36.352 2713 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 6.60 % Allowed : 28.06 % Favored : 65.33 % 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 are not related in a simple way. whole: -1.46 (0.16), residues: 2497 helix: -0.56 (0.22), residues: 528 sheet: -0.68 (0.22), residues: 602 loop : -1.23 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 528 TYR 0.017 0.002 TYR G 254 PHE 0.032 0.002 PHE C 281 TRP 0.010 0.002 TRP D 245 HIS 0.003 0.001 HIS Z 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 (20180) covalent geometry : angle 0.63010 / 0.33 (27299) hydrogen bonds : bond 0.03402 / 2.16 ( 636) hydrogen bonds : angle 5.45283 / 3.80 ( 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 415 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 268 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7754 (mp10) cc_final: 0.7268 (mp10) REVERT: B 305 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 561 ASP cc_start: 0.7369 (t0) cc_final: 0.7146 (t0) REVERT: B 575 CYS cc_start: 0.8889 (m) cc_final: 0.8419 (m) REVERT: B 589 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8411 (mmtt) REVERT: C 506 TYR cc_start: 0.8415 (m-80) cc_final: 0.7820 (m-80) REVERT: C 568 ASP cc_start: 0.8228 (m-30) cc_final: 0.7908 (m-30) REVERT: D 567 ASN cc_start: 0.7499 (t0) cc_final: 0.7185 (t0) REVERT: E 251 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: E 589 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8334 (tptp) REVERT: F 304 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6763 (tpp) REVERT: G 449 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8334 (tt) REVERT: G 458 ARG cc_start: 0.8868 (mmm-85) cc_final: 0.8626 (mtp85) REVERT: Z 62 ASP cc_start: 0.8051 (m-30) cc_final: 0.7682 (m-30) REVERT: Z 145 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: Z 177 GLN cc_start: 0.7635 (tp40) cc_final: 0.7402 (mm-40) outliers start: 147 outliers final: 106 residues processed: 385 average time/residue: 0.1266 time to fit residues: 77.7364 Evaluate side-chains 359 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 248 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 496 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 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 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 546 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 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 455 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain 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 175 THR Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 257 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 117 optimal weight: 0.0020 chunk 86 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124517 restraints weight = 31465.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128511 restraints weight = 16409.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131003 restraints weight = 10970.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132588 restraints weight = 8672.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133520 restraints weight = 7535.231| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20180 Z= 0.118 Angle : 0.547 9.803 27299 Z= 0.284 Chirality : 0.045 0.158 3090 Planarity : 0.004 0.058 3549 Dihedral : 4.767 32.548 2713 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.98 % Allowed : 29.64 % Favored : 65.38 % 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 are not related in a simple way. whole: -1.19 (0.17), residues: 2497 helix: -0.30 (0.23), residues: 528 sheet: -0.51 (0.22), residues: 615 loop : -1.08 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 76 TYR 0.020 0.001 TYR G 254 PHE 0.017 0.001 PHE C 281 TRP 0.034 0.002 TRP C 245 HIS 0.003 0.001 HIS Z 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20180) covalent geometry : angle 0.54673 / 0.28 (27299) hydrogen bonds : bond 0.02726 / 1.74 ( 636) hydrogen bonds : angle 5.21364 / 3.62 ( 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 395 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 284 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7712 (mp10) cc_final: 0.7271 (mp10) REVERT: A 403 MET cc_start: 0.8686 (ttm) cc_final: 0.8463 (ttt) REVERT: B 575 CYS cc_start: 0.8902 (m) cc_final: 0.8426 (m) REVERT: B 589 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8380 (mmtt) REVERT: C 432 ASN cc_start: 0.7527 (p0) cc_final: 0.7287 (p0) REVERT: C 506 TYR cc_start: 0.8324 (m-80) cc_final: 0.7546 (m-80) REVERT: C 568 ASP cc_start: 0.8172 (m-30) cc_final: 0.7854 (m-30) REVERT: D 469 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8098 (mtpt) REVERT: D 567 ASN cc_start: 0.7466 (t0) cc_final: 0.7144 (t0) REVERT: E 251 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: E 281 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8319 (p90) REVERT: E 589 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8272 (tptp) REVERT: F 304 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6825 (tpp) REVERT: F 535 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.5090 (mm) REVERT: G 449 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8203 (tt) REVERT: G 458 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8576 (mtp85) REVERT: Z 62 ASP cc_start: 0.7991 (m-30) cc_final: 0.7666 (m-30) REVERT: Z 71 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7921 (mmt-90) REVERT: Z 145 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: Z 177 GLN cc_start: 0.7426 (tp40) cc_final: 0.7207 (mm-40) outliers start: 111 outliers final: 82 residues processed: 373 average time/residue: 0.1323 time to fit residues: 79.1244 Evaluate side-chains 348 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 259 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 260 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 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 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 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 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain 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 288 GLU 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 535 LEU Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 455 PHE Chi-restraints excluded: chain F residue 478 LEU 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 243 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 396 TYR 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 484 SER 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 225 VAL 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: 5.9990 chunk 230 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3916 r_free = 0.3916 target = 0.151767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120720 restraints weight = 31616.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124332 restraints weight = 17220.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126585 restraints weight = 11852.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127934 restraints weight = 9523.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128761 restraints weight = 8401.497| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20180 Z= 0.301 Angle : 0.673 9.750 27299 Z= 0.355 Chirality : 0.050 0.175 3090 Planarity : 0.005 0.062 3549 Dihedral : 5.129 38.389 2713 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.65 % Allowed : 28.33 % Favored : 65.02 % 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 are not related in a simple way. whole: -1.57 (0.16), residues: 2497 helix: -0.57 (0.22), residues: 525 sheet: -0.89 (0.21), residues: 597 loop : -1.27 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 76 TYR 0.021 0.002 TYR G 254 PHE 0.035 0.002 PHE C 281 TRP 0.021 0.002 TRP C 245 HIS 0.004 0.001 HIS Z 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.30 (20180) covalent geometry : angle 0.67310 / 0.36 (27299) hydrogen bonds : bond 0.03494 / 2.20 ( 636) hydrogen bonds : angle 5.45157 / 3.81 ( 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 410 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 262 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7781 (mp10) cc_final: 0.7305 (mp10) REVERT: B 305 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 561 ASP cc_start: 0.7395 (t0) cc_final: 0.7178 (t0) REVERT: B 575 CYS cc_start: 0.8891 (m) cc_final: 0.8396 (m) REVERT: B 589 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8432 (mmtt) REVERT: C 506 TYR cc_start: 0.8436 (m-80) cc_final: 0.7850 (m-80) REVERT: C 568 ASP cc_start: 0.8253 (m-30) cc_final: 0.7905 (m-30) REVERT: D 469 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8115 (mtpt) REVERT: D 567 ASN cc_start: 0.7587 (t0) cc_final: 0.7270 (t0) REVERT: E 589 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8352 (tptp) REVERT: F 304 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.6707 (tpp) REVERT: F 428 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: F 429 ILE cc_start: 0.8856 (mt) cc_final: 0.8418 (pt) REVERT: F 535 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5132 (mm) REVERT: G 449 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8343 (tt) REVERT: G 458 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8626 (mtp85) REVERT: Z 62 ASP cc_start: 0.8114 (m-30) cc_final: 0.7722 (m-30) REVERT: Z 145 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7409 (tt0) outliers start: 148 outliers final: 110 residues processed: 382 average time/residue: 0.1275 time to fit residues: 78.3517 Evaluate side-chains 368 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 251 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 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 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 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 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 603 VAL Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 412 LEU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 455 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain Z residue 55 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 257 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 174 optimal weight: 7.9990 chunk 180 optimal weight: 0.1980 chunk 151 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 203 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124858 restraints weight = 31696.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128816 restraints weight = 16560.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131339 restraints weight = 11084.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132901 restraints weight = 8734.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133848 restraints weight = 7587.263| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1906 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= 0.110 Angle : 0.554 9.273 27299 Z= 0.289 Chirality : 0.045 0.164 3090 Planarity : 0.004 0.056 3549 Dihedral : 4.812 33.348 2713 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.18 % Allowed : 30.76 % Favored : 65.07 % 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 are not related in a simple way. whole: -1.17 (0.17), residues: 2497 helix: -0.26 (0.23), residues: 528 sheet: -0.56 (0.21), residues: 610 loop : -1.05 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 528 TYR 0.021 0.001 TYR G 254 PHE 0.013 0.001 PHE C 281 TRP 0.020 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20180) covalent geometry : angle 0.55399 / 0.29 (27299) hydrogen bonds : bond 0.02686 / 1.70 ( 636) hydrogen bonds : angle 5.18121 / 3.59 ( 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 377 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 284 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7724 (mp10) cc_final: 0.7280 (mp10) REVERT: B 464 TYR cc_start: 0.7848 (t80) cc_final: 0.7353 (t80) REVERT: B 561 ASP cc_start: 0.7392 (t0) cc_final: 0.7169 (t0) REVERT: B 575 CYS cc_start: 0.8893 (m) cc_final: 0.8399 (m) REVERT: C 506 TYR cc_start: 0.8353 (m-80) cc_final: 0.7711 (m-80) REVERT: C 568 ASP cc_start: 0.8185 (m-30) cc_final: 0.7848 (m-30) REVERT: D 511 ASP cc_start: 0.8710 (m-30) cc_final: 0.8389 (m-30) REVERT: D 567 ASN cc_start: 0.7538 (t0) cc_final: 0.7214 (t0) REVERT: E 281 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8188 (p90) REVERT: E 589 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8297 (tptp) REVERT: F 304 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.6788 (tpp) REVERT: F 535 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.5041 (mm) REVERT: G 449 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8263 (tt) REVERT: G 458 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8572 (mtp85) REVERT: Z 62 ASP cc_start: 0.8008 (m-30) cc_final: 0.7683 (m-30) REVERT: Z 145 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: Z 177 GLN cc_start: 0.7496 (tp40) cc_final: 0.7278 (mm-40) outliers start: 93 outliers final: 76 residues processed: 354 average time/residue: 0.1259 time to fit residues: 71.3775 Evaluate side-chains 350 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 260 ASN 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 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 507 ILE 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 393 VAL 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 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 404 TYR 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 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 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 272 THR 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 58 ASP Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 172 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 52 optimal weight: 0.0010 chunk 238 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123758 restraints weight = 31525.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127701 restraints weight = 16591.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130198 restraints weight = 11161.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131697 restraints weight = 8817.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132603 restraints weight = 7708.604| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20180 Z= 0.134 Angle : 0.562 7.904 27299 Z= 0.293 Chirality : 0.046 0.160 3090 Planarity : 0.004 0.055 3549 Dihedral : 4.720 32.189 2713 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.49 % Allowed : 30.71 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2497 helix: -0.20 (0.23), residues: 528 sheet: -0.55 (0.21), residues: 616 loop : -1.03 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 76 TYR 0.012 0.001 TYR G 254 PHE 0.017 0.001 PHE B 281 TRP 0.020 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (20180) covalent geometry : angle 0.56250 / 0.29 (27299) hydrogen bonds : bond 0.02731 / 1.73 ( 636) hydrogen bonds : angle 5.07984 / 3.52 ( 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 369 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 269 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 575 CYS cc_start: 0.8894 (m) cc_final: 0.8399 (m) REVERT: C 506 TYR cc_start: 0.8359 (m-80) cc_final: 0.7729 (m-80) REVERT: C 568 ASP cc_start: 0.8212 (m-30) cc_final: 0.7863 (m-30) REVERT: D 469 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: D 567 ASN cc_start: 0.7518 (t0) cc_final: 0.7166 (t0) REVERT: E 281 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8151 (p90) REVERT: E 589 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8302 (tptp) REVERT: F 288 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: F 535 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.5029 (mm) REVERT: G 449 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8209 (tt) REVERT: G 458 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.8599 (mtp85) REVERT: Z 62 ASP cc_start: 0.8017 (m-30) cc_final: 0.7692 (m-30) REVERT: Z 145 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: Z 177 GLN cc_start: 0.7510 (tp40) cc_final: 0.7289 (mm-40) outliers start: 100 outliers final: 82 residues processed: 346 average time/residue: 0.1269 time to fit residues: 70.2169 Evaluate side-chains 355 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 266 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 260 ASN 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 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 404 TYR 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 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 478 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 272 THR 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 58 ASP Chi-restraints excluded: chain Z residue 145 GLU 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 74 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 141 optimal weight: 0.0060 chunk 186 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.154222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122603 restraints weight = 31503.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126415 restraints weight = 16498.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128866 restraints weight = 11056.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130337 restraints weight = 8706.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131276 restraints weight = 7580.746| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20180 Z= 0.156 Angle : 0.581 8.741 27299 Z= 0.305 Chirality : 0.046 0.149 3090 Planarity : 0.004 0.055 3549 Dihedral : 4.737 31.762 2713 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.45 % Allowed : 30.62 % Favored : 64.93 % 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 are not related in a simple way. whole: -1.16 (0.17), residues: 2497 helix: -0.22 (0.23), residues: 528 sheet: -0.60 (0.21), residues: 621 loop : -1.03 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 76 TYR 0.012 0.001 TYR C 297 PHE 0.019 0.001 PHE B 281 TRP 0.022 0.002 TRP B 245 HIS 0.003 0.001 HIS Z 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20180) covalent geometry : angle 0.58083 / 0.30 (27299) hydrogen bonds : bond 0.02805 / 1.77 ( 636) hydrogen bonds : angle 5.10767 / 3.54 ( 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 372 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 273 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8472 (mm) REVERT: B 464 TYR cc_start: 0.7911 (t80) cc_final: 0.7502 (t80) REVERT: B 575 CYS cc_start: 0.8900 (m) cc_final: 0.8393 (m) REVERT: C 304 MET cc_start: 0.9034 (tpp) cc_final: 0.8818 (ttm) REVERT: C 506 TYR cc_start: 0.8407 (m-80) cc_final: 0.7849 (m-80) REVERT: C 568 ASP cc_start: 0.8211 (m-30) cc_final: 0.7867 (m-30) REVERT: D 469 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8088 (mtpt) REVERT: D 511 ASP cc_start: 0.8739 (m-30) cc_final: 0.8426 (m-30) REVERT: D 567 ASN cc_start: 0.7514 (t0) cc_final: 0.7162 (t0) REVERT: E 281 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8212 (p90) REVERT: E 589 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8328 (tptp) REVERT: F 288 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: F 535 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.5061 (mm) REVERT: G 449 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8213 (tt) REVERT: G 458 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.8590 (mtp85) REVERT: Z 62 ASP cc_start: 0.8052 (m-30) cc_final: 0.7731 (m-30) REVERT: Z 145 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: Z 177 GLN cc_start: 0.7501 (tp40) cc_final: 0.7290 (mm-40) outliers start: 99 outliers final: 87 residues processed: 351 average time/residue: 0.1214 time to fit residues: 68.2490 Evaluate side-chains 356 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 262 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 308 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 466 GLN Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 260 ASN 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 455 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 483 VAL 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 281 PHE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 404 TYR 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 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 478 LEU Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 272 THR 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 58 ASP 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: 0.2980 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 131 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124534 restraints weight = 31273.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128488 restraints weight = 16305.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131005 restraints weight = 10909.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132522 restraints weight = 8584.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133465 restraints weight = 7465.791| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20180 Z= 0.120 Angle : 0.559 7.686 27299 Z= 0.291 Chirality : 0.045 0.146 3090 Planarity : 0.004 0.054 3549 Dihedral : 4.660 33.050 2713 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.54 % Allowed : 30.44 % Favored : 65.02 % 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 are not related in a simple way. whole: -1.02 (0.17), residues: 2497 helix: -0.11 (0.23), residues: 527 sheet: -0.46 (0.21), residues: 614 loop : -0.96 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 528 TYR 0.012 0.001 TYR G 506 PHE 0.014 0.001 PHE B 281 TRP 0.023 0.001 TRP B 245 HIS 0.002 0.001 HIS Z 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (20180) covalent geometry : angle 0.55910 / 0.29 (27299) hydrogen bonds : bond 0.02608 / 1.65 ( 636) hydrogen bonds : angle 5.03312 / 3.48 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.47 seconds wall clock time: 60 minutes 22.68 seconds (3622.68 seconds total)