Starting phenix.real_space_refine on Thu May 22 18:57:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1a_36790/05_2025/8k1a_36790.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15280 2.51 5 N 4038 2.21 5 O 4555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24001 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6014 Classifications: {'peptide': 742} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 715} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6014 Classifications: {'peptide': 742} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 715} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 5955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5955 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 710} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 6018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6018 Classifications: {'peptide': 742} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 715} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 13.34, per 1000 atoms: 0.56 Number of scatterers: 24001 At special positions: 0 Unit cell: (115, 138, 138.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4555 8.00 N 4038 7.00 C 15280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.9 seconds 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 36 sheets defined 21.2% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.557A pdb=" N THR A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 removed outlier: 3.936A pdb=" N MET A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 423 through 429 removed outlier: 4.107A pdb=" N ARG A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 removed outlier: 4.123A pdb=" N LEU A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.806A pdb=" N VAL A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 464 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 520 removed outlier: 4.046A pdb=" N ILE A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.666A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 600 removed outlier: 4.440A pdb=" N PHE A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 636 removed outlier: 3.895A pdb=" N VAL A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.607A pdb=" N MET B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 361 Processing helix chain 'B' and resid 395 through 407 removed outlier: 4.381A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.575A pdb=" N LYS B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 464 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 removed outlier: 4.177A pdb=" N GLN B 498 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 520 removed outlier: 3.669A pdb=" N ILE B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 565 removed outlier: 4.587A pdb=" N LYS B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 removed outlier: 4.314A pdb=" N PHE B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 635 removed outlier: 4.838A pdb=" N SER B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU B 632 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 735 removed outlier: 3.535A pdb=" N LEU B 732 " --> pdb=" O TYR B 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.561A pdb=" N LEU C 49 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS C 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 50' Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.690A pdb=" N THR C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.540A pdb=" N MET C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 319 " --> pdb=" O ARG C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.753A pdb=" N ILE C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.529A pdb=" N ARG C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.716A pdb=" N MET C 464 " --> pdb=" O TYR C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 removed outlier: 3.941A pdb=" N GLN C 498 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 520 removed outlier: 3.700A pdb=" N ILE C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 565 removed outlier: 4.178A pdb=" N LYS C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 600 removed outlier: 4.433A pdb=" N PHE C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 618 removed outlier: 3.638A pdb=" N GLU C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 636 removed outlier: 3.574A pdb=" N LYS C 622 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU C 632 " --> pdb=" O LYS C 628 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 742 through 747 removed outlier: 3.814A pdb=" N LYS C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 305 through 320 removed outlier: 3.737A pdb=" N ALA D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 313 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 315 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 359 removed outlier: 3.583A pdb=" N ILE D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 407 Processing helix chain 'D' and resid 424 through 428 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.601A pdb=" N TRP D 432 " --> pdb=" O HIS D 429 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 433 " --> pdb=" O PRO D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 433' Processing helix chain 'D' and resid 454 through 471 removed outlier: 3.732A pdb=" N VAL D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET D 464 " --> pdb=" O TYR D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 498 removed outlier: 4.033A pdb=" N GLN D 498 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 520 removed outlier: 4.031A pdb=" N ILE D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 565 removed outlier: 3.779A pdb=" N LYS D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 600 removed outlier: 3.658A pdb=" N ARG D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.972A pdb=" N ILE D 634 " --> pdb=" O TYR D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 735 Processing helix chain 'D' and resid 742 through 748 removed outlier: 3.883A pdb=" N LYS D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.542A pdb=" N GLU A 11 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 14 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 20 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR A 36 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 22 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.745A pdb=" N ARG A 178 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 93 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 176 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.658A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 163 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL A 159 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A 233 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 196 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.658A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 163 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL A 159 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.652A pdb=" N PHE A 259 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 259 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 275 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 182 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.542A pdb=" N LEU A 524 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 410 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 335 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA8, first strand: chain 'A' and resid 639 through 644 removed outlier: 6.335A pdb=" N ALA A 653 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 664 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AB1, first strand: chain 'A' and resid 692 through 698 Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.530A pdb=" N GLU B 11 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 20 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR B 36 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 22 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.692A pdb=" N ARG B 178 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 93 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 176 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 182 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 275 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 259 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 215 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 104 through 112 removed outlier: 5.774A pdb=" N TYR B 105 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS B 139 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 107 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 145 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE B 233 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 196 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 235 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 104 through 112 removed outlier: 5.774A pdb=" N TYR B 105 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS B 139 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 107 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 145 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.406A pdb=" N THR B 546 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE B 525 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N TRP B 547 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER B 527 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 477 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 410 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LYS B 478 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 412 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE B 365 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N TRP B 413 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 335 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB8, first strand: chain 'B' and resid 639 through 644 removed outlier: 6.404A pdb=" N ALA B 653 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 652 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 654 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 667 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 755 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 698 " --> pdb=" O LEU B 755 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 680 through 682 removed outlier: 4.041A pdb=" N ILE B 680 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.677A pdb=" N TYR C 35 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 24 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN C 33 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 90 through 93 removed outlier: 3.580A pdb=" N ARG C 178 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 93 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 176 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 104 through 112 removed outlier: 6.963A pdb=" N THR C 137 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS C 108 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 135 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 110 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 133 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS C 112 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA C 131 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 154 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE C 233 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU C 196 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 235 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 104 through 112 removed outlier: 6.963A pdb=" N THR C 137 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS C 108 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 135 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 110 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 133 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS C 112 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA C 131 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 154 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.497A pdb=" N LEU C 334 " --> pdb=" O TYR C 605 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 411 through 414 Processing sheet with id=AC7, first strand: chain 'C' and resid 418 through 419 Processing sheet with id=AC8, first strand: chain 'C' and resid 639 through 644 removed outlier: 6.285A pdb=" N ALA C 653 " --> pdb=" O LEU C 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 696 through 698 removed outlier: 3.563A pdb=" N LYS C 723 " --> pdb=" O CYS C 697 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.902A pdb=" N TYR D 35 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG D 24 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN D 33 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 90 through 93 removed outlier: 6.125A pdb=" N THR D 91 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 174 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.637A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 107 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 150 " --> pdb=" O ASN D 163 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 163 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 154 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL D 159 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 234 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE D 233 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU D 196 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 112 removed outlier: 5.637A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 107 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 150 " --> pdb=" O ASN D 163 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 163 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 154 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL D 159 " --> pdb=" O TYR D 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 364 through 366 removed outlier: 6.565A pdb=" N LEU D 335 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 334 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET D 573 " --> pdb=" O THR D 602 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY D 604 " --> pdb=" O MET D 573 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER D 575 " --> pdb=" O GLY D 604 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 546 " --> pdb=" O GLY D 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AD7, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AD8, first strand: chain 'D' and resid 639 through 644 removed outlier: 3.610A pdb=" N VAL D 657 " --> pdb=" O ASP D 639 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 653 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 752 " --> pdb=" O GLN D 670 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU D 755 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP D 698 " --> pdb=" O LEU D 755 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 680 through 682 removed outlier: 4.002A pdb=" N ILE D 680 " --> pdb=" O ILE D 739 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2412 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: 8.74 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5484 1.33 - 1.45: 5630 1.45 - 1.57: 13208 1.57 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 24562 Sorted by residual: bond pdb=" CA SER B 220 " pdb=" CB SER B 220 " ideal model delta sigma weight residual 1.533 1.470 0.063 1.90e-02 2.77e+03 1.10e+01 bond pdb=" N ILE D 474 " pdb=" CA ILE D 474 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" N ASP B 45 " pdb=" CA ASP B 45 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.26e-02 6.30e+03 1.07e+01 bond pdb=" N ILE B 523 " pdb=" CA ILE B 523 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.24e-02 6.50e+03 9.96e+00 bond pdb=" N ILE B 477 " pdb=" CA ILE B 477 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 9.96e+00 ... (remaining 24557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 31808 1.86 - 3.73: 1233 3.73 - 5.59: 137 5.59 - 7.45: 28 7.45 - 9.31: 6 Bond angle restraints: 33212 Sorted by residual: angle pdb=" N LYS C 621 " pdb=" CA LYS C 621 " pdb=" C LYS C 621 " ideal model delta sigma weight residual 113.88 105.96 7.92 1.23e+00 6.61e-01 4.15e+01 angle pdb=" C PHE B 46 " pdb=" CA PHE B 46 " pdb=" CB PHE B 46 " ideal model delta sigma weight residual 112.07 103.07 9.00 1.54e+00 4.22e-01 3.41e+01 angle pdb=" N PRO C 118 " pdb=" CA PRO C 118 " pdb=" C PRO C 118 " ideal model delta sigma weight residual 110.70 117.80 -7.10 1.22e+00 6.72e-01 3.39e+01 angle pdb=" N LEU B 744 " pdb=" CA LEU B 744 " pdb=" C LEU B 744 " ideal model delta sigma weight residual 114.12 106.07 8.05 1.39e+00 5.18e-01 3.35e+01 angle pdb=" N LEU C 611 " pdb=" CA LEU C 611 " pdb=" C LEU C 611 " ideal model delta sigma weight residual 113.23 106.37 6.86 1.22e+00 6.72e-01 3.16e+01 ... (remaining 33207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13051 17.95 - 35.91: 1276 35.91 - 53.86: 239 53.86 - 71.81: 54 71.81 - 89.76: 24 Dihedral angle restraints: 14644 sinusoidal: 5974 harmonic: 8670 Sorted by residual: dihedral pdb=" CA PRO A 63 " pdb=" C PRO A 63 " pdb=" N GLU A 64 " pdb=" CA GLU A 64 " ideal model delta harmonic sigma weight residual 180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLU C 415 " pdb=" C GLU C 415 " pdb=" N LEU C 416 " pdb=" CA LEU C 416 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA MET A 539 " pdb=" C MET A 539 " pdb=" N LEU A 540 " pdb=" CA LEU A 540 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 14641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2526 0.051 - 0.102: 742 0.102 - 0.153: 196 0.153 - 0.204: 42 0.204 - 0.255: 9 Chirality restraints: 3515 Sorted by residual: chirality pdb=" CA PHE B 46 " pdb=" N PHE B 46 " pdb=" C PHE B 46 " pdb=" CB PHE B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ILE A 737 " pdb=" N ILE A 737 " pdb=" C ILE A 737 " pdb=" CB ILE A 737 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LEU B 744 " pdb=" N LEU B 744 " pdb=" C LEU B 744 " pdb=" CB LEU B 744 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3512 not shown) Planarity restraints: 4296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 466 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C ALA C 466 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA C 466 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 467 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 739 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C ILE B 739 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 739 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B 740 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 278 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO D 279 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 279 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 279 " -0.035 5.00e-02 4.00e+02 ... (remaining 4293 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1806 2.74 - 3.28: 21826 3.28 - 3.82: 36362 3.82 - 4.36: 46809 4.36 - 4.90: 83029 Nonbonded interactions: 189832 Sorted by model distance: nonbonded pdb=" O GLU C 76 " pdb=" OG SER C 183 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 48 " pdb=" OE2 GLU B 731 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR C 462 " pdb=" OE1 GLU C 519 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR D 462 " pdb=" OE1 GLU D 519 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG A 439 " pdb=" O LEU C 100 " model vdw 2.237 3.120 ... (remaining 189827 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 2 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 337 or (resid 338 and (name N or na \ me CA or name C or name O or name CB )) or resid 339 through 342 or (resid 343 a \ nd (name N or name CA or name C or name O or name CB )) or resid 346 through 358 \ or resid 360 through 469 or resid 472 through 761)) selection = (chain 'B' and (resid 2 through 337 or (resid 338 and (name N or name CA or name \ C or name O or name CB )) or resid 339 through 342 or (resid 343 and (name N or \ name CA or name C or name O or name CB )) or resid 346 through 358 or resid 360 \ through 469 or resid 472 through 745 or (resid 746 and (name N or name CA or na \ me C or name O or name CB )) or resid 747 through 761)) selection = (chain 'C' and (resid 2 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 745 or (resid 746 and (name N or na \ me CA or name C or name O or name CB )) or resid 747 through 761)) selection = (chain 'D' and (resid 2 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 337 or (resid 338 and (name N or na \ me CA or name C or name O or name CB )) or resid 339 through 342 or (resid 343 a \ nd (name N or name CA or name C or name O or name CB )) or resid 346 through 358 \ or resid 360 through 469 or resid 472 through 745 or (resid 746 and (name N or \ name CA or name C or name O or name CB )) or resid 747 through 761)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 52.700 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.005 0.063 24562 Z= 0.318 Angle : 0.802 9.313 33212 Z= 0.507 Chirality : 0.054 0.255 3515 Planarity : 0.005 0.065 4296 Dihedral : 14.950 89.765 9110 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 2941 helix: -1.74 (0.19), residues: 604 sheet: -0.33 (0.18), residues: 879 loop : -2.44 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 284 HIS 0.006 0.001 HIS A 219 PHE 0.041 0.002 PHE A 535 TYR 0.027 0.002 TYR B 541 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.17416 ( 776) hydrogen bonds : angle 6.66148 ( 2412) covalent geometry : bond 0.00512 (24562) covalent geometry : angle 0.80153 (33212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 2.766 Fit side-chains REVERT: A 481 MET cc_start: 0.7776 (tmm) cc_final: 0.7517 (tmm) REVERT: B 23 MET cc_start: 0.7040 (mtm) cc_final: 0.6766 (mtp) REVERT: B 685 GLN cc_start: 0.7891 (pm20) cc_final: 0.7538 (pt0) REVERT: C 352 LYS cc_start: 0.7663 (tttt) cc_final: 0.7024 (ttpp) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3532 time to fit residues: 180.9716 Evaluate side-chains 266 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 288 GLN B 13 HIS B 659 GLN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN C 582 ASN D 71 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119021 restraints weight = 33807.217| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.90 r_work: 0.3214 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24562 Z= 0.175 Angle : 0.649 9.559 33212 Z= 0.350 Chirality : 0.046 0.184 3515 Planarity : 0.005 0.053 4296 Dihedral : 5.222 22.870 3311 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.97 % Allowed : 9.00 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2941 helix: -1.18 (0.20), residues: 620 sheet: -0.09 (0.18), residues: 876 loop : -2.40 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 385 HIS 0.006 0.001 HIS A 219 PHE 0.025 0.002 PHE A 452 TYR 0.018 0.002 TYR A 111 ARG 0.004 0.000 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 776) hydrogen bonds : angle 5.04605 ( 2412) covalent geometry : bond 0.00410 (24562) covalent geometry : angle 0.64942 (33212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 2.661 Fit side-chains REVERT: A 648 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: B 23 MET cc_start: 0.7235 (mtm) cc_final: 0.6909 (mtp) REVERT: C 352 LYS cc_start: 0.7760 (tttt) cc_final: 0.7131 (ttpp) REVERT: C 630 TYR cc_start: 0.6623 (m-80) cc_final: 0.6284 (m-80) outliers start: 25 outliers final: 21 residues processed: 283 average time/residue: 0.3349 time to fit residues: 150.9141 Evaluate side-chains 279 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 203 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 277 optimal weight: 0.0010 chunk 210 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 337 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117375 restraints weight = 33615.131| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.91 r_work: 0.3201 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24562 Z= 0.179 Angle : 0.640 9.072 33212 Z= 0.345 Chirality : 0.046 0.185 3515 Planarity : 0.005 0.054 4296 Dihedral : 5.218 23.240 3311 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.71 % Allowed : 12.47 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2941 helix: -1.03 (0.20), residues: 620 sheet: -0.05 (0.18), residues: 868 loop : -2.36 (0.14), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 385 HIS 0.006 0.001 HIS A 219 PHE 0.027 0.002 PHE D 535 TYR 0.019 0.002 TYR C 249 ARG 0.004 0.000 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 776) hydrogen bonds : angle 4.91400 ( 2412) covalent geometry : bond 0.00424 (24562) covalent geometry : angle 0.63983 (33212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 3.114 Fit side-chains REVERT: A 364 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7951 (pp) REVERT: A 639 ASP cc_start: 0.7663 (m-30) cc_final: 0.7329 (m-30) REVERT: A 648 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: B 23 MET cc_start: 0.7320 (mtm) cc_final: 0.6963 (mtp) REVERT: B 733 MET cc_start: 0.8089 (mtt) cc_final: 0.7729 (mtt) REVERT: C 171 GLU cc_start: 0.6552 (tp30) cc_final: 0.6323 (tp30) REVERT: C 513 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.6268 (t80) REVERT: C 630 TYR cc_start: 0.6709 (m-80) cc_final: 0.6330 (m-80) outliers start: 44 outliers final: 30 residues processed: 301 average time/residue: 0.3332 time to fit residues: 161.2975 Evaluate side-chains 296 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 242 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122906 restraints weight = 32837.156| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 0.79 r_work: 0.3198 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24562 Z= 0.187 Angle : 0.644 9.182 33212 Z= 0.347 Chirality : 0.046 0.183 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.249 23.029 3311 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.14 % Allowed : 14.73 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.15), residues: 2941 helix: -0.98 (0.20), residues: 617 sheet: -0.16 (0.18), residues: 898 loop : -2.36 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 385 HIS 0.005 0.001 HIS A 219 PHE 0.019 0.002 PHE A 452 TYR 0.019 0.002 TYR C 249 ARG 0.003 0.000 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.05392 ( 776) hydrogen bonds : angle 4.88029 ( 2412) covalent geometry : bond 0.00446 (24562) covalent geometry : angle 0.64422 (33212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 2.831 Fit side-chains REVERT: A 364 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 481 MET cc_start: 0.7995 (tmm) cc_final: 0.7556 (tmm) REVERT: A 617 LEU cc_start: 0.7543 (tt) cc_final: 0.7261 (tp) REVERT: A 639 ASP cc_start: 0.7599 (m-30) cc_final: 0.7312 (m-30) REVERT: A 648 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6564 (pt0) REVERT: B 23 MET cc_start: 0.7342 (mtm) cc_final: 0.6973 (mtp) REVERT: B 733 MET cc_start: 0.8163 (mtt) cc_final: 0.7833 (mtt) REVERT: C 171 GLU cc_start: 0.6554 (tp30) cc_final: 0.6333 (tp30) REVERT: C 467 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5719 (tttm) REVERT: C 513 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6222 (t80) REVERT: D 347 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5929 (mt-10) REVERT: D 422 ASP cc_start: 0.6000 (t0) cc_final: 0.5753 (t0) outliers start: 55 outliers final: 38 residues processed: 306 average time/residue: 0.3276 time to fit residues: 161.6969 Evaluate side-chains 306 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 685 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 31 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 443 HIS ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN D 94 GLN D 262 GLN D 420 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122350 restraints weight = 32891.382| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.74 r_work: 0.3198 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24562 Z= 0.184 Angle : 0.635 9.117 33212 Z= 0.342 Chirality : 0.046 0.179 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.233 23.034 3311 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.92 % Allowed : 15.82 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2941 helix: -0.96 (0.20), residues: 622 sheet: -0.13 (0.18), residues: 895 loop : -2.37 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 385 HIS 0.005 0.001 HIS C 219 PHE 0.017 0.002 PHE A 452 TYR 0.020 0.002 TYR C 249 ARG 0.003 0.000 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 776) hydrogen bonds : angle 4.84613 ( 2412) covalent geometry : bond 0.00440 (24562) covalent geometry : angle 0.63496 (33212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 268 time to evaluate : 2.483 Fit side-chains REVERT: A 79 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 364 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7944 (pp) REVERT: A 481 MET cc_start: 0.8016 (tmm) cc_final: 0.7602 (tmm) REVERT: A 617 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7257 (tp) REVERT: A 639 ASP cc_start: 0.7630 (m-30) cc_final: 0.7324 (m-30) REVERT: A 648 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: B 9 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7783 (m) REVERT: B 23 MET cc_start: 0.7336 (mtm) cc_final: 0.6974 (mtp) REVERT: B 275 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 22 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 171 GLU cc_start: 0.6590 (tp30) cc_final: 0.6336 (tp30) REVERT: C 467 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5631 (tttm) REVERT: C 513 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6288 (t80) REVERT: D 347 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5945 (mt-10) REVERT: D 364 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7699 (pt) REVERT: D 382 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7412 (tt) REVERT: D 422 ASP cc_start: 0.5999 (t0) cc_final: 0.5777 (t0) outliers start: 75 outliers final: 46 residues processed: 322 average time/residue: 0.3251 time to fit residues: 169.7901 Evaluate side-chains 316 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 420 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 19 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 610 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122032 restraints weight = 32780.118| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.78 r_work: 0.3191 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24562 Z= 0.185 Angle : 0.637 9.095 33212 Z= 0.344 Chirality : 0.046 0.177 3515 Planarity : 0.005 0.054 4296 Dihedral : 5.238 23.081 3311 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.31 % Allowed : 16.36 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2941 helix: -0.94 (0.20), residues: 622 sheet: -0.17 (0.18), residues: 908 loop : -2.37 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 385 HIS 0.005 0.001 HIS C 219 PHE 0.016 0.002 PHE A 452 TYR 0.019 0.002 TYR C 249 ARG 0.002 0.000 ARG D 631 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 776) hydrogen bonds : angle 4.83104 ( 2412) covalent geometry : bond 0.00442 (24562) covalent geometry : angle 0.63714 (33212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 262 time to evaluate : 2.641 Fit side-chains REVERT: A 79 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (m) REVERT: A 364 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7940 (pp) REVERT: A 639 ASP cc_start: 0.7693 (m-30) cc_final: 0.7398 (m-30) REVERT: A 648 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: B 9 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7768 (m) REVERT: B 23 MET cc_start: 0.7364 (mtm) cc_final: 0.7006 (mtp) REVERT: B 275 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 684 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7836 (pp) REVERT: B 733 MET cc_start: 0.8181 (mtt) cc_final: 0.7891 (mtt) REVERT: C 22 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8249 (tt) REVERT: C 171 GLU cc_start: 0.6617 (tp30) cc_final: 0.6368 (tp30) REVERT: C 467 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5626 (tttm) REVERT: C 513 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6283 (t80) REVERT: D 271 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8173 (m) REVERT: D 364 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7701 (pt) REVERT: D 382 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7484 (tt) outliers start: 85 outliers final: 58 residues processed: 326 average time/residue: 0.3573 time to fit residues: 190.5072 Evaluate side-chains 327 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 214 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN B 216 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121200 restraints weight = 32890.584| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.79 r_work: 0.3169 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24562 Z= 0.252 Angle : 0.725 9.731 33212 Z= 0.389 Chirality : 0.049 0.202 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.576 24.638 3311 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.54 % Allowed : 17.37 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.15), residues: 2941 helix: -1.14 (0.20), residues: 622 sheet: -0.25 (0.18), residues: 911 loop : -2.46 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 284 HIS 0.007 0.001 HIS C 219 PHE 0.021 0.002 PHE A 452 TYR 0.023 0.002 TYR C 249 ARG 0.003 0.001 ARG D 557 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 776) hydrogen bonds : angle 5.04518 ( 2412) covalent geometry : bond 0.00612 (24562) covalent geometry : angle 0.72549 (33212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 266 time to evaluate : 2.684 Fit side-chains REVERT: A 364 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8075 (pp) REVERT: A 639 ASP cc_start: 0.7741 (m-30) cc_final: 0.7465 (m-30) REVERT: A 648 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: B 275 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 648 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: B 684 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7924 (pp) REVERT: B 685 GLN cc_start: 0.7482 (pm20) cc_final: 0.7245 (tt0) REVERT: C 171 GLU cc_start: 0.6630 (tp30) cc_final: 0.6354 (tp30) REVERT: C 467 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5816 (tttm) REVERT: C 513 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.6304 (t80) REVERT: C 585 MET cc_start: 0.5561 (OUTLIER) cc_final: 0.5086 (mmm) REVERT: D 364 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7764 (pt) REVERT: D 382 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7432 (tt) REVERT: D 422 ASP cc_start: 0.6032 (t0) cc_final: 0.5777 (t0) outliers start: 91 outliers final: 69 residues processed: 335 average time/residue: 0.3147 time to fit residues: 170.1776 Evaluate side-chains 338 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 696 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 676 ASN B 216 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115083 restraints weight = 33971.377| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 0.92 r_work: 0.3170 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24562 Z= 0.220 Angle : 0.687 9.354 33212 Z= 0.369 Chirality : 0.048 0.185 3515 Planarity : 0.005 0.056 4296 Dihedral : 5.489 24.259 3311 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.66 % Allowed : 17.41 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2941 helix: -1.11 (0.20), residues: 622 sheet: -0.25 (0.18), residues: 911 loop : -2.47 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 385 HIS 0.006 0.001 HIS C 219 PHE 0.016 0.002 PHE A 452 TYR 0.021 0.002 TYR C 249 ARG 0.003 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 776) hydrogen bonds : angle 4.96610 ( 2412) covalent geometry : bond 0.00532 (24562) covalent geometry : angle 0.68673 (33212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 262 time to evaluate : 2.914 Fit side-chains REVERT: A 364 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 639 ASP cc_start: 0.7820 (m-30) cc_final: 0.7564 (m-30) REVERT: A 648 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: B 275 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 684 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7892 (pp) REVERT: B 685 GLN cc_start: 0.7454 (pm20) cc_final: 0.7214 (tt0) REVERT: C 171 GLU cc_start: 0.6624 (tp30) cc_final: 0.6339 (tp30) REVERT: C 467 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5764 (tttm) REVERT: C 513 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6243 (t80) REVERT: C 585 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.5076 (mmm) REVERT: C 632 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: D 271 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8161 (m) REVERT: D 364 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7675 (pt) REVERT: D 382 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7350 (tt) REVERT: D 422 ASP cc_start: 0.6010 (t0) cc_final: 0.5795 (t0) REVERT: D 539 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6618 (mmp) outliers start: 94 outliers final: 73 residues processed: 331 average time/residue: 0.3444 time to fit residues: 186.0557 Evaluate side-chains 343 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 258 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 151 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121674 restraints weight = 33011.206| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.75 r_work: 0.3180 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24562 Z= 0.186 Angle : 0.648 9.084 33212 Z= 0.349 Chirality : 0.046 0.185 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.357 23.866 3311 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.54 % Allowed : 17.88 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2941 helix: -1.01 (0.20), residues: 622 sheet: -0.20 (0.18), residues: 908 loop : -2.44 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 385 HIS 0.006 0.001 HIS C 219 PHE 0.014 0.002 PHE D 668 TYR 0.019 0.002 TYR C 249 ARG 0.003 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.05374 ( 776) hydrogen bonds : angle 4.87786 ( 2412) covalent geometry : bond 0.00444 (24562) covalent geometry : angle 0.64769 (33212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 260 time to evaluate : 2.929 Fit side-chains REVERT: A 364 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 639 ASP cc_start: 0.7777 (m-30) cc_final: 0.7514 (m-30) REVERT: A 648 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: B 275 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8497 (mp) REVERT: B 648 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6493 (pm20) REVERT: B 684 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7900 (pp) REVERT: C 171 GLU cc_start: 0.6620 (tp30) cc_final: 0.6363 (tp30) REVERT: C 467 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5725 (tttm) REVERT: C 513 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.6289 (t80) REVERT: C 585 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5137 (mmm) REVERT: C 616 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5523 (mm-30) REVERT: C 632 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: D 240 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: D 271 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8168 (m) REVERT: D 364 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7705 (pt) REVERT: D 382 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (tt) REVERT: D 539 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6630 (mmp) outliers start: 91 outliers final: 73 residues processed: 326 average time/residue: 0.3151 time to fit residues: 166.9342 Evaluate side-chains 341 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 253 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 104 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 676 ASN B 216 GLN B 582 ASN D 420 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.123273 restraints weight = 32803.636| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.80 r_work: 0.3197 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24562 Z= 0.161 Angle : 0.612 8.744 33212 Z= 0.330 Chirality : 0.045 0.189 3515 Planarity : 0.005 0.056 4296 Dihedral : 5.163 23.495 3311 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.51 % Allowed : 17.96 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2941 helix: -0.89 (0.20), residues: 622 sheet: -0.19 (0.18), residues: 911 loop : -2.38 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 385 HIS 0.006 0.001 HIS C 219 PHE 0.013 0.002 PHE D 668 TYR 0.017 0.002 TYR C 249 ARG 0.003 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 776) hydrogen bonds : angle 4.75388 ( 2412) covalent geometry : bond 0.00380 (24562) covalent geometry : angle 0.61210 (33212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 257 time to evaluate : 2.717 Fit side-chains REVERT: A 639 ASP cc_start: 0.7803 (m-30) cc_final: 0.7536 (m-30) REVERT: A 648 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6614 (pt0) REVERT: B 275 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 648 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: B 684 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7895 (pp) REVERT: C 171 GLU cc_start: 0.6634 (tp30) cc_final: 0.6382 (tp30) REVERT: C 467 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5769 (tttm) REVERT: C 513 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.6348 (t80) REVERT: C 585 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5082 (mmm) REVERT: C 616 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5517 (mm-30) REVERT: C 632 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: D 240 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: D 271 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8202 (m) REVERT: D 364 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7650 (pt) REVERT: D 382 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7492 (tt) REVERT: D 539 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6708 (mmp) outliers start: 90 outliers final: 67 residues processed: 321 average time/residue: 0.3161 time to fit residues: 165.4032 Evaluate side-chains 333 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 513 TYR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 699 MET Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 34 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 259 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** D 420 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 = 0.3484 r_free = 0.3484 target = 0.134195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125325 restraints weight = 32505.132| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 0.79 r_work: 0.3225 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24562 Z= 0.116 Angle : 0.553 8.309 33212 Z= 0.300 Chirality : 0.043 0.185 3515 Planarity : 0.004 0.055 4296 Dihedral : 4.834 22.521 3311 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.69 % Allowed : 18.82 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2941 helix: -0.68 (0.21), residues: 625 sheet: 0.11 (0.18), residues: 857 loop : -2.26 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 385 HIS 0.004 0.001 HIS C 219 PHE 0.011 0.001 PHE C 668 TYR 0.015 0.001 TYR C 249 ARG 0.002 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 776) hydrogen bonds : angle 4.53534 ( 2412) covalent geometry : bond 0.00263 (24562) covalent geometry : angle 0.55349 (33212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10514.57 seconds wall clock time: 183 minutes 5.46 seconds (10985.46 seconds total)