Starting phenix.real_space_refine on Sun Aug 24 21:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1a_36790/08_2025/8k1a_36790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1a_36790/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k1a_36790/08_2025/8k1a_36790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1a_36790/08_2025/8k1a_36790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1a_36790/08_2025/8k1a_36790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1a_36790/08_2025/8k1a_36790.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'PHE:plan': 1, 'GLU: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: 6.54, per 1000 atoms: 0.27 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: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.05 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: 5.75 Time building geometry restraints manager: 2.79 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.680 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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 : 8.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.000 ARG C 74 TYR 0.027 0.002 TYR B 541 PHE 0.041 0.002 PHE A 535 TRP 0.026 0.002 TRP C 284 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00512 (24562) covalent geometry : angle 0.80153 (33212) hydrogen bonds : bond 0.17416 ( 776) hydrogen bonds : angle 6.66148 ( 2412) *********************** 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 : 1.010 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: 0.1720 time to fit residues: 88.9142 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 : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 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 A 288 GLN A 610 ASN B 659 GLN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN C 582 ASN D 71 GLN D 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115997 restraints weight = 34182.132| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.90 r_work: 0.3177 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24562 Z= 0.258 Angle : 0.766 12.071 33212 Z= 0.409 Chirality : 0.050 0.202 3515 Planarity : 0.006 0.056 4296 Dihedral : 5.673 24.723 3311 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.32 % Allowed : 10.32 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.15), residues: 2941 helix: -1.40 (0.20), residues: 614 sheet: -0.36 (0.18), residues: 915 loop : -2.47 (0.14), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 631 TYR 0.022 0.002 TYR C 249 PHE 0.035 0.003 PHE D 535 TRP 0.019 0.003 TRP D 385 HIS 0.009 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00623 (24562) covalent geometry : angle 0.76568 (33212) hydrogen bonds : bond 0.06594 ( 776) hydrogen bonds : angle 5.27974 ( 2412) *********************** 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 294 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.721 Fit side-chains REVERT: A 639 ASP cc_start: 0.7735 (m-30) cc_final: 0.7371 (m-30) REVERT: A 648 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: B 502 MET cc_start: 0.7753 (mtt) cc_final: 0.7222 (mtt) REVERT: B 685 GLN cc_start: 0.8069 (pm20) cc_final: 0.7642 (pt0) REVERT: B 733 MET cc_start: 0.8070 (mtt) cc_final: 0.7691 (mtt) REVERT: C 352 LYS cc_start: 0.7771 (tttt) cc_final: 0.7139 (ttpp) REVERT: D 422 ASP cc_start: 0.6019 (t0) cc_final: 0.5718 (t0) outliers start: 34 outliers final: 29 residues processed: 280 average time/residue: 0.1578 time to fit residues: 71.3227 Evaluate side-chains 282 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 161 THR 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 117 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 341 THR 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 105 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 B 13 HIS ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118545 restraints weight = 33941.986| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.97 r_work: 0.3208 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24562 Z= 0.133 Angle : 0.590 8.563 33212 Z= 0.320 Chirality : 0.044 0.179 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.108 22.405 3311 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.25 % Allowed : 13.21 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.15), residues: 2941 helix: -0.98 (0.21), residues: 620 sheet: -0.03 (0.18), residues: 868 loop : -2.34 (0.14), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 631 TYR 0.016 0.001 TYR C 249 PHE 0.012 0.001 PHE A 452 TRP 0.016 0.001 TRP D 385 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00300 (24562) covalent geometry : angle 0.59037 (33212) hydrogen bonds : bond 0.04866 ( 776) hydrogen bonds : angle 4.84580 ( 2412) *********************** 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 310 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.011 Fit side-chains REVERT: A 364 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7939 (pp) REVERT: A 639 ASP cc_start: 0.7683 (m-30) cc_final: 0.7366 (m-30) REVERT: A 648 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: C 171 GLU cc_start: 0.6527 (tp30) cc_final: 0.6295 (tp30) REVERT: C 513 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.6277 (t80) outliers start: 32 outliers final: 19 residues processed: 298 average time/residue: 0.1710 time to fit residues: 81.8711 Evaluate side-chains 286 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 61 CYS 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 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 40 ILE Chi-restraints excluded: chain C residue 101 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 1 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 A 650 ASN D 71 GLN D 94 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115411 restraints weight = 34119.203| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.91 r_work: 0.3169 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24562 Z= 0.239 Angle : 0.714 10.240 33212 Z= 0.383 Chirality : 0.049 0.190 3515 Planarity : 0.005 0.055 4296 Dihedral : 5.536 24.450 3311 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.45 % Allowed : 15.35 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.15), residues: 2941 helix: -1.12 (0.20), residues: 616 sheet: -0.25 (0.18), residues: 912 loop : -2.44 (0.14), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 631 TYR 0.021 0.002 TYR C 249 PHE 0.023 0.002 PHE A 452 TRP 0.017 0.002 TRP B 413 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00577 (24562) covalent geometry : angle 0.71446 (33212) hydrogen bonds : bond 0.06115 ( 776) hydrogen bonds : angle 5.06279 ( 2412) *********************** 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 325 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 1.068 Fit side-chains REVERT: A 639 ASP cc_start: 0.7755 (m-30) cc_final: 0.7468 (m-30) REVERT: A 648 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: B 685 GLN cc_start: 0.7921 (pm20) cc_final: 0.7690 (pm20) REVERT: C 171 GLU cc_start: 0.6606 (tp30) cc_final: 0.6344 (tp30) REVERT: C 467 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5773 (tttm) REVERT: C 513 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6293 (t80) REVERT: D 347 GLU cc_start: 0.6269 (mt-10) cc_final: 0.6000 (mt-10) REVERT: D 364 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (pp) REVERT: D 422 ASP cc_start: 0.5975 (t0) cc_final: 0.5718 (t0) outliers start: 63 outliers final: 44 residues processed: 310 average time/residue: 0.1613 time to fit residues: 81.1618 Evaluate side-chains 312 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 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 C residue 40 ILE 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 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 102 ASP Chi-restraints excluded: chain D residue 134 LEU 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 364 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 206 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 276 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 D 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115861 restraints weight = 34023.274| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.91 r_work: 0.3173 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24562 Z= 0.215 Angle : 0.681 9.724 33212 Z= 0.367 Chirality : 0.048 0.183 3515 Planarity : 0.005 0.056 4296 Dihedral : 5.461 24.040 3311 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.23 % Allowed : 16.05 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.15), residues: 2941 helix: -1.11 (0.20), residues: 622 sheet: -0.20 (0.18), residues: 898 loop : -2.46 (0.14), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 631 TYR 0.021 0.002 TYR C 249 PHE 0.019 0.002 PHE A 452 TRP 0.018 0.002 TRP D 385 HIS 0.006 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00520 (24562) covalent geometry : angle 0.68142 (33212) hydrogen bonds : bond 0.05725 ( 776) hydrogen bonds : angle 4.98303 ( 2412) *********************** 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 353 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 0.850 Fit side-chains REVERT: A 316 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 639 ASP cc_start: 0.7808 (m-30) cc_final: 0.7522 (m-30) REVERT: A 648 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6728 (pt0) REVERT: B 9 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7728 (m) REVERT: B 733 MET cc_start: 0.8209 (mtt) cc_final: 0.7973 (mtt) REVERT: C 22 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (tt) REVERT: C 171 GLU cc_start: 0.6629 (tp30) cc_final: 0.6370 (tp30) REVERT: C 467 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5798 (tttm) REVERT: C 513 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6329 (t80) REVERT: D 271 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8147 (m) REVERT: D 347 GLU cc_start: 0.6243 (mt-10) cc_final: 0.6013 (mt-10) REVERT: D 364 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7718 (pp) REVERT: D 382 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7196 (tt) REVERT: D 422 ASP cc_start: 0.5964 (t0) cc_final: 0.5747 (t0) outliers start: 83 outliers final: 55 residues processed: 333 average time/residue: 0.1546 time to fit residues: 83.8409 Evaluate side-chains 321 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 402 LYS 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 234 ILE 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 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 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 102 ASP 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 382 LEU Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 216 GLN B 582 ASN B 685 GLN D 71 GLN D 420 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124240 restraints weight = 32728.279| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.74 r_work: 0.3210 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24562 Z= 0.142 Angle : 0.587 8.663 33212 Z= 0.318 Chirality : 0.045 0.171 3515 Planarity : 0.004 0.055 4296 Dihedral : 5.071 23.069 3311 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.00 % Allowed : 17.53 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.15), residues: 2941 helix: -0.90 (0.21), residues: 625 sheet: 0.00 (0.18), residues: 867 loop : -2.33 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 587 TYR 0.016 0.001 TYR C 249 PHE 0.012 0.001 PHE D 668 TRP 0.017 0.002 TRP D 385 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00330 (24562) covalent geometry : angle 0.58662 (33212) hydrogen bonds : bond 0.04690 ( 776) hydrogen bonds : angle 4.72088 ( 2412) *********************** 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 348 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 271 time to evaluate : 0.956 Fit side-chains REVERT: A 79 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7229 (m) REVERT: A 364 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8103 (pp) REVERT: A 481 MET cc_start: 0.8003 (tmm) cc_final: 0.7648 (tmm) REVERT: A 639 ASP cc_start: 0.7664 (m-30) cc_final: 0.7362 (m-30) REVERT: A 648 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6473 (pt0) REVERT: B 9 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7776 (m) REVERT: B 733 MET cc_start: 0.8215 (mtt) cc_final: 0.7952 (mtt) REVERT: C 22 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8206 (tt) REVERT: C 171 GLU cc_start: 0.6622 (tp30) cc_final: 0.6376 (tp30) REVERT: C 467 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5601 (tttm) REVERT: C 513 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.6339 (t80) REVERT: C 632 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: D 364 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7692 (pp) REVERT: D 422 ASP cc_start: 0.5930 (t0) cc_final: 0.5687 (t0) outliers start: 77 outliers final: 48 residues processed: 329 average time/residue: 0.1550 time to fit residues: 82.6885 Evaluate side-chains 318 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 145 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 580 VAL Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 THR 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 134 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 MET 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 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 685 GLN 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 101 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 217 SER 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 632 GLU Chi-restraints excluded: chain C residue 639 ASP 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 242 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 465 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 9.9990 chunk 104 optimal weight: 0.0470 chunk 66 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- 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** A 610 ASN A 676 ASN B 685 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121633 restraints weight = 32910.595| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.78 r_work: 0.3185 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24562 Z= 0.190 Angle : 0.645 8.978 33212 Z= 0.347 Chirality : 0.046 0.179 3515 Planarity : 0.005 0.054 4296 Dihedral : 5.247 23.296 3311 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.54 % Allowed : 17.69 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.15), residues: 2941 helix: -0.95 (0.20), residues: 622 sheet: -0.15 (0.18), residues: 908 loop : -2.39 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 587 TYR 0.019 0.002 TYR C 249 PHE 0.016 0.002 PHE D 668 TRP 0.016 0.002 TRP D 385 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00454 (24562) covalent geometry : angle 0.64477 (33212) hydrogen bonds : bond 0.05343 ( 776) hydrogen bonds : angle 4.82626 ( 2412) *********************** 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 349 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 258 time to evaluate : 0.874 Fit side-chains REVERT: A 481 MET cc_start: 0.8050 (tmm) cc_final: 0.7638 (tmm) REVERT: A 639 ASP cc_start: 0.7731 (m-30) cc_final: 0.7445 (m-30) REVERT: A 648 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6614 (pt0) REVERT: B 9 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7825 (m) REVERT: B 733 MET cc_start: 0.8226 (mtt) cc_final: 0.7952 (mtt) REVERT: C 22 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 171 GLU cc_start: 0.6635 (tp30) cc_final: 0.6378 (tp30) REVERT: C 467 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5618 (tttm) REVERT: C 513 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.6353 (t80) REVERT: C 632 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: D 240 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: D 271 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8165 (m) REVERT: D 422 ASP cc_start: 0.6071 (t0) cc_final: 0.5805 (t0) REVERT: D 539 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6786 (mmp) outliers start: 91 outliers final: 69 residues processed: 328 average time/residue: 0.1392 time to fit residues: 75.1554 Evaluate side-chains 334 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 256 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 28 ASN 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 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 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 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 274 MET 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 685 GLN Chi-restraints excluded: chain C residue 22 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 217 SER 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 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 240 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 368 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 221 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 A 676 ASN B 685 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118765 restraints weight = 33634.130| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.95 r_work: 0.3221 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24562 Z= 0.110 Angle : 0.544 8.354 33212 Z= 0.295 Chirality : 0.043 0.175 3515 Planarity : 0.004 0.055 4296 Dihedral : 4.807 22.315 3311 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.65 % Allowed : 18.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.15), residues: 2941 helix: -0.70 (0.21), residues: 625 sheet: 0.10 (0.18), residues: 867 loop : -2.24 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 587 TYR 0.014 0.001 TYR C 249 PHE 0.011 0.001 PHE C 668 TRP 0.016 0.001 TRP D 385 HIS 0.003 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00244 (24562) covalent geometry : angle 0.54378 (33212) hydrogen bonds : bond 0.04123 ( 776) hydrogen bonds : angle 4.55262 ( 2412) *********************** 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 341 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 0.954 Fit side-chains REVERT: A 79 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7214 (m) REVERT: A 464 MET cc_start: 0.8149 (mtm) cc_final: 0.7702 (mtp) REVERT: A 481 MET cc_start: 0.7960 (tmm) cc_final: 0.7641 (tmm) REVERT: A 639 ASP cc_start: 0.7693 (m-30) cc_final: 0.7400 (m-30) REVERT: A 648 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: B 9 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7684 (m) REVERT: B 189 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7757 (ptt) REVERT: B 648 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: B 733 MET cc_start: 0.8156 (mtt) cc_final: 0.7852 (mtt) REVERT: C 22 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8151 (tt) REVERT: C 171 GLU cc_start: 0.6616 (tp30) cc_final: 0.6338 (tp30) REVERT: C 467 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5617 (tttm) REVERT: C 513 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.6348 (t80) REVERT: C 616 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5374 (mm-30) REVERT: D 539 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6678 (mmp) outliers start: 68 outliers final: 49 residues processed: 323 average time/residue: 0.1348 time to fit residues: 71.1151 Evaluate side-chains 323 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 61 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 161 THR 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 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 9 THR 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 134 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 234 ILE 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 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 C residue 22 LEU 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 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 616 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 D residue 19 VAL 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 134 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 609 LEU 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 176 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 273 optimal weight: 0.9990 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 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN B 685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123403 restraints weight = 32840.208| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.79 r_work: 0.3205 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24562 Z= 0.159 Angle : 0.603 8.680 33212 Z= 0.325 Chirality : 0.045 0.180 3515 Planarity : 0.005 0.053 4296 Dihedral : 4.990 22.695 3311 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.00 % Allowed : 18.74 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.15), residues: 2941 helix: -0.77 (0.21), residues: 625 sheet: 0.04 (0.18), residues: 881 loop : -2.25 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 741 TYR 0.017 0.002 TYR C 249 PHE 0.015 0.002 PHE D 668 TRP 0.015 0.002 TRP B 413 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00377 (24562) covalent geometry : angle 0.60333 (33212) hydrogen bonds : bond 0.04847 ( 776) hydrogen bonds : angle 4.63821 ( 2412) *********************** 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 340 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 263 time to evaluate : 0.761 Fit side-chains REVERT: A 79 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7192 (m) REVERT: A 368 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6807 (t70) REVERT: A 481 MET cc_start: 0.8041 (tmm) cc_final: 0.7679 (tmm) REVERT: A 639 ASP cc_start: 0.7647 (m-30) cc_final: 0.7348 (m-30) REVERT: A 648 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: B 9 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7843 (m) REVERT: C 22 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 171 GLU cc_start: 0.6635 (tp30) cc_final: 0.6382 (tp30) REVERT: C 326 TRP cc_start: 0.6210 (m100) cc_final: 0.6002 (m100) REVERT: C 467 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5631 (tttm) REVERT: C 513 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.6388 (t80) REVERT: C 616 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5567 (mm-30) REVERT: C 630 TYR cc_start: 0.6819 (m-80) cc_final: 0.6407 (m-80) REVERT: C 632 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: D 240 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: D 271 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8208 (m) REVERT: D 539 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6820 (mmp) outliers start: 77 outliers final: 57 residues processed: 322 average time/residue: 0.1363 time to fit residues: 71.5034 Evaluate side-chains 330 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 28 ASN 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 145 THR Chi-restraints excluded: chain A residue 161 THR 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 368 ASP 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 9 THR 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 134 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 234 ILE 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 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 685 GLN Chi-restraints excluded: chain C residue 22 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 217 SER 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 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 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 134 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 539 MET 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 28 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 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 610 ASN A 676 ASN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114776 restraints weight = 34075.084| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.91 r_work: 0.3160 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24562 Z= 0.253 Angle : 0.730 10.097 33212 Z= 0.389 Chirality : 0.049 0.204 3515 Planarity : 0.005 0.054 4296 Dihedral : 5.482 24.541 3311 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.31 % Allowed : 18.50 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2941 helix: -1.04 (0.20), residues: 622 sheet: -0.07 (0.18), residues: 881 loop : -2.41 (0.14), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 741 TYR 0.024 0.002 TYR C 249 PHE 0.019 0.002 PHE A 668 TRP 0.016 0.002 TRP D 479 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00613 (24562) covalent geometry : angle 0.72997 (33212) hydrogen bonds : bond 0.06073 ( 776) hydrogen bonds : angle 4.95595 ( 2412) ********************** 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 342 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 1.003 Fit side-chains REVERT: A 26 MET cc_start: 0.7261 (mtm) cc_final: 0.6985 (mtp) REVERT: A 368 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6862 (t70) REVERT: A 639 ASP cc_start: 0.7843 (m-30) cc_final: 0.7577 (m-30) REVERT: A 648 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: B 733 MET cc_start: 0.8273 (mtt) cc_final: 0.8002 (mtt) REVERT: C 22 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8262 (tt) REVERT: C 171 GLU cc_start: 0.6628 (tp30) cc_final: 0.6339 (tp30) REVERT: C 326 TRP cc_start: 0.6300 (m100) cc_final: 0.6060 (m100) REVERT: C 467 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5704 (tttm) REVERT: C 513 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.6290 (t80) REVERT: C 632 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: D 240 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: D 271 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8184 (m) REVERT: D 539 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6827 (mmp) outliers start: 85 outliers final: 69 residues processed: 321 average time/residue: 0.1398 time to fit residues: 73.2054 Evaluate side-chains 332 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 28 ASN 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 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 368 ASP 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 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 274 MET 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 702 SER Chi-restraints excluded: chain C residue 22 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 217 SER 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 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 117 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 145 THR 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 368 ASP 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 246 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 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 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 676 ASN ** B 685 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 = 0.3393 r_free = 0.3393 target = 0.126992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116551 restraints weight = 33887.548| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.92 r_work: 0.3190 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1563 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 : 0.616 9.257 33212 Z= 0.332 Chirality : 0.045 0.187 3515 Planarity : 0.005 0.054 4296 Dihedral : 5.168 23.199 3311 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.00 % Allowed : 18.85 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.15), residues: 2941 helix: -0.87 (0.21), residues: 622 sheet: 0.07 (0.18), residues: 857 loop : -2.35 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 594 TYR 0.017 0.002 TYR C 249 PHE 0.013 0.002 PHE D 668 TRP 0.016 0.002 TRP D 385 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00381 (24562) covalent geometry : angle 0.61643 (33212) hydrogen bonds : bond 0.04963 ( 776) hydrogen bonds : angle 4.73346 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.01 seconds wall clock time: 84 minutes 7.42 seconds (5047.42 seconds total)