Starting phenix.real_space_refine on Sun Sep 13 20:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nr3_0488/09_2026/6nr3_0488.map" } resolution = 3.4 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= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 108 5.16 5 C 16432 2.51 5 N 4252 2.21 5 O 4372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25180 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6112 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 21, 'TRANS': 808} Chain breaks: 13 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 899 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'UNK:plan-1': 22, 'TYR:plan': 6, 'ARG:plan': 13, 'ASP:plan': 21, 'GLU:plan': 30, 'GLN:plan1': 2, 'ASN:plan1': 8, 'PHE:plan': 7, 'HIS:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 416 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' CA': 1, 'KX7': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Restraints were copied for chains: B, C, D Time building chain proxies: 9.58, per 1000 atoms: 0.38 Number of scatterers: 25180 At special positions: 0 Unit cell: (150.12, 150.12, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 12 15.00 O 4372 8.00 N 4252 7.00 C 16432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D1042 " distance=2.03 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6568 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 12 sheets defined 79.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.106A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.727A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 352 through 362 removed outlier: 4.471A pdb=" N GLU A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.849A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.137A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.077A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.536A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.576A pdb=" N THR A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.655A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 586 through 603 removed outlier: 3.628A pdb=" N SER A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.623A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.117A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 683 removed outlier: 3.511A pdb=" N GLN A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.549A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.651A pdb=" N GLY A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 Processing helix chain 'A' and resid 733 through 756 Processing helix chain 'A' and resid 765 through 789 removed outlier: 3.901A pdb=" N ASN A 789 " --> pdb=" O GLN A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.842A pdb=" N PHE A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.879A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 810 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 840 Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.850A pdb=" N VAL A 848 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 849 " --> pdb=" O PHE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 889 removed outlier: 4.443A pdb=" N ILE A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 912 Proline residue: A 906 - end of helix Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 955 through 979 removed outlier: 4.045A pdb=" N VAL A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1007 removed outlier: 3.716A pdb=" N SER A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1013 No H-bonds generated for 'chain 'A' and resid 1011 through 1013' Processing helix chain 'A' and resid 1014 through 1025 removed outlier: 4.305A pdb=" N ALA A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1069 removed outlier: 3.924A pdb=" N ASN A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1100 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 187 through 203 removed outlier: 4.106A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.727A pdb=" N ASN B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 Processing helix chain 'B' and resid 352 through 362 removed outlier: 4.472A pdb=" N GLU B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.849A pdb=" N ILE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.137A pdb=" N ASN B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.077A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.537A pdb=" N LEU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.577A pdb=" N THR B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.655A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.628A pdb=" N SER B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.623A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.118A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 683 removed outlier: 3.510A pdb=" N GLN B 675 " --> pdb=" O GLN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.549A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.651A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 732 Processing helix chain 'B' and resid 733 through 756 Processing helix chain 'B' and resid 765 through 789 removed outlier: 3.900A pdb=" N ASN B 789 " --> pdb=" O GLN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 796 removed outlier: 3.842A pdb=" N PHE B 794 " --> pdb=" O GLY B 790 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 796 " --> pdb=" O LYS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.879A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 810 " --> pdb=" O ILE B 806 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 840 Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.850A pdb=" N VAL B 848 " --> pdb=" O ILE B 845 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 849 " --> pdb=" O PHE B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 889 removed outlier: 4.443A pdb=" N ILE B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 912 Proline residue: B 906 - end of helix Processing helix chain 'B' and resid 952 through 954 No H-bonds generated for 'chain 'B' and resid 952 through 954' Processing helix chain 'B' and resid 955 through 979 removed outlier: 4.045A pdb=" N VAL B 959 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1007 removed outlier: 3.716A pdb=" N SER B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1013 No H-bonds generated for 'chain 'B' and resid 1011 through 1013' Processing helix chain 'B' and resid 1014 through 1025 removed outlier: 4.305A pdb=" N ALA B1018 " --> pdb=" O PHE B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1069 removed outlier: 3.925A pdb=" N ASN B1049 " --> pdb=" O ARG B1045 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B1054 " --> pdb=" O GLU B1050 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B1069 " --> pdb=" O LYS B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1100 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.106A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.727A pdb=" N ASN C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 352 through 362 removed outlier: 4.472A pdb=" N GLU C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.850A pdb=" N ILE C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 Processing helix chain 'C' and resid 403 through 419 removed outlier: 4.136A pdb=" N ASN C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 4.077A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 removed outlier: 3.536A pdb=" N LEU C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.576A pdb=" N THR C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.655A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 586 through 603 removed outlier: 3.628A pdb=" N SER C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.623A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 645 Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 665 through 670 removed outlier: 4.117A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.511A pdb=" N GLN C 675 " --> pdb=" O GLN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.549A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 708 removed outlier: 3.651A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 732 Processing helix chain 'C' and resid 733 through 756 Processing helix chain 'C' and resid 765 through 789 removed outlier: 3.901A pdb=" N ASN C 789 " --> pdb=" O GLN C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 796 removed outlier: 3.842A pdb=" N PHE C 794 " --> pdb=" O GLY C 790 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 796 " --> pdb=" O LYS C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.879A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 810 " --> pdb=" O ILE C 806 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 840 Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.850A pdb=" N VAL C 848 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 849 " --> pdb=" O PHE C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 889 removed outlier: 4.443A pdb=" N ILE C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 865 " --> pdb=" O ARG C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 912 Proline residue: C 906 - end of helix Processing helix chain 'C' and resid 952 through 954 No H-bonds generated for 'chain 'C' and resid 952 through 954' Processing helix chain 'C' and resid 955 through 979 removed outlier: 4.045A pdb=" N VAL C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1007 removed outlier: 3.716A pdb=" N SER C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1013 No H-bonds generated for 'chain 'C' and resid 1011 through 1013' Processing helix chain 'C' and resid 1014 through 1025 removed outlier: 4.305A pdb=" N ALA C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1069 removed outlier: 3.925A pdb=" N ASN C1049 " --> pdb=" O ARG C1045 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP C1054 " --> pdb=" O GLU C1050 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C1069 " --> pdb=" O LYS C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1100 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.105A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.727A pdb=" N ASN D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 352 through 362 removed outlier: 4.472A pdb=" N GLU D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.849A pdb=" N ILE D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 Processing helix chain 'D' and resid 403 through 419 removed outlier: 4.137A pdb=" N ASN D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.077A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 468 removed outlier: 3.536A pdb=" N LEU D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 468 " --> pdb=" O THR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.576A pdb=" N THR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 533 " --> pdb=" O GLU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.655A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 586 through 603 removed outlier: 3.629A pdb=" N SER D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.623A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 665 through 670 removed outlier: 4.117A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 683 removed outlier: 3.511A pdb=" N GLN D 675 " --> pdb=" O GLN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.549A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 708 removed outlier: 3.651A pdb=" N GLY D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 732 Processing helix chain 'D' and resid 733 through 756 Processing helix chain 'D' and resid 765 through 789 removed outlier: 3.900A pdb=" N ASN D 789 " --> pdb=" O GLN D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 796 removed outlier: 3.842A pdb=" N PHE D 794 " --> pdb=" O GLY D 790 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 796 " --> pdb=" O LYS D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 818 removed outlier: 3.879A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 810 " --> pdb=" O ILE D 806 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 840 Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.849A pdb=" N VAL D 848 " --> pdb=" O ILE D 845 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 849 " --> pdb=" O PHE D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 889 removed outlier: 4.444A pdb=" N ILE D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP D 865 " --> pdb=" O ARG D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 912 Proline residue: D 906 - end of helix Processing helix chain 'D' and resid 952 through 954 No H-bonds generated for 'chain 'D' and resid 952 through 954' Processing helix chain 'D' and resid 955 through 979 removed outlier: 4.045A pdb=" N VAL D 959 " --> pdb=" O THR D 955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1007 removed outlier: 3.716A pdb=" N SER D1006 " --> pdb=" O GLN D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1013 No H-bonds generated for 'chain 'D' and resid 1011 through 1013' Processing helix chain 'D' and resid 1014 through 1025 removed outlier: 4.304A pdb=" N ALA D1018 " --> pdb=" O PHE D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1069 removed outlier: 3.925A pdb=" N ASN D1049 " --> pdb=" O ARG D1045 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D1069 " --> pdb=" O LYS D1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1100 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 5.853A pdb=" N ARG A 119 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.984A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS A 326 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 394 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 328 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 647 through 648 removed outlier: 4.301A pdb=" N CYS A 648 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 654 " --> pdb=" O CYS A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 120 removed outlier: 5.853A pdb=" N ARG B 119 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.984A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 326 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 394 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 328 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 647 through 648 removed outlier: 4.301A pdb=" N CYS B 648 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 654 " --> pdb=" O CYS B 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 120 removed outlier: 5.853A pdb=" N ARG C 119 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 179 removed outlier: 6.984A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS C 326 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 394 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 328 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 647 through 648 removed outlier: 4.301A pdb=" N CYS C 648 " --> pdb=" O SER C 654 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 654 " --> pdb=" O CYS C 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 120 removed outlier: 5.853A pdb=" N ARG D 119 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 178 through 179 removed outlier: 6.984A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS D 326 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE D 394 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 328 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 647 through 648 removed outlier: 4.301A pdb=" N CYS D 648 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 654 " --> pdb=" O CYS D 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1700 hydrogen bonds defined for protein. 5052 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: 5.01 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3928 1.30 - 1.43: 7183 1.43 - 1.56: 14421 1.56 - 1.69: 20 1.69 - 1.82: 156 Bond restraints: 25708 Sorted by residual: bond pdb=" N21 KX7 D1201 " pdb=" O23 KX7 D1201 " ideal model delta sigma weight residual 1.208 1.403 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" N21 KX7 C1201 " pdb=" O23 KX7 C1201 " ideal model delta sigma weight residual 1.208 1.403 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" N21 KX7 B1201 " pdb=" O23 KX7 B1201 " ideal model delta sigma weight residual 1.208 1.403 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" N21 KX7 A1201 " pdb=" O23 KX7 A1201 " ideal model delta sigma weight residual 1.208 1.403 -0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C05 KX7 A1201 " pdb=" N07 KX7 A1201 " ideal model delta sigma weight residual 1.355 1.498 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 25703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 34517 3.72 - 7.45: 431 7.45 - 11.17: 88 11.17 - 14.90: 0 14.90 - 18.62: 8 Bond angle restraints: 35044 Sorted by residual: angle pdb=" N GLN D 583 " pdb=" CA GLN D 583 " pdb=" C GLN D 583 " ideal model delta sigma weight residual 111.36 122.31 -10.95 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N GLN C 583 " pdb=" CA GLN C 583 " pdb=" C GLN C 583 " ideal model delta sigma weight residual 111.36 122.28 -10.92 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N GLN A 583 " pdb=" CA GLN A 583 " pdb=" C GLN A 583 " ideal model delta sigma weight residual 111.36 122.28 -10.92 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N GLN B 583 " pdb=" CA GLN B 583 " pdb=" C GLN B 583 " ideal model delta sigma weight residual 111.36 122.25 -10.89 1.09e+00 8.42e-01 9.99e+01 angle pdb=" N VAL D 848 " pdb=" CA VAL D 848 " pdb=" C VAL D 848 " ideal model delta sigma weight residual 110.62 119.64 -9.02 1.02e+00 9.61e-01 7.82e+01 ... (remaining 35039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 14291 17.13 - 34.26: 593 34.26 - 51.38: 128 51.38 - 68.51: 36 68.51 - 85.64: 20 Dihedral angle restraints: 15068 sinusoidal: 5044 harmonic: 10024 Sorted by residual: dihedral pdb=" CA THR C 557 " pdb=" C THR C 557 " pdb=" N ARG C 558 " pdb=" CA ARG C 558 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA THR A 557 " pdb=" C THR A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA THR B 557 " pdb=" C THR B 557 " pdb=" N ARG B 558 " pdb=" CA ARG B 558 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3197 0.059 - 0.118: 723 0.118 - 0.178: 180 0.178 - 0.237: 32 0.237 - 0.296: 20 Chirality restraints: 4152 Sorted by residual: chirality pdb=" CA TYR D1004 " pdb=" N TYR D1004 " pdb=" C TYR D1004 " pdb=" CB TYR D1004 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA TYR B1004 " pdb=" N TYR B1004 " pdb=" C TYR B1004 " pdb=" CB TYR B1004 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA TYR A1004 " pdb=" N TYR A1004 " pdb=" C TYR A1004 " pdb=" CB TYR A1004 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4149 not shown) Planarity restraints: 4340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 KX7 A1201 " 0.613 2.00e-02 2.50e+03 3.99e-01 2.78e+03 pdb=" C03 KX7 A1201 " -0.364 2.00e-02 2.50e+03 pdb=" C05 KX7 A1201 " 0.116 2.00e-02 2.50e+03 pdb=" C08 KX7 A1201 " -0.668 2.00e-02 2.50e+03 pdb=" N04 KX7 A1201 " -0.174 2.00e-02 2.50e+03 pdb=" N07 KX7 A1201 " 0.207 2.00e-02 2.50e+03 pdb=" O06 KX7 A1201 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 KX7 B1201 " 0.613 2.00e-02 2.50e+03 3.99e-01 2.78e+03 pdb=" C03 KX7 B1201 " -0.364 2.00e-02 2.50e+03 pdb=" C05 KX7 B1201 " 0.116 2.00e-02 2.50e+03 pdb=" C08 KX7 B1201 " -0.668 2.00e-02 2.50e+03 pdb=" N04 KX7 B1201 " -0.174 2.00e-02 2.50e+03 pdb=" N07 KX7 B1201 " 0.207 2.00e-02 2.50e+03 pdb=" O06 KX7 B1201 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 KX7 C1201 " -0.613 2.00e-02 2.50e+03 3.99e-01 2.78e+03 pdb=" C03 KX7 C1201 " 0.363 2.00e-02 2.50e+03 pdb=" C05 KX7 C1201 " -0.116 2.00e-02 2.50e+03 pdb=" C08 KX7 C1201 " 0.667 2.00e-02 2.50e+03 pdb=" N04 KX7 C1201 " 0.175 2.00e-02 2.50e+03 pdb=" N07 KX7 C1201 " -0.207 2.00e-02 2.50e+03 pdb=" O06 KX7 C1201 " -0.270 2.00e-02 2.50e+03 ... (remaining 4337 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 168 2.63 - 3.20: 22094 3.20 - 3.76: 37349 3.76 - 4.33: 46888 4.33 - 4.90: 78880 Nonbonded interactions: 185379 Sorted by model distance: nonbonded pdb=" O43 KXP D1202 " pdb=" O46 KXP D1202 " model vdw 2.059 3.040 nonbonded pdb=" O43 KXP A1202 " pdb=" O46 KXP A1202 " model vdw 2.060 3.040 nonbonded pdb=" O43 KXP B1202 " pdb=" O46 KXP B1202 " model vdw 2.060 3.040 nonbonded pdb=" O43 KXP C1202 " pdb=" O46 KXP C1202 " model vdw 2.060 3.040 nonbonded pdb=" NE2 GLN D 562 " pdb=" OG1 THR D 584 " model vdw 2.280 3.120 ... (remaining 185374 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.130 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.390 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.009 0.195 25712 Z= 0.430 Angle : 1.125 18.619 35052 Z= 0.634 Chirality : 0.058 0.296 4152 Planarity : 0.014 0.399 4340 Dihedral : 11.441 85.638 8488 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.54 % Allowed : 4.13 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3136 helix: -0.72 (0.10), residues: 2268 sheet: -0.37 (0.55), residues: 104 loop : -3.26 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 485 TYR 0.018 0.002 TYR D 808 PHE 0.025 0.003 PHE C 501 TRP 0.026 0.003 TRP D 993 HIS 0.008 0.002 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.43 (25708) covalent geometry : angle 1.12406 / 0.63 (35044) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 3.21896 / 1.60 ( 8) hydrogen bonds : bond 0.15972 / 11.29 ( 1700) hydrogen bonds : angle 5.51490 / 3.87 ( 5052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 668 time to evaluate : 0.945 Fit side-chains REVERT: A 654 SER cc_start: 0.8889 (t) cc_final: 0.8607 (p) REVERT: A 1058 MET cc_start: 0.8015 (mmm) cc_final: 0.7724 (mmt) REVERT: B 654 SER cc_start: 0.8887 (t) cc_final: 0.8599 (p) REVERT: B 1058 MET cc_start: 0.8020 (mmm) cc_final: 0.7729 (mmt) REVERT: C 654 SER cc_start: 0.8888 (t) cc_final: 0.8602 (p) REVERT: C 1058 MET cc_start: 0.8019 (mmm) cc_final: 0.7726 (mmt) REVERT: D 654 SER cc_start: 0.8889 (t) cc_final: 0.8607 (p) REVERT: D 1058 MET cc_start: 0.8018 (mmm) cc_final: 0.7731 (mmt) outliers start: 12 outliers final: 4 residues processed: 676 average time/residue: 0.1611 time to fit residues: 176.3005 Evaluate side-chains 419 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 415 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain D residue 740 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 256 ASN A 438 GLN A 844 HIS B 208 ASN B 256 ASN B 438 GLN B 844 HIS C 208 ASN C 256 ASN C 438 GLN C 844 HIS D 208 ASN D 256 ASN D 438 GLN D 844 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122486 restraints weight = 40478.262| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.98 r_work: 0.3131 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25712 Z= 0.160 Angle : 0.594 6.710 35052 Z= 0.305 Chirality : 0.039 0.140 4152 Planarity : 0.004 0.044 4340 Dihedral : 9.619 88.862 3832 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.09 % Allowed : 10.66 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3136 helix: 0.86 (0.10), residues: 2296 sheet: -0.27 (0.50), residues: 128 loop : -3.04 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 841 TYR 0.014 0.001 TYR A1004 PHE 0.021 0.001 PHE A 744 TRP 0.012 0.002 TRP D 876 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (25708) covalent geometry : angle 0.59313 / 0.30 (35044) SS BOND : bond 0.00053 / 0.03 ( 4) SS BOND : angle 1.54037 / 0.76 ( 8) hydrogen bonds : bond 0.05163 / 3.56 ( 1700) hydrogen bonds : angle 3.82795 / 2.71 ( 5052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 0.967 Fit side-chains REVERT: A 824 TRP cc_start: 0.6194 (t60) cc_final: 0.5755 (t60) REVERT: A 850 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: B 824 TRP cc_start: 0.6205 (t60) cc_final: 0.5766 (t60) REVERT: B 850 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7922 (ttm-80) REVERT: C 824 TRP cc_start: 0.6185 (t60) cc_final: 0.5748 (t60) REVERT: C 850 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7920 (ttm-80) REVERT: D 824 TRP cc_start: 0.6263 (t60) cc_final: 0.5836 (t60) REVERT: D 850 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7913 (ttm-80) outliers start: 68 outliers final: 44 residues processed: 460 average time/residue: 0.1486 time to fit residues: 114.5489 Evaluate side-chains 412 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 368 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 832 CYS Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 832 CYS Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 832 CYS Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 328 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 75 optimal weight: 50.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 HIS B 559 HIS C 559 HIS D 559 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116376 restraints weight = 40674.525| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.42 r_work: 0.3012 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 25712 Z= 0.318 Angle : 0.711 7.749 35052 Z= 0.367 Chirality : 0.043 0.146 4152 Planarity : 0.005 0.045 4340 Dihedral : 9.080 92.024 3832 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.49 % Allowed : 12.07 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3136 helix: 1.10 (0.11), residues: 2296 sheet: -1.38 (0.43), residues: 148 loop : -2.74 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 160 TYR 0.015 0.002 TYR D 646 PHE 0.020 0.002 PHE A 998 TRP 0.019 0.002 TRP A 682 HIS 0.004 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.32 (25708) covalent geometry : angle 0.70975 / 0.37 (35044) SS BOND : bond 0.00279 / 0.14 ( 4) SS BOND : angle 2.55486 / 1.28 ( 8) hydrogen bonds : bond 0.06384 / 4.41 ( 1700) hydrogen bonds : angle 4.03523 / 2.87 ( 5052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 357 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 824 TRP cc_start: 0.6542 (t60) cc_final: 0.6260 (t60) REVERT: A 859 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 752 PHE cc_start: 0.7988 (t80) cc_final: 0.7715 (t80) REVERT: B 824 TRP cc_start: 0.6551 (t60) cc_final: 0.6267 (t60) REVERT: B 859 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 869 PHE cc_start: 0.7590 (m-80) cc_final: 0.7380 (m-80) REVERT: C 752 PHE cc_start: 0.7985 (t80) cc_final: 0.7719 (t80) REVERT: C 824 TRP cc_start: 0.6551 (t60) cc_final: 0.6264 (t60) REVERT: C 859 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8187 (mp) REVERT: D 752 PHE cc_start: 0.7996 (t80) cc_final: 0.7725 (t80) REVERT: D 824 TRP cc_start: 0.6535 (t60) cc_final: 0.6265 (t60) REVERT: D 859 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (mp) REVERT: D 869 PHE cc_start: 0.7589 (m-80) cc_final: 0.7381 (m-80) outliers start: 99 outliers final: 79 residues processed: 426 average time/residue: 0.1399 time to fit residues: 102.3809 Evaluate side-chains 422 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 339 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 832 CYS Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 832 CYS Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1009 THR Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 93 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 187 optimal weight: 0.0020 chunk 74 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120436 restraints weight = 40236.174| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.96 r_work: 0.3101 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25712 Z= 0.129 Angle : 0.534 7.165 35052 Z= 0.271 Chirality : 0.037 0.139 4152 Planarity : 0.004 0.050 4340 Dihedral : 8.603 86.980 3832 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.72 % Allowed : 15.25 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3136 helix: 1.76 (0.11), residues: 2292 sheet: -0.35 (0.48), residues: 132 loop : -2.78 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 688 TYR 0.011 0.001 TYR A1004 PHE 0.020 0.001 PHE B 998 TRP 0.015 0.001 TRP A 651 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25708) covalent geometry : angle 0.53365 / 0.27 (35044) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 1.08833 / 0.54 ( 8) hydrogen bonds : bond 0.04302 / 2.97 ( 1700) hydrogen bonds : angle 3.52669 / 2.50 ( 5052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 391 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 786 TRP cc_start: 0.8380 (t60) cc_final: 0.8141 (t60) REVERT: A 824 TRP cc_start: 0.5956 (t60) cc_final: 0.5648 (t60) REVERT: B 752 PHE cc_start: 0.7990 (t80) cc_final: 0.7729 (t80) REVERT: B 786 TRP cc_start: 0.8382 (t60) cc_final: 0.8134 (t60) REVERT: B 824 TRP cc_start: 0.6022 (t60) cc_final: 0.5706 (t60) REVERT: C 752 PHE cc_start: 0.7996 (t80) cc_final: 0.7736 (t80) REVERT: C 786 TRP cc_start: 0.8378 (t60) cc_final: 0.8134 (t60) REVERT: C 824 TRP cc_start: 0.6026 (t60) cc_final: 0.5712 (t60) REVERT: D 752 PHE cc_start: 0.7994 (t80) cc_final: 0.7732 (t80) REVERT: D 786 TRP cc_start: 0.8380 (t60) cc_final: 0.8138 (t60) REVERT: D 824 TRP cc_start: 0.6049 (t60) cc_final: 0.5733 (t60) outliers start: 60 outliers final: 40 residues processed: 425 average time/residue: 0.1484 time to fit residues: 106.9675 Evaluate side-chains 391 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 57 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 269 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117932 restraints weight = 40029.647| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.35 r_work: 0.3040 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25712 Z= 0.224 Angle : 0.617 8.078 35052 Z= 0.313 Chirality : 0.039 0.141 4152 Planarity : 0.004 0.048 4340 Dihedral : 8.699 89.843 3832 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.86 % Allowed : 16.65 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3136 helix: 1.76 (0.11), residues: 2300 sheet: -1.66 (0.39), residues: 172 loop : -2.39 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 558 TYR 0.016 0.001 TYR A 835 PHE 0.017 0.002 PHE A 998 TRP 0.017 0.002 TRP D 651 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (25708) covalent geometry : angle 0.61649 / 0.31 (35044) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 1.82104 / 0.91 ( 8) hydrogen bonds : bond 0.05283 / 3.64 ( 1700) hydrogen bonds : angle 3.70500 / 2.63 ( 5052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8719 (m-80) cc_final: 0.8475 (m-80) REVERT: B 731 PHE cc_start: 0.8716 (m-80) cc_final: 0.8471 (m-80) REVERT: B 824 TRP cc_start: 0.6287 (t60) cc_final: 0.6075 (t60) REVERT: C 731 PHE cc_start: 0.8714 (m-80) cc_final: 0.8467 (m-80) REVERT: C 824 TRP cc_start: 0.6287 (t60) cc_final: 0.6078 (t60) REVERT: D 731 PHE cc_start: 0.8716 (m-80) cc_final: 0.8474 (m-80) REVERT: D 824 TRP cc_start: 0.6292 (t60) cc_final: 0.6087 (t60) REVERT: D 1055 GLU cc_start: 0.8315 (tt0) cc_final: 0.8083 (tt0) outliers start: 85 outliers final: 61 residues processed: 403 average time/residue: 0.1432 time to fit residues: 97.6155 Evaluate side-chains 402 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 310 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 160 optimal weight: 50.0000 chunk 120 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 ASN C 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117000 restraints weight = 40506.608| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.39 r_work: 0.3021 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 25712 Z= 0.245 Angle : 0.634 7.860 35052 Z= 0.322 Chirality : 0.040 0.138 4152 Planarity : 0.004 0.051 4340 Dihedral : 8.758 90.360 3832 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.99 % Allowed : 17.15 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3136 helix: 1.73 (0.11), residues: 2300 sheet: -2.10 (0.38), residues: 168 loop : -2.25 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 558 TYR 0.020 0.001 TYR A 835 PHE 0.021 0.002 PHE A 752 TRP 0.018 0.002 TRP B 682 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (25708) covalent geometry : angle 0.63305 / 0.32 (35044) SS BOND : bond 0.00129 / 0.06 ( 4) SS BOND : angle 1.83169 / 0.92 ( 8) hydrogen bonds : bond 0.05405 / 3.73 ( 1700) hydrogen bonds : angle 3.77672 / 2.68 ( 5052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 76 residues processed: 403 average time/residue: 0.1437 time to fit residues: 99.1004 Evaluate side-chains 407 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 331 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 832 CYS Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 995 PHE Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 832 CYS Chi-restraints excluded: chain D residue 839 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 170 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 274 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 203 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118286 restraints weight = 39894.348| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.32 r_work: 0.3045 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 25712 Z= 0.198 Angle : 0.589 7.305 35052 Z= 0.299 Chirality : 0.038 0.134 4152 Planarity : 0.004 0.048 4340 Dihedral : 8.660 88.918 3832 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.90 % Allowed : 18.28 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3136 helix: 1.85 (0.11), residues: 2300 sheet: -1.23 (0.45), residues: 128 loop : -2.32 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.011 0.001 TYR B1004 PHE 0.017 0.001 PHE D 998 TRP 0.018 0.002 TRP B 651 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (25708) covalent geometry : angle 0.58883 / 0.30 (35044) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 1.48120 / 0.74 ( 8) hydrogen bonds : bond 0.04876 / 3.37 ( 1700) hydrogen bonds : angle 3.65101 / 2.58 ( 5052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7952 (ttm170) REVERT: A 859 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8084 (tt) REVERT: B 850 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: B 859 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8073 (tt) REVERT: C 850 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7945 (ttm170) REVERT: C 859 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8062 (tt) REVERT: D 850 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: D 859 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8069 (tt) outliers start: 86 outliers final: 63 residues processed: 410 average time/residue: 0.1497 time to fit residues: 103.4955 Evaluate side-chains 406 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 SER Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 849 SER Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 40 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 169 optimal weight: 50.0000 chunk 275 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120698 restraints weight = 39967.839| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.34 r_work: 0.3075 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25712 Z= 0.134 Angle : 0.532 7.446 35052 Z= 0.267 Chirality : 0.037 0.132 4152 Planarity : 0.004 0.048 4340 Dihedral : 8.482 86.365 3832 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.18 % Allowed : 19.42 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 3136 helix: 2.04 (0.11), residues: 2296 sheet: -0.67 (0.48), residues: 132 loop : -2.34 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 558 TYR 0.009 0.001 TYR B1004 PHE 0.016 0.001 PHE D 998 TRP 0.014 0.001 TRP B 651 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (25708) covalent geometry : angle 0.53207 / 0.27 (35044) SS BOND : bond 0.00053 / 0.03 ( 4) SS BOND : angle 0.97373 / 0.49 ( 8) hydrogen bonds : bond 0.04015 / 2.78 ( 1700) hydrogen bonds : angle 3.45785 / 2.44 ( 5052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8762 (tptt) cc_final: 0.8025 (mmtp) REVERT: A 863 MET cc_start: 0.7061 (mmm) cc_final: 0.6740 (ttp) REVERT: A 1060 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 863 MET cc_start: 0.7050 (mmm) cc_final: 0.6733 (ttp) REVERT: B 1060 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8492 (mm-30) REVERT: C 863 MET cc_start: 0.7052 (mmm) cc_final: 0.6731 (ttp) REVERT: C 1060 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 863 MET cc_start: 0.7055 (mmm) cc_final: 0.6733 (ttp) outliers start: 70 outliers final: 49 residues processed: 382 average time/residue: 0.1516 time to fit residues: 95.6670 Evaluate side-chains 379 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 308 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 303 optimal weight: 0.0670 chunk 140 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 305 optimal weight: 0.8980 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122728 restraints weight = 40027.767| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.11 r_work: 0.3116 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25712 Z= 0.112 Angle : 0.509 7.492 35052 Z= 0.254 Chirality : 0.036 0.130 4152 Planarity : 0.004 0.047 4340 Dihedral : 8.291 84.917 3832 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 21.05 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3136 helix: 2.22 (0.11), residues: 2300 sheet: -0.36 (0.48), residues: 132 loop : -2.17 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 688 TYR 0.015 0.001 TYR D 835 PHE 0.015 0.001 PHE A 998 TRP 0.024 0.001 TRP A 786 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (25708) covalent geometry : angle 0.50859 / 0.25 (35044) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 0.76551 / 0.39 ( 8) hydrogen bonds : bond 0.03492 / 2.42 ( 1700) hydrogen bonds : angle 3.29376 / 2.33 ( 5052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 MET cc_start: 0.6924 (mmm) cc_final: 0.6699 (ttp) REVERT: A 1060 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8420 (mm-30) REVERT: B 1060 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8470 (mm-30) REVERT: C 863 MET cc_start: 0.6925 (mmm) cc_final: 0.6708 (ttp) REVERT: C 1060 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8447 (mm-30) REVERT: D 1055 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: D 1060 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8411 (mm-30) outliers start: 45 outliers final: 40 residues processed: 370 average time/residue: 0.1513 time to fit residues: 94.2633 Evaluate side-chains 362 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 105 optimal weight: 6.9990 chunk 338 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113521 restraints weight = 40393.178| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.31 r_work: 0.2967 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 25712 Z= 0.390 Angle : 0.757 7.199 35052 Z= 0.388 Chirality : 0.045 0.142 4152 Planarity : 0.005 0.047 4340 Dihedral : 8.895 92.802 3832 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.63 % Allowed : 20.69 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3136 helix: 1.58 (0.11), residues: 2300 sheet: -2.32 (0.38), residues: 168 loop : -2.03 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 494 TYR 0.021 0.002 TYR C 835 PHE 0.016 0.002 PHE B 165 TRP 0.027 0.003 TRP D 786 HIS 0.005 0.001 HIS D 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.39 (25708) covalent geometry : angle 0.75652 / 0.39 (35044) SS BOND : bond 0.00167 / 0.08 ( 4) SS BOND : angle 2.48304 / 1.27 ( 8) hydrogen bonds : bond 0.06546 / 4.51 ( 1700) hydrogen bonds : angle 4.05293 / 2.87 ( 5052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1055 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (tt0) outliers start: 58 outliers final: 54 residues processed: 384 average time/residue: 0.1458 time to fit residues: 94.1944 Evaluate side-chains 394 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 740 TRP Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 1068 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 698 CYS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 1068 THR Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain D residue 740 TRP Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1068 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 8 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 255 optimal weight: 20.0000 chunk 13 optimal weight: 0.0060 chunk 22 optimal weight: 10.0000 chunk 337 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 ASN C 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122027 restraints weight = 39472.070| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.10 r_work: 0.3121 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25712 Z= 0.110 Angle : 0.528 7.454 35052 Z= 0.266 Chirality : 0.036 0.131 4152 Planarity : 0.004 0.049 4340 Dihedral : 8.396 84.008 3832 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 22.05 % Favored : 76.18 % 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 are not related in a simple way. whole: 1.65 (0.15), residues: 3136 helix: 2.15 (0.11), residues: 2296 sheet: -0.80 (0.47), residues: 132 loop : -2.24 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 558 TYR 0.016 0.001 TYR B 835 PHE 0.017 0.001 PHE B 998 TRP 0.021 0.001 TRP A 786 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (25708) covalent geometry : angle 0.52772 / 0.27 (35044) SS BOND : bond 0.00010 / 0.00 ( 4) SS BOND : angle 0.55111 / 0.28 ( 8) hydrogen bonds : bond 0.03636 / 2.52 ( 1700) hydrogen bonds : angle 3.45891 / 2.44 ( 5052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.25 seconds wall clock time: 100 minutes 30.26 seconds (6030.26 seconds total)