Starting phenix.real_space_refine on Tue Aug 26 06:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9a_36982/08_2025/8k9a_36982.cif" } resolution = 3.9 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 22033 2.51 5 N 5506 2.21 5 O 6366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 8081 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 950} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 8057 Classifications: {'peptide': 969} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 949} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 8091 Classifications: {'peptide': 971} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 950} Chain breaks: 3 Chain: "D" Number of atoms: 8093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8093 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 9.33, per 1000 atoms: 0.27 Number of scatterers: 34035 At special positions: 0 Unit cell: (102, 130.05, 275.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 6366 8.00 N 5506 7.00 C 22033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7830 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 16 sheets defined 65.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.447A pdb=" N GLU A 13 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.580A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.659A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.543A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.710A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.548A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.991A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.610A pdb=" N ILE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.632A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.703A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.723A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.661A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.856A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.357A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.623A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.772A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 702 removed outlier: 3.653A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 702 " --> pdb=" O GLN A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.956A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.623A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.729A pdb=" N LYS A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.804A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.745A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.654A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.749A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.693A pdb=" N ILE A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 896 Processing helix chain 'A' and resid 913 through 922 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.685A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.575A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.025A pdb=" N TRP A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 977 through 991 Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.958A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.776A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.890A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.506A pdb=" N ALA B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.667A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.814A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 299 removed outlier: 3.567A pdb=" N TYR B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.513A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.558A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.913A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 468 through 492 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.796A pdb=" N ALA B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.656A pdb=" N MET B 531 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.792A pdb=" N TYR B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.973A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.116A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.897A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.565A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.421A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.279A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.584A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.783A pdb=" N GLU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.600A pdb=" N LEU B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.937A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 872 removed outlier: 3.523A pdb=" N MET B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.694A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 4.257A pdb=" N TRP B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.241A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.772A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.650A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.638A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.792A pdb=" N CYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.045A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.848A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.605A pdb=" N SER C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.580A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 417 through 427 removed outlier: 4.002A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 496 Processing helix chain 'C' and resid 508 through 520 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.734A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 571 removed outlier: 3.723A pdb=" N TYR C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C 557 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 571 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.766A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.626A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 removed outlier: 3.500A pdb=" N LYS C 675 " --> pdb=" O SER C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 701 removed outlier: 3.743A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 removed outlier: 4.040A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.579A pdb=" N LYS C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.580A pdb=" N ILE C 772 " --> pdb=" O PRO C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 removed outlier: 4.020A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.764A pdb=" N CYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 840 removed outlier: 3.633A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'C' and resid 846 through 854 Processing helix chain 'C' and resid 862 through 872 removed outlier: 3.739A pdb=" N ASN C 867 " --> pdb=" O ASN C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 896 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 933 removed outlier: 3.981A pdb=" N PHE C 933 " --> pdb=" O MET C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 removed outlier: 3.700A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.704A pdb=" N LYS C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 962 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 976 through 991 removed outlier: 4.712A pdb=" N GLU C 982 " --> pdb=" O HIS C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1003 Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.979A pdb=" N GLU D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.639A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 53' Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.641A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.854A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.531A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.718A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.644A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.824A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.502A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.943A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.857A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 493 removed outlier: 3.842A pdb=" N ASN D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.786A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.494A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.639A pdb=" N ASN D 563 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.679A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.770A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.599A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 681 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.765A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.513A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.922A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.651A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.535A pdb=" N ILE D 835 " --> pdb=" O LYS D 831 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 855 removed outlier: 3.534A pdb=" N SER D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 871 removed outlier: 4.067A pdb=" N MET D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 896 Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.596A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 934 removed outlier: 3.825A pdb=" N GLU D 931 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 955 through 961 removed outlier: 3.506A pdb=" N TRP D 958 " --> pdb=" O ILE D 955 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 960 " --> pdb=" O SER D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 977 through 991 Processing helix chain 'D' and resid 993 through 1003 Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'F' and resid 10 through 13 removed outlier: 3.554A pdb=" N ASP F 13 " --> pdb=" O ALA F 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 95 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.281A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 341 removed outlier: 3.675A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.306A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.171A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 246 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.348A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.938A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.279A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 71 through 72 removed outlier: 8.831A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 46 " --> pdb=" O GLU F 115 " (cutoff:3.500A) 1726 hydrogen bonds defined for protein. 4977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10786 1.34 - 1.46: 8697 1.46 - 1.58: 15115 1.58 - 1.70: 0 1.70 - 1.82: 214 Bond restraints: 34812 Sorted by residual: bond pdb=" N VAL C 859 " pdb=" CA VAL C 859 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C VAL C 859 " pdb=" N GLU C 860 " ideal model delta sigma weight residual 1.331 1.289 0.041 1.31e-02 5.83e+03 1.00e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.462 1.495 -0.032 1.06e-02 8.90e+03 9.27e+00 bond pdb=" N VAL E 99 " pdb=" CA VAL E 99 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.74e+00 bond pdb=" N ILE B 138 " pdb=" CA ILE B 138 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.41e-02 5.03e+03 8.01e+00 ... (remaining 34807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 46269 2.35 - 4.70: 519 4.70 - 7.06: 79 7.06 - 9.41: 23 9.41 - 11.76: 9 Bond angle restraints: 46899 Sorted by residual: angle pdb=" N THR E 11 " pdb=" CA THR E 11 " pdb=" C THR E 11 " ideal model delta sigma weight residual 113.37 107.26 6.11 1.38e+00 5.25e-01 1.96e+01 angle pdb=" N TYR C 650 " pdb=" CA TYR C 650 " pdb=" C TYR C 650 " ideal model delta sigma weight residual 111.71 106.66 5.05 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N ILE C 138 " pdb=" CA ILE C 138 " pdb=" C ILE C 138 " ideal model delta sigma weight residual 112.98 107.76 5.22 1.25e+00 6.40e-01 1.75e+01 angle pdb=" N THR C 555 " pdb=" CA THR C 555 " pdb=" C THR C 555 " ideal model delta sigma weight residual 112.90 107.59 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" CA THR C 555 " pdb=" CB THR C 555 " pdb=" OG1 THR C 555 " ideal model delta sigma weight residual 109.60 103.56 6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 46894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17358 17.86 - 35.72: 2530 35.72 - 53.59: 683 53.59 - 71.45: 125 71.45 - 89.31: 41 Dihedral angle restraints: 20737 sinusoidal: 8568 harmonic: 12169 Sorted by residual: dihedral pdb=" CA MET C 647 " pdb=" C MET C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASN B 705 " pdb=" C ASN B 705 " pdb=" N VAL B 706 " pdb=" CA VAL B 706 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS B 505 " pdb=" C LYS B 505 " pdb=" N PRO B 506 " pdb=" CA PRO B 506 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4171 0.055 - 0.110: 736 0.110 - 0.164: 83 0.164 - 0.219: 10 0.219 - 0.274: 3 Chirality restraints: 5003 Sorted by residual: chirality pdb=" CG LEU D 922 " pdb=" CB LEU D 922 " pdb=" CD1 LEU D 922 " pdb=" CD2 LEU D 922 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 859 " pdb=" CA VAL C 859 " pdb=" CG1 VAL C 859 " pdb=" CG2 VAL C 859 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 661 " pdb=" CA ILE C 661 " pdb=" CG1 ILE C 661 " pdb=" CG2 ILE C 661 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 5000 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 462 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C SER B 462 " 0.049 2.00e-02 2.50e+03 pdb=" O SER B 462 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 463 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 660 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C LYS D 660 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS D 660 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE D 661 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 458 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ILE B 458 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 458 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 459 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 397 2.63 - 3.19: 31273 3.19 - 3.76: 52758 3.76 - 4.33: 68558 4.33 - 4.90: 112387 Nonbonded interactions: 265373 Sorted by model distance: nonbonded pdb=" OH TYR C 687 " pdb=" OE2 GLU C 715 " model vdw 2.057 3.040 nonbonded pdb=" O GLU C 516 " pdb=" OG1 THR C 520 " model vdw 2.127 3.040 nonbonded pdb=" O ILE C 458 " pdb=" OG SER C 462 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASP C 630 " pdb=" OG SER D 991 " model vdw 2.147 3.040 ... (remaining 265368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 747 or resid 749 through 753 or (resid 754 and (name \ N or name CA or name C or name O or name CB )) or resid 755 through 787 or resi \ d 794 through 896 or resid 910 through 1005)) selection = (chain 'B' and (resid 22 through 463 or resid 465 through 566 or resid 578 throu \ gh 747 or resid 749 through 759 or (resid 760 and (name N or name CA or name C o \ r name O or name CB )) or resid 761 through 787 or resid 794 through 857 or resi \ d 861 through 896 or resid 910 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 974 or resid 976 through \ 1005)) selection = (chain 'C' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 504 or (resid 505 and (name N or name CA or name C o \ r name O or name CB )) or resid 506 through 566 or resid 578 through 753 or (res \ id 754 and (name N or name CA or name C or name O or name CB )) or resid 755 thr \ ough 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) \ or resid 761 through 787 or resid 794 through 857 or resid 861 through 896 or re \ sid 910 through 911 or (resid 912 and (name N or name CA or name C or name O or \ name CB )) or resid 913 through 974 or resid 976 through 1005)) selection = (chain 'D' and (resid 22 through 142 or resid 145 through 498 or resid 503 throu \ gh 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 747 or resid 749 through 753 or (resid 754 and (name N or nam \ e CA or name C or name O or name CB )) or resid 755 through 759 or (resid 760 an \ d (name N or name CA or name C or name O or name CB )) or resid 761 through 787 \ or resid 794 through 857 or resid 861 through 896 or resid 910 through 1005)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 10 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 120)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.950 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.003 0.045 34812 Z= 0.165 Angle : 0.639 11.761 46899 Z= 0.344 Chirality : 0.042 0.274 5003 Planarity : 0.004 0.059 5976 Dihedral : 17.913 89.311 12907 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 2.33 % Allowed : 29.78 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 4060 helix: 0.97 (0.11), residues: 2380 sheet: -1.59 (0.35), residues: 214 loop : -1.17 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 669 TYR 0.037 0.001 TYR D 888 PHE 0.038 0.001 PHE C 778 TRP 0.022 0.002 TRP B 757 HIS 0.005 0.001 HIS C 979 Details of bonding type rmsd covalent geometry : bond 0.00303 (34812) covalent geometry : angle 0.63924 (46899) hydrogen bonds : bond 0.14562 ( 1724) hydrogen bonds : angle 5.61292 ( 4977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 246 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7738 (t80) REVERT: B 647 MET cc_start: 0.8087 (pmm) cc_final: 0.7751 (pmm) REVERT: C 651 ASP cc_start: 0.8686 (t70) cc_final: 0.8413 (t0) REVERT: C 751 ILE cc_start: 0.8529 (mp) cc_final: 0.8205 (tp) REVERT: D 519 MET cc_start: 0.8287 (mtm) cc_final: 0.7929 (mpp) outliers start: 87 outliers final: 68 residues processed: 316 average time/residue: 0.2041 time to fit residues: 110.4184 Evaluate side-chains 291 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 757 TRP Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 1004 PHE Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0030 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 297 GLN B 339 HIS B 382 ASN B 391 ASN B 415 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN C 58 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 HIS C 658 HIS ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 ASN C 867 ASN C 895 ASN D 224 ASN D 477 ASN D 786 HIS D 789 GLN D 832 GLN E 17 HIS F 54 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065467 restraints weight = 94176.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.066137 restraints weight = 72800.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.066835 restraints weight = 53856.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067665 restraints weight = 44489.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067742 restraints weight = 40968.027| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34812 Z= 0.217 Angle : 0.604 9.856 46899 Z= 0.314 Chirality : 0.041 0.171 5003 Planarity : 0.004 0.054 5976 Dihedral : 6.126 59.322 4613 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 4.17 % Allowed : 27.21 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.13), residues: 4060 helix: 1.11 (0.11), residues: 2416 sheet: -1.51 (0.37), residues: 192 loop : -1.17 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 669 TYR 0.028 0.002 TYR D 888 PHE 0.016 0.001 PHE A 916 TRP 0.014 0.001 TRP C 143 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00506 (34812) covalent geometry : angle 0.60359 (46899) hydrogen bonds : bond 0.04560 ( 1724) hydrogen bonds : angle 4.38166 ( 4977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 241 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 GLU cc_start: 0.9112 (tp30) cc_final: 0.8890 (tp30) REVERT: A 744 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8346 (t80) REVERT: B 115 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: B 342 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8608 (t) REVERT: B 517 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7036 (ttp80) REVERT: B 838 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5818 (mm) REVERT: B 866 MET cc_start: 0.5116 (mpp) cc_final: 0.4848 (mpp) REVERT: B 936 MET cc_start: 0.3385 (OUTLIER) cc_final: 0.3177 (mmt) REVERT: B 1001 MET cc_start: 0.6335 (tpp) cc_final: 0.6110 (tpp) REVERT: C 124 MET cc_start: 0.9001 (mmm) cc_final: 0.8705 (mmm) REVERT: C 347 VAL cc_start: 0.9592 (OUTLIER) cc_final: 0.9315 (m) REVERT: C 396 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: C 599 CYS cc_start: 0.7650 (t) cc_final: 0.7274 (t) REVERT: C 741 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 913 MET cc_start: 0.7057 (ppp) cc_final: 0.6721 (ttt) REVERT: C 978 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8378 (p90) REVERT: D 200 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9045 (mm) REVERT: D 825 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7515 (mm) REVERT: E 67 PHE cc_start: 0.7809 (m-80) cc_final: 0.7298 (m-80) REVERT: F 49 ASN cc_start: 0.8937 (t0) cc_final: 0.8737 (t0) outliers start: 156 outliers final: 79 residues processed: 367 average time/residue: 0.1886 time to fit residues: 117.6389 Evaluate side-chains 310 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 220 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 7 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 406 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 HIS ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065393 restraints weight = 94118.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066841 restraints weight = 64801.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067209 restraints weight = 45605.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.067656 restraints weight = 42621.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.067656 restraints weight = 38528.177| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34812 Z= 0.186 Angle : 0.563 8.650 46899 Z= 0.294 Chirality : 0.041 0.241 5003 Planarity : 0.004 0.053 5976 Dihedral : 5.565 59.000 4549 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 4.36 % Allowed : 27.02 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.13), residues: 4060 helix: 1.16 (0.11), residues: 2427 sheet: -1.61 (0.36), residues: 198 loop : -1.20 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 819 TYR 0.018 0.001 TYR D 888 PHE 0.041 0.001 PHE D 839 TRP 0.014 0.001 TRP A 143 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00435 (34812) covalent geometry : angle 0.56331 (46899) hydrogen bonds : bond 0.04219 ( 1724) hydrogen bonds : angle 4.18619 ( 4977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 244 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8680 (ttp-110) REVERT: A 802 ARG cc_start: 0.8312 (ptt90) cc_final: 0.7905 (tmt-80) REVERT: B 342 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8634 (t) REVERT: B 647 MET cc_start: 0.8812 (pmm) cc_final: 0.8546 (pmm) REVERT: B 802 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6575 (ttm170) REVERT: B 838 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5847 (mm) REVERT: B 919 TRP cc_start: 0.6957 (m-10) cc_final: 0.6544 (m-10) REVERT: B 936 MET cc_start: 0.3515 (OUTLIER) cc_final: 0.3240 (mmt) REVERT: B 954 PHE cc_start: 0.5278 (t80) cc_final: 0.4997 (t80) REVERT: C 124 MET cc_start: 0.9027 (mmm) cc_final: 0.8697 (mmm) REVERT: C 134 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7759 (p90) REVERT: C 396 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: C 738 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8757 (tptt) REVERT: C 751 ILE cc_start: 0.8585 (mp) cc_final: 0.8355 (tp) REVERT: C 1005 ILE cc_start: 0.8162 (mm) cc_final: 0.7680 (pt) REVERT: D 230 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8645 (t0) REVERT: D 396 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7450 (mmt) REVERT: D 825 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 930 MET cc_start: 0.8159 (pmm) cc_final: 0.7742 (pmm) REVERT: D 936 MET cc_start: 0.3694 (mtt) cc_final: 0.3391 (mtt) REVERT: E 67 PHE cc_start: 0.7762 (m-80) cc_final: 0.7348 (m-80) REVERT: F 49 ASN cc_start: 0.8975 (t0) cc_final: 0.8651 (t0) outliers start: 163 outliers final: 86 residues processed: 377 average time/residue: 0.1804 time to fit residues: 116.1419 Evaluate side-chains 322 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 225 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 142 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 293 optimal weight: 0.7980 chunk 365 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 408 optimal weight: 0.2980 chunk 282 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 341 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 467 ASN B 491 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 GLN C 829 GLN C 848 ASN C 895 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067493 restraints weight = 92985.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068892 restraints weight = 63278.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069337 restraints weight = 44825.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069740 restraints weight = 42125.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069841 restraints weight = 37520.151| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34812 Z= 0.102 Angle : 0.523 12.255 46899 Z= 0.268 Chirality : 0.039 0.195 5003 Planarity : 0.003 0.053 5976 Dihedral : 5.186 57.894 4541 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 3.29 % Allowed : 27.56 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.14), residues: 4060 helix: 1.36 (0.11), residues: 2420 sheet: -1.52 (0.37), residues: 186 loop : -1.08 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 502 TYR 0.025 0.001 TYR D 888 PHE 0.043 0.001 PHE A 839 TRP 0.012 0.001 TRP C 143 HIS 0.006 0.001 HIS C 503 Details of bonding type rmsd covalent geometry : bond 0.00225 (34812) covalent geometry : angle 0.52287 (46899) hydrogen bonds : bond 0.03415 ( 1724) hydrogen bonds : angle 3.92199 ( 4977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 262 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.9175 (tt0) cc_final: 0.8546 (tm-30) REVERT: A 744 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8388 (t80) REVERT: A 802 ARG cc_start: 0.8289 (ptt90) cc_final: 0.7884 (tmt-80) REVERT: A 936 MET cc_start: 0.3646 (OUTLIER) cc_final: 0.2774 (ptp) REVERT: B 115 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: B 342 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 460 LEU cc_start: 0.9217 (pp) cc_final: 0.8776 (mm) REVERT: B 467 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7207 (p0) REVERT: B 517 ARG cc_start: 0.7851 (ptt-90) cc_final: 0.7172 (ttp80) REVERT: B 647 MET cc_start: 0.8824 (pmm) cc_final: 0.8551 (pmm) REVERT: B 648 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: B 838 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5765 (mm) REVERT: B 919 TRP cc_start: 0.6885 (m-10) cc_final: 0.6565 (m-10) REVERT: B 936 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.3164 (mmt) REVERT: C 124 MET cc_start: 0.9011 (mmm) cc_final: 0.8695 (mmm) REVERT: C 134 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7704 (p90) REVERT: C 279 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: C 359 ARG cc_start: 0.8588 (tpt170) cc_final: 0.8377 (tpt-90) REVERT: C 396 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: C 588 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8953 (tp) REVERT: C 599 CYS cc_start: 0.7453 (t) cc_final: 0.7110 (t) REVERT: C 751 ILE cc_start: 0.8623 (mp) cc_final: 0.8302 (tp) REVERT: C 892 ARG cc_start: 0.8065 (mmp-170) cc_final: 0.7270 (ptm-80) REVERT: C 1005 ILE cc_start: 0.8188 (mm) cc_final: 0.7650 (pt) REVERT: D 188 ASP cc_start: 0.8557 (t0) cc_final: 0.8129 (t0) REVERT: D 230 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8418 (t0) REVERT: D 825 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 930 MET cc_start: 0.8130 (pmm) cc_final: 0.7724 (pmm) REVERT: D 936 MET cc_start: 0.3786 (mtt) cc_final: 0.3504 (mtt) REVERT: E 16 TYR cc_start: 0.6979 (t80) cc_final: 0.6447 (t80) REVERT: E 67 PHE cc_start: 0.7664 (m-80) cc_final: 0.7339 (m-80) REVERT: E 110 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: F 47 CYS cc_start: 0.7908 (t) cc_final: 0.7540 (t) REVERT: F 49 ASN cc_start: 0.8967 (t0) cc_final: 0.8676 (t0) REVERT: F 51 TYR cc_start: 0.8589 (m-10) cc_final: 0.8333 (m-10) REVERT: F 117 VAL cc_start: 0.9016 (t) cc_final: 0.8816 (p) outliers start: 123 outliers final: 62 residues processed: 353 average time/residue: 0.1746 time to fit residues: 104.3519 Evaluate side-chains 307 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 87 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 356 optimal weight: 0.0270 chunk 325 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 361 optimal weight: 0.5980 chunk 318 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070291 restraints weight = 93280.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069087 restraints weight = 65247.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068779 restraints weight = 58113.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.069026 restraints weight = 56556.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069389 restraints weight = 48948.900| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34812 Z= 0.101 Angle : 0.515 10.934 46899 Z= 0.263 Chirality : 0.039 0.222 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.874 57.183 4533 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 3.37 % Allowed : 27.16 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.14), residues: 4060 helix: 1.44 (0.11), residues: 2421 sheet: -1.30 (0.38), residues: 176 loop : -1.03 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 247 TYR 0.021 0.001 TYR D 888 PHE 0.022 0.001 PHE D 839 TRP 0.017 0.001 TRP C 143 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00220 (34812) covalent geometry : angle 0.51467 (46899) hydrogen bonds : bond 0.03255 ( 1724) hydrogen bonds : angle 3.84192 ( 4977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 264 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.9200 (tt0) cc_final: 0.8606 (tm-30) REVERT: A 744 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8400 (t80) REVERT: A 802 ARG cc_start: 0.8301 (ptt90) cc_final: 0.7869 (tmt-80) REVERT: A 936 MET cc_start: 0.3720 (OUTLIER) cc_final: 0.2837 (ptp) REVERT: B 115 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (m-40) REVERT: B 283 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8993 (tt) REVERT: B 342 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8636 (t) REVERT: B 460 LEU cc_start: 0.9270 (pp) cc_final: 0.8891 (mm) REVERT: B 647 MET cc_start: 0.8824 (pmm) cc_final: 0.8179 (pmm) REVERT: B 648 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 835 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6631 (mp) REVERT: B 838 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5781 (mm) REVERT: B 936 MET cc_start: 0.3229 (OUTLIER) cc_final: 0.2999 (mmt) REVERT: C 124 MET cc_start: 0.9035 (mmm) cc_final: 0.8707 (mmm) REVERT: C 134 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7699 (p90) REVERT: C 279 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: C 359 ARG cc_start: 0.8648 (tpt170) cc_final: 0.8405 (tpt-90) REVERT: C 396 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: C 421 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8163 (pmt) REVERT: C 460 LEU cc_start: 0.8355 (mt) cc_final: 0.8117 (mm) REVERT: C 588 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8979 (tp) REVERT: C 599 CYS cc_start: 0.7447 (t) cc_final: 0.7124 (t) REVERT: C 892 ARG cc_start: 0.8157 (mmp-170) cc_final: 0.7434 (ptm-80) REVERT: C 1005 ILE cc_start: 0.8137 (mm) cc_final: 0.7522 (pt) REVERT: D 230 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8420 (t0) REVERT: D 825 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7635 (mm) REVERT: D 930 MET cc_start: 0.8166 (pmm) cc_final: 0.7652 (pmm) REVERT: D 936 MET cc_start: 0.3783 (mtt) cc_final: 0.3473 (mtt) REVERT: E 16 TYR cc_start: 0.6987 (t80) cc_final: 0.6662 (t80) REVERT: E 47 CYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5832 (t) REVERT: E 67 PHE cc_start: 0.7709 (m-80) cc_final: 0.7387 (m-80) REVERT: E 110 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: F 47 CYS cc_start: 0.8043 (t) cc_final: 0.7602 (t) REVERT: F 49 ASN cc_start: 0.8971 (t0) cc_final: 0.8634 (t0) REVERT: F 51 TYR cc_start: 0.8577 (m-10) cc_final: 0.8293 (m-10) REVERT: F 71 LYS cc_start: 0.8715 (tptt) cc_final: 0.8486 (tptt) outliers start: 126 outliers final: 64 residues processed: 363 average time/residue: 0.1812 time to fit residues: 111.8040 Evaluate side-chains 319 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 62 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 352 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** 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 = 0.3742 r_free = 0.3742 target = 0.105720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074793 restraints weight = 92956.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073123 restraints weight = 76074.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074162 restraints weight = 74597.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074166 restraints weight = 54434.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074353 restraints weight = 47190.328| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34812 Z= 0.121 Angle : 0.521 10.726 46899 Z= 0.268 Chirality : 0.039 0.253 5003 Planarity : 0.003 0.050 5976 Dihedral : 4.768 59.288 4527 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 3.39 % Allowed : 27.02 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.14), residues: 4060 helix: 1.45 (0.11), residues: 2423 sheet: -1.29 (0.38), residues: 176 loop : -1.04 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 247 TYR 0.022 0.001 TYR D 888 PHE 0.020 0.001 PHE F 59 TRP 0.014 0.001 TRP C 143 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00278 (34812) covalent geometry : angle 0.52077 (46899) hydrogen bonds : bond 0.03374 ( 1724) hydrogen bonds : angle 3.84249 ( 4977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 243 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.9139 (tt0) cc_final: 0.8569 (tm-30) REVERT: A 744 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8420 (t80) REVERT: A 802 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7765 (tmt-80) REVERT: A 913 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5017 (pp-130) REVERT: A 936 MET cc_start: 0.3182 (OUTLIER) cc_final: 0.2101 (ptp) REVERT: A 939 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8327 (pp30) REVERT: A 1004 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6853 (t80) REVERT: B 283 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 342 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (t) REVERT: B 460 LEU cc_start: 0.9217 (pp) cc_final: 0.8749 (mm) REVERT: B 517 ARG cc_start: 0.7757 (ptt-90) cc_final: 0.7023 (ttp80) REVERT: B 647 MET cc_start: 0.8892 (pmm) cc_final: 0.8352 (pmm) REVERT: B 648 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: B 835 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6416 (mp) REVERT: B 838 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5701 (mm) REVERT: B 913 MET cc_start: 0.4768 (mpp) cc_final: 0.4144 (mpp) REVERT: B 936 MET cc_start: 0.2766 (OUTLIER) cc_final: 0.2536 (mmt) REVERT: C 124 MET cc_start: 0.9065 (mmm) cc_final: 0.8738 (mmm) REVERT: C 134 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7614 (p90) REVERT: C 279 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: C 359 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8147 (tpp-160) REVERT: C 396 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: C 421 MET cc_start: 0.8720 (pmt) cc_final: 0.8088 (pmt) REVERT: C 588 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8326 (tp) REVERT: C 599 CYS cc_start: 0.7611 (t) cc_final: 0.7228 (t) REVERT: C 738 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8671 (tptt) REVERT: C 749 LEU cc_start: 0.7041 (mp) cc_final: 0.6748 (tp) REVERT: C 1005 ILE cc_start: 0.8136 (mm) cc_final: 0.7501 (pt) REVERT: D 223 TYR cc_start: 0.7901 (t80) cc_final: 0.7669 (t80) REVERT: D 230 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8458 (t0) REVERT: D 825 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (mm) REVERT: D 930 MET cc_start: 0.7782 (pmm) cc_final: 0.7400 (pmm) REVERT: D 936 MET cc_start: 0.3458 (mtt) cc_final: 0.3251 (mtt) REVERT: E 16 TYR cc_start: 0.6717 (t80) cc_final: 0.6497 (t80) REVERT: E 110 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: F 49 ASN cc_start: 0.8984 (t0) cc_final: 0.8643 (t0) REVERT: F 51 TYR cc_start: 0.8478 (m-10) cc_final: 0.8189 (m-10) outliers start: 127 outliers final: 79 residues processed: 349 average time/residue: 0.1851 time to fit residues: 109.5018 Evaluate side-chains 325 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 227 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 296 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 364 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 357 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** 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 = 0.3742 r_free = 0.3742 target = 0.105801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067108 restraints weight = 93263.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068428 restraints weight = 62917.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068664 restraints weight = 48546.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069205 restraints weight = 42541.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069233 restraints weight = 38249.031| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34812 Z= 0.115 Angle : 0.517 10.647 46899 Z= 0.265 Chirality : 0.039 0.295 5003 Planarity : 0.003 0.051 5976 Dihedral : 4.680 58.901 4525 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 3.23 % Allowed : 27.37 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 4060 helix: 1.46 (0.11), residues: 2422 sheet: -1.29 (0.37), residues: 176 loop : -1.01 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 819 TYR 0.021 0.001 TYR D 888 PHE 0.021 0.001 PHE D 839 TRP 0.013 0.001 TRP C 143 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00262 (34812) covalent geometry : angle 0.51710 (46899) hydrogen bonds : bond 0.03311 ( 1724) hydrogen bonds : angle 3.79998 ( 4977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 240 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7742 (t80) REVERT: A 711 GLN cc_start: 0.9184 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 744 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8459 (t80) REVERT: A 802 ARG cc_start: 0.8341 (ptt90) cc_final: 0.7831 (ttt180) REVERT: A 913 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5929 (pp-130) REVERT: A 936 MET cc_start: 0.3702 (OUTLIER) cc_final: 0.2925 (ptp) REVERT: A 939 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (pp30) REVERT: A 1004 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 115 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7690 (m110) REVERT: B 283 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9009 (tt) REVERT: B 342 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 421 MET cc_start: 0.7670 (pmm) cc_final: 0.7291 (pmm) REVERT: B 460 LEU cc_start: 0.9269 (pp) cc_final: 0.8849 (mm) REVERT: B 517 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7149 (ttp80) REVERT: B 647 MET cc_start: 0.8804 (pmm) cc_final: 0.8177 (pmm) REVERT: B 648 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: B 835 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6665 (mp) REVERT: B 838 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5782 (mm) REVERT: C 124 MET cc_start: 0.9046 (mmm) cc_final: 0.8746 (mmm) REVERT: C 134 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7743 (p90) REVERT: C 359 ARG cc_start: 0.8622 (tpt170) cc_final: 0.8202 (tpp-160) REVERT: C 396 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: C 421 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8223 (pmt) REVERT: C 588 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8993 (tp) REVERT: C 599 CYS cc_start: 0.7408 (t) cc_final: 0.7078 (t) REVERT: C 738 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8725 (tptt) REVERT: C 1005 ILE cc_start: 0.8095 (mm) cc_final: 0.7395 (pt) REVERT: D 223 TYR cc_start: 0.7849 (t80) cc_final: 0.7609 (t80) REVERT: D 230 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8469 (t0) REVERT: D 543 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: D 825 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7635 (mm) REVERT: D 930 MET cc_start: 0.8155 (pmm) cc_final: 0.7712 (pmm) REVERT: E 16 TYR cc_start: 0.7025 (t80) cc_final: 0.6674 (t80) REVERT: E 47 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5902 (t) REVERT: E 67 PHE cc_start: 0.8112 (m-80) cc_final: 0.7701 (t80) REVERT: E 110 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: F 49 ASN cc_start: 0.9034 (t0) cc_final: 0.8637 (t0) REVERT: F 51 TYR cc_start: 0.8629 (m-10) cc_final: 0.8298 (m-10) outliers start: 121 outliers final: 75 residues processed: 339 average time/residue: 0.1803 time to fit residues: 104.4015 Evaluate side-chains 324 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 227 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 214 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 658 HIS ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 810 HIS D 109 GLN ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.064589 restraints weight = 93525.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065914 restraints weight = 64350.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.066447 restraints weight = 45907.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066895 restraints weight = 42029.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066884 restraints weight = 38200.530| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34812 Z= 0.205 Angle : 0.593 14.940 46899 Z= 0.305 Chirality : 0.041 0.248 5003 Planarity : 0.004 0.054 5976 Dihedral : 4.904 59.730 4525 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 3.31 % Allowed : 27.35 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.13), residues: 4060 helix: 1.28 (0.11), residues: 2434 sheet: -1.57 (0.37), residues: 178 loop : -1.10 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 760 TYR 0.021 0.002 TYR B 755 PHE 0.022 0.002 PHE D 839 TRP 0.014 0.001 TRP B 919 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00482 (34812) covalent geometry : angle 0.59290 (46899) hydrogen bonds : bond 0.04208 ( 1724) hydrogen bonds : angle 4.05700 ( 4977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 233 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8448 (t80) REVERT: A 802 ARG cc_start: 0.8292 (ptt90) cc_final: 0.7915 (tmt-80) REVERT: A 913 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5953 (pp-130) REVERT: A 936 MET cc_start: 0.4007 (OUTLIER) cc_final: 0.2116 (ptm) REVERT: A 939 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8450 (pp30) REVERT: A 1004 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 145 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6122 (tmm-80) REVERT: B 283 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9025 (tt) REVERT: B 467 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7939 (p0) REVERT: B 647 MET cc_start: 0.8727 (pmm) cc_final: 0.8103 (pmm) REVERT: B 648 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: B 835 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6759 (mp) REVERT: B 838 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5829 (mm) REVERT: C 124 MET cc_start: 0.9103 (mmm) cc_final: 0.8825 (mmm) REVERT: C 134 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7781 (p90) REVERT: C 359 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8298 (tpp-160) REVERT: C 396 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8011 (mmm) REVERT: C 421 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8115 (pmt) REVERT: C 588 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9008 (tp) REVERT: C 738 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8718 (tptt) REVERT: C 1005 ILE cc_start: 0.8183 (mm) cc_final: 0.7529 (pt) REVERT: D 223 TYR cc_start: 0.8034 (t80) cc_final: 0.7779 (t80) REVERT: D 230 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8472 (t0) REVERT: D 543 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 616 MET cc_start: 0.9230 (tpp) cc_final: 0.8912 (mmt) REVERT: D 825 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7693 (mm) REVERT: D 930 MET cc_start: 0.8115 (pmm) cc_final: 0.7458 (pmm) REVERT: E 47 CYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6001 (t) REVERT: E 67 PHE cc_start: 0.8060 (m-80) cc_final: 0.7707 (m-80) REVERT: E 110 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: F 13 ASP cc_start: 0.8537 (t70) cc_final: 0.8132 (t0) REVERT: F 49 ASN cc_start: 0.9083 (t0) cc_final: 0.8689 (t0) REVERT: F 51 TYR cc_start: 0.8643 (m-10) cc_final: 0.8278 (m-10) outliers start: 124 outliers final: 82 residues processed: 335 average time/residue: 0.1820 time to fit residues: 103.3096 Evaluate side-chains 323 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 220 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 106 optimal weight: 0.5980 chunk 343 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 323 optimal weight: 0.9990 chunk 404 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.105655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.067259 restraints weight = 92809.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068479 restraints weight = 62117.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.068350 restraints weight = 46323.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068789 restraints weight = 44573.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068957 restraints weight = 41008.090| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34812 Z= 0.105 Angle : 0.542 14.861 46899 Z= 0.274 Chirality : 0.040 0.239 5003 Planarity : 0.003 0.053 5976 Dihedral : 4.685 59.325 4523 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 2.70 % Allowed : 28.12 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.14), residues: 4060 helix: 1.40 (0.11), residues: 2424 sheet: -1.33 (0.37), residues: 176 loop : -1.01 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.024 0.001 TYR A1003 PHE 0.020 0.001 PHE D 839 TRP 0.016 0.001 TRP B 919 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00232 (34812) covalent geometry : angle 0.54245 (46899) hydrogen bonds : bond 0.03281 ( 1724) hydrogen bonds : angle 3.82641 ( 4977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 235 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8506 (t80) REVERT: A 802 ARG cc_start: 0.8300 (ptt90) cc_final: 0.7910 (tmt-80) REVERT: A 913 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5817 (pp-130) REVERT: A 936 MET cc_start: 0.4202 (OUTLIER) cc_final: 0.2214 (ptm) REVERT: A 939 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8424 (pp30) REVERT: A 1004 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6689 (t80) REVERT: B 283 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 421 MET cc_start: 0.7559 (pmm) cc_final: 0.7243 (pmm) REVERT: B 517 ARG cc_start: 0.7876 (ptt-90) cc_final: 0.7260 (ttp80) REVERT: B 519 MET cc_start: 0.8229 (mmp) cc_final: 0.8006 (mmp) REVERT: B 647 MET cc_start: 0.8792 (pmm) cc_final: 0.8148 (pmm) REVERT: B 648 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: B 835 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6752 (mp) REVERT: B 838 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5774 (mm) REVERT: B 930 MET cc_start: 0.3599 (ptt) cc_final: 0.2797 (mmt) REVERT: C 124 MET cc_start: 0.9028 (mmm) cc_final: 0.8756 (mmm) REVERT: C 134 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7682 (p90) REVERT: C 359 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8298 (tpp-160) REVERT: C 396 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7874 (mmm) REVERT: C 421 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8222 (pmt) REVERT: C 599 CYS cc_start: 0.7415 (t) cc_final: 0.7063 (t) REVERT: C 738 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8757 (tptt) REVERT: C 892 ARG cc_start: 0.8239 (mmp-170) cc_final: 0.7492 (ptm-80) REVERT: D 230 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8478 (t0) REVERT: D 543 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: D 825 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (mm) REVERT: D 930 MET cc_start: 0.8145 (pmm) cc_final: 0.7502 (pmm) REVERT: D 936 MET cc_start: 0.3681 (mtt) cc_final: 0.2783 (mtp) REVERT: D 960 LYS cc_start: 0.9344 (mttt) cc_final: 0.9104 (mttm) REVERT: E 16 TYR cc_start: 0.6892 (t80) cc_final: 0.6332 (t80) REVERT: E 47 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5964 (t) REVERT: E 67 PHE cc_start: 0.8111 (m-80) cc_final: 0.7745 (m-80) REVERT: E 110 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: F 49 ASN cc_start: 0.9037 (t0) cc_final: 0.8649 (t0) REVERT: F 51 TYR cc_start: 0.8642 (m-10) cc_final: 0.8266 (m-10) REVERT: F 71 LYS cc_start: 0.8730 (tptt) cc_final: 0.8528 (tptt) outliers start: 101 outliers final: 68 residues processed: 317 average time/residue: 0.1803 time to fit residues: 97.3762 Evaluate side-chains 311 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 225 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 240 optimal weight: 0.9990 chunk 58 optimal weight: 0.0020 chunk 408 optimal weight: 2.9990 chunk 380 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 74 optimal weight: 0.0010 chunk 375 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** E 88 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.106493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068729 restraints weight = 93130.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069427 restraints weight = 62630.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069544 restraints weight = 48076.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.070083 restraints weight = 43773.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070266 restraints weight = 39924.470| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 34812 Z= 0.098 Angle : 0.541 14.923 46899 Z= 0.271 Chirality : 0.039 0.256 5003 Planarity : 0.003 0.051 5976 Dihedral : 4.515 57.165 4523 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 2.17 % Allowed : 28.74 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 4060 helix: 1.48 (0.11), residues: 2423 sheet: -1.24 (0.38), residues: 166 loop : -1.00 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 247 TYR 0.021 0.001 TYR A 709 PHE 0.019 0.001 PHE D 839 TRP 0.016 0.001 TRP C 143 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00214 (34812) covalent geometry : angle 0.54072 (46899) hydrogen bonds : bond 0.03015 ( 1724) hydrogen bonds : angle 3.76646 ( 4977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 244 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8582 (t80) REVERT: A 802 ARG cc_start: 0.8295 (ptt90) cc_final: 0.7894 (tmt-80) REVERT: A 936 MET cc_start: 0.4211 (OUTLIER) cc_final: 0.2164 (ptm) REVERT: A 939 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (pp30) REVERT: B 283 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8937 (tt) REVERT: B 421 MET cc_start: 0.7491 (pmm) cc_final: 0.7249 (pmm) REVERT: B 460 LEU cc_start: 0.9195 (pp) cc_final: 0.8727 (mm) REVERT: B 517 ARG cc_start: 0.7861 (ptt-90) cc_final: 0.7253 (ttp80) REVERT: B 519 MET cc_start: 0.8231 (mmp) cc_final: 0.8028 (mmp) REVERT: B 647 MET cc_start: 0.8801 (pmm) cc_final: 0.8156 (pmm) REVERT: B 648 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: B 835 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 838 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5746 (mm) REVERT: B 930 MET cc_start: 0.3740 (ptt) cc_final: 0.2871 (mmt) REVERT: B 989 LYS cc_start: 0.9326 (ptmm) cc_final: 0.8993 (tptt) REVERT: C 124 MET cc_start: 0.9029 (mmm) cc_final: 0.8717 (mmm) REVERT: C 134 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7572 (p90) REVERT: C 359 ARG cc_start: 0.8663 (tpt170) cc_final: 0.8024 (tpp-160) REVERT: C 396 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: C 421 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8453 (pmm) REVERT: C 599 CYS cc_start: 0.7481 (t) cc_final: 0.7116 (t) REVERT: C 738 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8779 (tptt) REVERT: C 892 ARG cc_start: 0.8283 (mmp-170) cc_final: 0.7533 (ptm-80) REVERT: D 230 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8509 (t0) REVERT: D 616 MET cc_start: 0.9319 (tpp) cc_final: 0.9099 (mmt) REVERT: D 913 MET cc_start: 0.8086 (pmm) cc_final: 0.7798 (ppp) REVERT: D 922 LEU cc_start: 0.8502 (mm) cc_final: 0.8009 (tp) REVERT: D 930 MET cc_start: 0.8160 (pmm) cc_final: 0.7589 (pmm) REVERT: D 936 MET cc_start: 0.3820 (mtt) cc_final: 0.2902 (mtp) REVERT: D 960 LYS cc_start: 0.9335 (mttt) cc_final: 0.9084 (mttm) REVERT: E 16 TYR cc_start: 0.6911 (t80) cc_final: 0.6392 (t80) REVERT: E 47 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.5937 (t) REVERT: E 67 PHE cc_start: 0.8111 (m-80) cc_final: 0.7710 (t80) REVERT: E 110 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: F 49 ASN cc_start: 0.9018 (t0) cc_final: 0.8640 (t0) REVERT: F 51 TYR cc_start: 0.8637 (m-10) cc_final: 0.8283 (m-10) outliers start: 81 outliers final: 62 residues processed: 309 average time/residue: 0.1850 time to fit residues: 97.3400 Evaluate side-chains 308 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 232 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 311 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 364 optimal weight: 0.9980 chunk 387 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 333 optimal weight: 0.0270 chunk 290 optimal weight: 10.0000 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.105760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.066488 restraints weight = 92356.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069067 restraints weight = 61020.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.069162 restraints weight = 41955.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.069553 restraints weight = 37039.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.069641 restraints weight = 35851.963| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34812 Z= 0.112 Angle : 0.549 14.368 46899 Z= 0.273 Chirality : 0.040 0.350 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.478 57.111 4521 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 2.22 % Allowed : 28.95 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 4060 helix: 1.49 (0.11), residues: 2424 sheet: -1.23 (0.38), residues: 166 loop : -0.99 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 247 TYR 0.021 0.001 TYR D 888 PHE 0.026 0.001 PHE A 301 TRP 0.016 0.001 TRP B 919 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00256 (34812) covalent geometry : angle 0.54912 (46899) hydrogen bonds : bond 0.03167 ( 1724) hydrogen bonds : angle 3.77673 ( 4977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4893.30 seconds wall clock time: 85 minutes 56.03 seconds (5156.03 seconds total)