Starting phenix.real_space_refine on Tue Aug 26 06:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w56_37272/08_2025/8w56_37272.map" } resolution = 3.59 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 128 5.16 5 C 22036 2.51 5 N 5503 2.21 5 O 6384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s 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: 34051 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 8076 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 953} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8059 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8095 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 3 Chain: "D" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 8113 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 953} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 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 Chain: "F" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 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: 7.51, per 1000 atoms: 0.22 Number of scatterers: 34051 At special positions: 0 Unit cell: (102.85, 131.75, 273.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 6384 8.00 N 5503 7.00 C 22036 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7844 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 16 sheets defined 65.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.741A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.870A 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 70 removed outlier: 3.578A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 4.079A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.563A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.678A 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 154 through 158 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.706A pdb=" N ASN A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.511A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 4.065A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.675A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.820A 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 367 through 372 removed outlier: 3.622A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.749A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.563A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.722A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.436A 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: 3.957A pdb=" N LEU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.904A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 3.649A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 702 removed outlier: 3.649A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.130A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 removed outlier: 4.805A pdb=" N ALA A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.803A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.887A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.671A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 895 Processing helix chain 'A' and resid 912 through 922 removed outlier: 4.426A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.939A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 961 removed outlier: 3.874A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 removed outlier: 3.729A pdb=" N GLY A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 991 Processing helix chain 'A' and resid 993 through 1004 removed outlier: 3.605A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.595A 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 124 removed outlier: 3.554A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.688A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 4.589A pdb=" N LYS B 176 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.775A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 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 233 removed outlier: 3.591A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.734A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.814A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.905A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.602A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.580A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 495 Processing helix chain 'B' and resid 508 through 520 removed outlier: 4.102A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 550 removed outlier: 5.874A pdb=" N ASN B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 572 removed outlier: 3.568A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 4.224A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 593 " --> pdb=" O TYR B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.958A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.562A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.064A 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 661 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.800A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 723 removed outlier: 4.471A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.260A 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 762 Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.900A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 removed outlier: 3.950A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 840 removed outlier: 3.714A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 4.202A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 872 Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 930 through 934 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 955 through 962 removed outlier: 4.045A pdb=" N TRP B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.028A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 4.028A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.772A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.644A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.581A pdb=" N TYR C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) 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 removed outlier: 3.510A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.613A pdb=" N LYS C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.670A pdb=" N ASN C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 183 " --> pdb=" O GLY C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' 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 removed outlier: 3.552A pdb=" N SER C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.627A pdb=" N TYR C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 321 removed outlier: 3.712A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 321' Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.879A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 334' Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.861A 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: 3.700A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 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 removed outlier: 4.351A pdb=" N ASN C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 495 " --> pdb=" O GLN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 550 removed outlier: 3.683A pdb=" N ASP C 547 " --> pdb=" O PHE C 544 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN C 548 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE C 550 " --> pdb=" O ASP C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 571 removed outlier: 3.593A pdb=" N VAL C 556 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 557 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 571 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 597 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.829A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.947A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 4.209A pdb=" N LEU C 634 " --> pdb=" O ASP C 630 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 680 through 699 Processing helix chain 'C' and resid 705 through 723 removed outlier: 4.451A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) 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 743 Processing helix chain 'C' and resid 750 through 762 Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.700A pdb=" N ILE C 772 " --> pdb=" O PRO C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 removed outlier: 3.737A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 808 " --> pdb=" O TYR C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.651A pdb=" N SER C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.774A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 855 removed outlier: 4.045A pdb=" N SER C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 872 Processing helix chain 'C' and resid 878 through 896 removed outlier: 3.505A pdb=" N GLU C 882 " --> pdb=" O THR C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 928 through 933 removed outlier: 3.730A pdb=" N GLU C 931 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 944 removed outlier: 3.901A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 954 removed outlier: 3.748A pdb=" N LYS C 953 " --> pdb=" O ASP C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 962 removed outlier: 3.693A 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: 4.470A pdb=" N GLU C 982 " --> pdb=" O HIS C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1004 removed outlier: 4.094A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C1004 " --> pdb=" O LEU C1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.601A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.122A 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: 3.601A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 115 through 123 removed outlier: 3.875A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.800A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 159' Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.684A pdb=" N ASN D 182 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 183 " --> pdb=" O GLY D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 183' 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 234 removed outlier: 3.715A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 282 through 298 removed outlier: 3.526A pdb=" N TYR D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.784A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.631A pdb=" N LEU D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.701A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.757A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.873A 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 467 through 493 removed outlier: 4.108A pdb=" N TYR D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 519 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.302A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 removed outlier: 3.533A pdb=" N THR D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 removed outlier: 4.016A pdb=" N ASN D 563 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.927A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.706A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.556A 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 702 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.742A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.563A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 4.269A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 805 " --> pdb=" O SER D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.596A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 841 Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 857 removed outlier: 3.915A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.890A pdb=" N ILE D 871 " --> pdb=" O ASN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 896 removed outlier: 3.615A pdb=" N TYR D 896 " --> pdb=" O ARG D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 922 removed outlier: 4.244A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.887A pdb=" N GLU D 932 " --> pdb=" O LYS D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.705A pdb=" N ASP D 941 " --> pdb=" O ASP D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.619A pdb=" N LYS D 953 " --> pdb=" O ASP D 950 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 962 removed outlier: 3.784A pdb=" N TYR D 962 " --> pdb=" O LEU D 959 " (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 106 Processing helix chain 'F' and resid 95 through 104 removed outlier: 4.331A pdb=" N GLU F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.179A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 216 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.124A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.177A 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 341 removed outlier: 3.652A pdb=" N THR B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.310A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.123A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 247 Processing sheet with id=AA8, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.615A pdb=" N VAL C 346 " --> pdb=" O CYS C 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 573 through 575 removed outlier: 5.945A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.272A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 338 through 341 Processing sheet with id=AB3, first strand: chain 'E' and resid 65 through 68 removed outlier: 4.975A pdb=" N GLU E 38 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 33 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN E 40 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 31 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE E 44 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 10.243A pdb=" N VAL E 27 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 65 through 68 removed outlier: 10.055A pdb=" N GLU E 115 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE E 44 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'F' and resid 71 through 72 removed outlier: 4.170A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 88 1726 hydrogen bonds defined for protein. 4935 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: 6.88 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.55: 34593 1.55 - 1.87: 236 1.87 - 2.19: 0 2.19 - 2.52: 0 2.52 - 2.84: 1 Bond restraints: 34830 Sorted by residual: bond pdb=" C ARG B 747 " pdb=" N LEU B 749 " ideal model delta sigma weight residual 1.332 2.840 -1.507 1.40e-02 5.10e+03 1.16e+04 bond pdb=" C ARG B 819 " pdb=" N LEU B 820 " ideal model delta sigma weight residual 1.333 1.224 0.109 1.49e-02 4.50e+03 5.39e+01 bond pdb=" N VAL E 113 " pdb=" CA VAL E 113 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE E 20 " pdb=" CA ILE E 20 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.18e+01 bond pdb=" N ILE B 676 " pdb=" CA ILE B 676 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.20e-02 6.94e+03 1.14e+01 ... (remaining 34825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.94: 46932 10.94 - 21.87: 4 21.87 - 32.81: 0 32.81 - 43.75: 0 43.75 - 54.68: 2 Bond angle restraints: 46938 Sorted by residual: angle pdb=" O ARG B 747 " pdb=" C ARG B 747 " pdb=" N LEU B 749 " ideal model delta sigma weight residual 122.59 67.91 54.68 1.33e+00 5.65e-01 1.69e+03 angle pdb=" C ARG B 747 " pdb=" N LEU B 749 " pdb=" CA LEU B 749 " ideal model delta sigma weight residual 121.54 168.30 -46.76 1.91e+00 2.74e-01 5.99e+02 angle pdb=" N ILE E 20 " pdb=" CA ILE E 20 " pdb=" C ILE E 20 " ideal model delta sigma weight residual 113.10 107.53 5.57 9.70e-01 1.06e+00 3.29e+01 angle pdb=" N ARG A 10 " pdb=" CA ARG A 10 " pdb=" C ARG A 10 " ideal model delta sigma weight residual 113.72 106.68 7.04 1.30e+00 5.92e-01 2.93e+01 angle pdb=" N ALA B 806 " pdb=" CA ALA B 806 " pdb=" C ALA B 806 " ideal model delta sigma weight residual 112.34 106.06 6.28 1.30e+00 5.92e-01 2.34e+01 ... (remaining 46933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 17343 17.68 - 35.36: 2543 35.36 - 53.03: 686 53.03 - 70.71: 138 70.71 - 88.39: 30 Dihedral angle restraints: 20740 sinusoidal: 8545 harmonic: 12195 Sorted by residual: dihedral pdb=" CA MET A 704 " pdb=" C MET A 704 " pdb=" N ASN A 705 " pdb=" CA ASN A 705 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C ASN B 115 " pdb=" N ASN B 115 " pdb=" CA ASN B 115 " pdb=" CB ASN B 115 " ideal model delta harmonic sigma weight residual -122.60 -113.33 -9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA LEU C 767 " pdb=" C LEU C 767 " pdb=" N PRO C 768 " pdb=" CA PRO C 768 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 20737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3853 0.049 - 0.097: 861 0.097 - 0.146: 234 0.146 - 0.194: 43 0.194 - 0.243: 20 Chirality restraints: 5011 Sorted by residual: chirality pdb=" CA ILE E 53 " pdb=" N ILE E 53 " pdb=" C ILE E 53 " pdb=" CB ILE E 53 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE A 246 " pdb=" N ILE A 246 " pdb=" C ILE A 246 " pdb=" CB ILE A 246 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN B 115 " pdb=" N ASN B 115 " pdb=" C ASN B 115 " pdb=" CB ASN B 115 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 5008 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 747 " 0.205 2.00e-02 2.50e+03 2.91e-01 8.45e+02 pdb=" C ARG B 747 " -0.480 2.00e-02 2.50e+03 pdb=" O ARG B 747 " 0.255 2.00e-02 2.50e+03 pdb=" N LEU B 749 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 777 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ASP D 777 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP D 777 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE D 778 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 490 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C THR A 490 " 0.054 2.00e-02 2.50e+03 pdb=" O THR A 490 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 491 " -0.018 2.00e-02 2.50e+03 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 755 2.69 - 3.24: 34282 3.24 - 3.80: 53415 3.80 - 4.35: 68015 4.35 - 4.90: 110117 Nonbonded interactions: 266584 Sorted by model distance: nonbonded pdb=" OD2 ASP A 632 " pdb=" OG SER B 991 " model vdw 2.139 3.040 nonbonded pdb=" OG SER D 579 " pdb=" OD1 ASP D 581 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR D 589 " pdb=" OD1 ASP D 651 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR A 828 " pdb=" OD1 ASP A 830 " model vdw 2.188 3.040 nonbonded pdb=" N GLU C 284 " pdb=" OE1 GLU C 284 " model vdw 2.189 3.120 ... (remaining 266579 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 464 or (resid 465 and \ (name N or name CA or name C or name O or name CB )) or resid 466 through 504 or \ (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 6 through 637 or (resid 638 through 639 and (name N or name CA or name C or name \ O or name CB )) or resid 640 through 747 or resid 749 through 818 or (resid 819 \ and (name N or name CA or name C or name O or name CB )) or resid 820 through 8 \ 96 or resid 910 through 984 or (resid 985 and (name N or name CA or name C or na \ me O or name CB )) or resid 986 through 1005)) selection = (chain 'B' and (resid 22 through 497 or (resid 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 through 501 or (resid 502 and (name N o \ r name CA or name C or name O or name CB )) or resid 503 through 563 or (resid 5 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 565 or (res \ id 566 and (name N or name CA or name C or name O or name CB )) or (resid 578 an \ d (name N or name CA or name C or name O or name CB )) or resid 579 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 resid 789 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 97 \ 4 or resid 976 through 1000 or (resid 1001 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1002 through 1005)) selection = (chain 'C' and (resid 22 through 464 or (resid 465 and (name N or name CA or nam \ e C or name O or name CB )) or resid 466 through 497 or (resid 498 and (name N o \ r name CA or name C or name O or name CB )) or resid 499 through 501 or (resid 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 503 through \ 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or r \ esid 506 through 563 or (resid 564 and (name N or name CA or name C or name O or \ name CB )) or resid 565 or (resid 566 and (name N or name CA or name C or name \ O or name CB )) or (resid 578 and (name N or name CA or name C or name O or name \ CB )) or resid 579 through 637 or (resid 638 through 639 and (name N or name CA \ or name C or name O or name CB )) or resid 640 through 676 or (resid 677 and (n \ ame N or name CA or name C or name O or name CB )) or resid 678 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 resid 789 through 818 or (resid 819 and (name N or name CA or nam \ e C or name O or name CB )) or resid 820 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 91 \ 3 through 974 or resid 976 through 984 or (resid 985 and (name N or name CA or n \ ame C or name O or name CB )) or resid 986 through 1000 or (resid 1001 and (name \ N or name CA or name C or name O or name CB )) or resid 1002 through 1005)) selection = (chain 'D' and (resid 22 through 142 or resid 145 through 464 or (resid 465 and \ (name N or name CA or name C or name O or name CB )) or resid 466 through 497 or \ (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 9 through 501 or (resid 502 and (name N or name CA or name C or name O or name C \ B )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C or \ name O or name CB )) or resid 506 through 563 or (resid 564 and (name N or name \ CA or name C or name O or name CB )) or resid 565 or (resid 566 through 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 637 or \ (resid 638 through 639 and (name N or name CA or name C or name O or name CB )) \ or resid 640 through 676 or (resid 677 and (name N or name CA or name C or name \ O or name CB )) or resid 678 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 8 \ 18 or (resid 819 and (name N or name CA or name C or name O or name CB )) or res \ id 820 through 896 or resid 910 through 984 or (resid 985 and (name N or name CA \ or name C or name O or name CB )) or resid 986 through 1000 or (resid 1001 and \ (name N or name CA or name C or name O or name CB )) or resid 1002 through 1005) \ ) } ncs_group { reference = (chain 'E' and (resid 10 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 120)) selection = (chain 'F' and (resid 10 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 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: 11.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.680 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.507 34830 Z= 0.643 Angle : 0.784 54.681 46938 Z= 0.487 Chirality : 0.047 0.243 5011 Planarity : 0.006 0.291 5988 Dihedral : 17.836 88.388 12896 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.49 % Favored : 95.24 % Rotamer: Outliers : 2.92 % Allowed : 26.91 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.13), residues: 4072 helix: 0.94 (0.11), residues: 2334 sheet: -0.94 (0.42), residues: 150 loop : -1.12 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 819 TYR 0.016 0.001 TYR B 888 PHE 0.028 0.001 PHE D 638 TRP 0.018 0.001 TRP A 958 HIS 0.012 0.001 HIS A 810 Details of bonding type rmsd covalent geometry : bond 0.00909 (34830) covalent geometry : angle 0.78378 (46938) hydrogen bonds : bond 0.14322 ( 1722) hydrogen bonds : angle 5.72864 ( 4935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 246 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8247 (tpp) cc_final: 0.7826 (tpp) REVERT: A 678 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 936 MET cc_start: 0.3491 (ptm) cc_final: -0.0376 (mmt) REVERT: B 276 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8409 (p0) REVERT: B 279 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7819 (tp30) REVERT: B 547 ASP cc_start: 0.8557 (t0) cc_final: 0.8176 (t0) REVERT: B 929 LYS cc_start: 0.8517 (mttm) cc_final: 0.8277 (tmtt) REVERT: B 960 LYS cc_start: 0.7362 (mmpt) cc_final: 0.7159 (mmtp) REVERT: D 812 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4725 (tm-30) REVERT: E 63 SER cc_start: 0.4438 (m) cc_final: 0.4098 (p) REVERT: E 110 PHE cc_start: 0.7393 (m-80) cc_final: 0.7029 (m-80) REVERT: F 67 PHE cc_start: 0.8551 (m-80) cc_final: 0.7980 (m-10) outliers start: 109 outliers final: 69 residues processed: 347 average time/residue: 0.1778 time to fit residues: 104.0490 Evaluate side-chains 293 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 753 LYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 1002 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.0770 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 109 GLN A 125 ASN A 477 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN B 182 ASN B 297 GLN B 339 HIS B 404 ASN B 457 ASN B 493 ASN B 549 GLN B 789 GLN B 978 HIS C 89 GLN C 93 ASN C 297 GLN C 382 ASN C 477 ASN C 666 ASN C 681 GLN C 782 GLN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN D 192 ASN D 211 HIS D 332 HIS D 339 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN D 477 ASN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN D 609 HIS D 789 GLN D 810 HIS ** D 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.112353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071561 restraints weight = 94463.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073712 restraints weight = 50740.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075063 restraints weight = 35245.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075857 restraints weight = 28472.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076378 restraints weight = 25214.770| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34830 Z= 0.131 Angle : 0.533 8.298 46938 Z= 0.279 Chirality : 0.040 0.290 5011 Planarity : 0.003 0.053 5988 Dihedral : 5.807 58.102 4632 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 3.40 % Allowed : 24.63 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.13), residues: 4074 helix: 1.14 (0.11), residues: 2416 sheet: -1.43 (0.38), residues: 185 loop : -1.09 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 747 TYR 0.019 0.001 TYR E 43 PHE 0.031 0.001 PHE A 839 TRP 0.018 0.001 TRP D 958 HIS 0.005 0.001 HIS B 979 Details of bonding type rmsd covalent geometry : bond 0.00295 (34830) covalent geometry : angle 0.53326 (46938) hydrogen bonds : bond 0.03712 ( 1722) hydrogen bonds : angle 4.26457 ( 4935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 245 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7493 (p0) REVERT: A 190 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 319 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9351 (mm) REVERT: A 421 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7163 (tpp) REVERT: A 441 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 778 PHE cc_start: 0.7270 (t80) cc_final: 0.6511 (t80) REVERT: A 936 MET cc_start: 0.3094 (ptm) cc_final: -0.0827 (mmt) REVERT: B 276 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7996 (p0) REVERT: B 378 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: B 425 ILE cc_start: 0.7742 (pp) cc_final: 0.7440 (pt) REVERT: B 647 MET cc_start: 0.8653 (mmm) cc_final: 0.7744 (tpt) REVERT: B 923 GLU cc_start: 0.4400 (mp0) cc_final: 0.3422 (pm20) REVERT: B 929 LYS cc_start: 0.8505 (mttm) cc_final: 0.8281 (tmtt) REVERT: C 115 ASN cc_start: 0.8383 (t0) cc_final: 0.8087 (t0) REVERT: C 963 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8016 (p0) REVERT: D 504 TYR cc_start: 0.7875 (m-10) cc_final: 0.7568 (m-10) REVERT: D 812 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.4886 (tm-30) REVERT: D 839 PHE cc_start: 0.8610 (m-10) cc_final: 0.8371 (m-10) REVERT: D 936 MET cc_start: 0.2779 (OUTLIER) cc_final: 0.0903 (tpt) REVERT: F 67 PHE cc_start: 0.8734 (m-80) cc_final: 0.8310 (m-10) outliers start: 127 outliers final: 61 residues processed: 359 average time/residue: 0.1834 time to fit residues: 111.3245 Evaluate side-chains 298 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 753 LYS Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1002 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 377 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 191 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN C 666 ASN ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.112570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072338 restraints weight = 93930.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075623 restraints weight = 53049.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075835 restraints weight = 31238.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076154 restraints weight = 27947.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076289 restraints weight = 27053.442| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34830 Z= 0.108 Angle : 0.492 8.886 46938 Z= 0.257 Chirality : 0.039 0.295 5011 Planarity : 0.003 0.051 5988 Dihedral : 5.138 58.410 4565 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 2.81 % Allowed : 24.82 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 4074 helix: 1.30 (0.11), residues: 2414 sheet: -1.42 (0.38), residues: 185 loop : -1.03 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 760 TYR 0.015 0.001 TYR B 804 PHE 0.019 0.001 PHE E 48 TRP 0.012 0.001 TRP A 958 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00239 (34830) covalent geometry : angle 0.49214 (46938) hydrogen bonds : bond 0.03367 ( 1722) hydrogen bonds : angle 4.06033 ( 4935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 248 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7643 (p0) REVERT: A 190 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8183 (t80) REVERT: A 414 TYR cc_start: 0.8339 (t80) cc_final: 0.8124 (t80) REVERT: A 421 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7211 (tpp) REVERT: A 441 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 778 PHE cc_start: 0.7343 (t80) cc_final: 0.7031 (t80) REVERT: A 866 MET cc_start: -0.1632 (ptp) cc_final: -0.1868 (mtt) REVERT: A 936 MET cc_start: 0.2769 (ptm) cc_final: -0.1225 (mmt) REVERT: B 134 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8419 (p90) REVERT: B 348 ARG cc_start: 0.8911 (tmm-80) cc_final: 0.8595 (ptm-80) REVERT: B 421 MET cc_start: 0.8676 (tpp) cc_final: 0.8398 (tpp) REVERT: B 425 ILE cc_start: 0.7704 (pp) cc_final: 0.7380 (pt) REVERT: B 647 MET cc_start: 0.8713 (mmm) cc_final: 0.7492 (tpp) REVERT: B 708 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5276 (m-10) REVERT: B 929 LYS cc_start: 0.8501 (mttm) cc_final: 0.8270 (tmtt) REVERT: C 115 ASN cc_start: 0.8332 (t0) cc_final: 0.8072 (t0) REVERT: C 811 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6784 (t80) REVERT: C 963 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7948 (p0) REVERT: D 504 TYR cc_start: 0.8033 (m-10) cc_final: 0.7707 (m-10) REVERT: D 839 PHE cc_start: 0.8729 (m-10) cc_final: 0.8448 (m-10) REVERT: D 930 MET cc_start: 0.7985 (pmm) cc_final: 0.7715 (pmm) REVERT: D 936 MET cc_start: 0.2561 (OUTLIER) cc_final: 0.0674 (tpt) REVERT: D 940 TYR cc_start: 0.8198 (t80) cc_final: 0.7950 (t80) REVERT: F 67 PHE cc_start: 0.8763 (m-80) cc_final: 0.8405 (m-10) REVERT: F 72 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7886 (mmm160) outliers start: 105 outliers final: 56 residues processed: 334 average time/residue: 0.1763 time to fit residues: 98.0775 Evaluate side-chains 296 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 811 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1002 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 362 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 408 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 299 ASN A 461 ASN A 491 GLN A 493 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B1002 ASN C 658 HIS C 848 ASN ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 125 ASN D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071027 restraints weight = 92534.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070877 restraints weight = 59067.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071396 restraints weight = 42928.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071444 restraints weight = 40457.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071921 restraints weight = 35352.867| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34830 Z= 0.269 Angle : 0.602 8.729 46938 Z= 0.317 Chirality : 0.043 0.273 5011 Planarity : 0.004 0.048 5988 Dihedral : 5.299 57.409 4553 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 3.69 % Allowed : 24.79 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.13), residues: 4074 helix: 1.09 (0.11), residues: 2416 sheet: -1.72 (0.37), residues: 185 loop : -1.05 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 10 TYR 0.021 0.002 TYR C 436 PHE 0.023 0.002 PHE A 839 TRP 0.012 0.002 TRP A 958 HIS 0.007 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00632 (34830) covalent geometry : angle 0.60162 (46938) hydrogen bonds : bond 0.04408 ( 1722) hydrogen bonds : angle 4.37862 ( 4935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 234 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8375 (t80) REVERT: A 319 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9389 (mm) REVERT: A 421 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7299 (tpp) REVERT: A 441 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8423 (t80) REVERT: A 647 MET cc_start: 0.7651 (pp-130) cc_final: 0.6907 (pp-130) REVERT: A 766 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5815 (tm-30) REVERT: A 778 PHE cc_start: 0.7356 (t80) cc_final: 0.7052 (t80) REVERT: A 866 MET cc_start: -0.1470 (ptp) cc_final: -0.1729 (mtt) REVERT: A 936 MET cc_start: 0.2736 (ptm) cc_final: -0.1446 (mmt) REVERT: B 647 MET cc_start: 0.8648 (mmm) cc_final: 0.7555 (tpp) REVERT: B 708 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5681 (m-10) REVERT: B 744 PHE cc_start: 0.7380 (t80) cc_final: 0.7159 (t80) REVERT: B 929 LYS cc_start: 0.8504 (mttm) cc_final: 0.8262 (tmtt) REVERT: B 976 MET cc_start: 0.1876 (pmm) cc_final: 0.0966 (ppp) REVERT: C 179 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (mtmt) REVERT: C 720 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9448 (mm) REVERT: C 722 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8793 (t80) REVERT: C 877 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5837 (p90) REVERT: C 930 MET cc_start: 0.7184 (mmp) cc_final: 0.6943 (mmm) REVERT: C 963 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8056 (p0) REVERT: D 502 ARG cc_start: 0.7216 (tpt170) cc_final: 0.6889 (tpm170) REVERT: D 504 TYR cc_start: 0.8179 (m-10) cc_final: 0.7771 (m-10) REVERT: D 812 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5074 (tm-30) REVERT: D 839 PHE cc_start: 0.8676 (m-10) cc_final: 0.8380 (m-10) REVERT: D 930 MET cc_start: 0.8245 (pmm) cc_final: 0.7862 (pmm) REVERT: D 936 MET cc_start: 0.2562 (OUTLIER) cc_final: 0.0587 (tpt) REVERT: D 940 TYR cc_start: 0.8291 (t80) cc_final: 0.8076 (t80) REVERT: F 40 ASN cc_start: 0.8393 (m-40) cc_final: 0.7793 (t0) REVERT: F 69 GLU cc_start: 0.8813 (mp0) cc_final: 0.8472 (mp0) REVERT: F 72 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8147 (mmm160) REVERT: F 101 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.8105 (p-80) outliers start: 138 outliers final: 85 residues processed: 355 average time/residue: 0.2108 time to fit residues: 127.2544 Evaluate side-chains 317 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 218 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 811 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 42 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 281 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 372 optimal weight: 6.9990 chunk 390 optimal weight: 0.0870 chunk 284 optimal weight: 0.9990 chunk 290 optimal weight: 0.0370 chunk 190 optimal weight: 9.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 926 ASN ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.111808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071402 restraints weight = 93908.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074778 restraints weight = 52846.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074953 restraints weight = 30984.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075453 restraints weight = 27424.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075542 restraints weight = 26050.417| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34830 Z= 0.095 Angle : 0.494 10.906 46938 Z= 0.257 Chirality : 0.039 0.259 5011 Planarity : 0.003 0.052 5988 Dihedral : 4.798 57.972 4542 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 2.75 % Allowed : 25.70 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.14), residues: 4074 helix: 1.26 (0.11), residues: 2422 sheet: -1.57 (0.37), residues: 185 loop : -0.98 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 870 TYR 0.016 0.001 TYR E 16 PHE 0.026 0.001 PHE D 533 TRP 0.028 0.001 TRP D 919 HIS 0.006 0.001 HIS C 786 Details of bonding type rmsd covalent geometry : bond 0.00203 (34830) covalent geometry : angle 0.49424 (46938) hydrogen bonds : bond 0.03233 ( 1722) hydrogen bonds : angle 4.01673 ( 4935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 253 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 421 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7237 (tpp) REVERT: A 441 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8423 (t80) REVERT: A 586 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 766 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: A 778 PHE cc_start: 0.7312 (t80) cc_final: 0.7002 (t80) REVERT: A 866 MET cc_start: -0.1515 (ptp) cc_final: -0.1836 (mtt) REVERT: A 936 MET cc_start: 0.2714 (ptm) cc_final: -0.1462 (tpp) REVERT: B 348 ARG cc_start: 0.8918 (tmm-80) cc_final: 0.8651 (ptm-80) REVERT: B 647 MET cc_start: 0.8612 (mmm) cc_final: 0.7548 (tpp) REVERT: B 708 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5578 (m-10) REVERT: B 744 PHE cc_start: 0.7301 (t80) cc_final: 0.7012 (t80) REVERT: B 929 LYS cc_start: 0.8502 (mttm) cc_final: 0.8268 (tmtt) REVERT: C 722 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8630 (t80) REVERT: C 866 MET cc_start: 0.7591 (pp-130) cc_final: 0.7326 (ptt) REVERT: C 877 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5903 (p90) REVERT: C 963 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8020 (p0) REVERT: D 504 TYR cc_start: 0.7982 (m-10) cc_final: 0.7679 (m-10) REVERT: D 812 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4956 (tm-30) REVERT: D 930 MET cc_start: 0.8048 (pmm) cc_final: 0.7724 (pmm) REVERT: D 936 MET cc_start: 0.2388 (OUTLIER) cc_final: 0.0391 (tpt) REVERT: E 67 PHE cc_start: 0.8689 (t80) cc_final: 0.8347 (t80) REVERT: E 112 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7714 (mt) REVERT: F 72 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7977 (mmm160) REVERT: F 101 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.8087 (p-80) outliers start: 103 outliers final: 57 residues processed: 341 average time/residue: 0.2167 time to fit residues: 124.5719 Evaluate side-chains 296 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 811 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 61 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 221 optimal weight: 0.0670 chunk 391 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.109863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069756 restraints weight = 91105.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072874 restraints weight = 52891.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073116 restraints weight = 30916.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073523 restraints weight = 27354.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073683 restraints weight = 26718.363| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34830 Z= 0.162 Angle : 0.530 12.454 46938 Z= 0.274 Chirality : 0.040 0.250 5011 Planarity : 0.003 0.049 5988 Dihedral : 4.730 56.536 4540 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 2.97 % Allowed : 26.16 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 4074 helix: 1.30 (0.11), residues: 2410 sheet: -1.62 (0.37), residues: 185 loop : -0.98 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 593 TYR 0.020 0.001 TYR D 888 PHE 0.027 0.001 PHE A 839 TRP 0.021 0.001 TRP D 919 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00380 (34830) covalent geometry : angle 0.52965 (46938) hydrogen bonds : bond 0.03586 ( 1722) hydrogen bonds : angle 4.07347 ( 4935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 229 time to evaluate : 1.375 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 190 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 319 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9373 (mm) REVERT: A 421 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7310 (tpp) REVERT: A 441 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8476 (t80) REVERT: A 586 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8712 (mp) REVERT: A 766 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5638 (tm-30) REVERT: A 778 PHE cc_start: 0.7375 (t80) cc_final: 0.7042 (t80) REVERT: A 866 MET cc_start: -0.1215 (ptp) cc_final: -0.1580 (mtt) REVERT: A 936 MET cc_start: 0.2750 (ptm) cc_final: -0.1403 (tpp) REVERT: B 348 ARG cc_start: 0.8902 (tmm-80) cc_final: 0.8624 (ptm-80) REVERT: B 647 MET cc_start: 0.8543 (mmm) cc_final: 0.7594 (tpp) REVERT: B 708 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5647 (m-10) REVERT: B 929 LYS cc_start: 0.8476 (mttm) cc_final: 0.8252 (tmtt) REVERT: B 976 MET cc_start: 0.1917 (pmm) cc_final: 0.0776 (ppp) REVERT: C 722 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8716 (t80) REVERT: C 866 MET cc_start: 0.7532 (pp-130) cc_final: 0.7311 (ptt) REVERT: C 877 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.6015 (p90) REVERT: C 963 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8027 (p0) REVERT: D 502 ARG cc_start: 0.6759 (tpt170) cc_final: 0.6419 (tpm170) REVERT: D 812 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5004 (tm-30) REVERT: D 930 MET cc_start: 0.8158 (pmm) cc_final: 0.7851 (pmm) REVERT: D 936 MET cc_start: 0.2335 (OUTLIER) cc_final: 0.0267 (tpt) REVERT: E 112 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7762 (mt) REVERT: F 40 ASN cc_start: 0.8304 (m-40) cc_final: 0.7714 (t0) REVERT: F 69 GLU cc_start: 0.8714 (mp0) cc_final: 0.8350 (mp0) outliers start: 111 outliers final: 76 residues processed: 325 average time/residue: 0.2043 time to fit residues: 113.7374 Evaluate side-chains 308 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 219 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 810 HIS Chi-restraints excluded: chain C residue 811 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 915 THR Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 390 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 364 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 374 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS C 765 ASN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067759 restraints weight = 92010.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069706 restraints weight = 50527.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070996 restraints weight = 35279.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071743 restraints weight = 28635.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072200 restraints weight = 25397.654| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34830 Z= 0.226 Angle : 0.592 11.514 46938 Z= 0.306 Chirality : 0.042 0.275 5011 Planarity : 0.003 0.058 5988 Dihedral : 4.873 55.318 4536 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.94 % Rotamer: Outliers : 3.69 % Allowed : 25.46 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.13), residues: 4074 helix: 1.12 (0.11), residues: 2428 sheet: -1.75 (0.35), residues: 195 loop : -1.08 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 72 TYR 0.018 0.002 TYR C 436 PHE 0.027 0.002 PHE D 533 TRP 0.018 0.001 TRP D 919 HIS 0.011 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00530 (34830) covalent geometry : angle 0.59242 (46938) hydrogen bonds : bond 0.04122 ( 1722) hydrogen bonds : angle 4.27458 ( 4935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 233 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8219 (p90) REVERT: A 190 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8331 (t80) REVERT: A 319 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9400 (mm) REVERT: A 421 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7164 (tpp) REVERT: A 441 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8342 (t80) REVERT: A 586 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 636 PHE cc_start: 0.7247 (m-10) cc_final: 0.6755 (m-10) REVERT: A 766 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5515 (tm-30) REVERT: A 778 PHE cc_start: 0.7425 (t80) cc_final: 0.7122 (t80) REVERT: A 866 MET cc_start: -0.1238 (ptp) cc_final: -0.1535 (mtt) REVERT: A 936 MET cc_start: 0.3034 (ptm) cc_final: -0.1464 (mmt) REVERT: B 348 ARG cc_start: 0.8864 (tmm-80) cc_final: 0.8607 (ptm-80) REVERT: B 504 TYR cc_start: 0.6894 (m-10) cc_final: 0.6645 (m-10) REVERT: B 511 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6845 (t80) REVERT: B 560 GLU cc_start: 0.8099 (mp0) cc_final: 0.7865 (mp0) REVERT: B 647 MET cc_start: 0.8394 (mmm) cc_final: 0.7636 (tpp) REVERT: B 708 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.5803 (m-10) REVERT: B 929 LYS cc_start: 0.8491 (mttm) cc_final: 0.8281 (tmtt) REVERT: B 976 MET cc_start: 0.1893 (pmm) cc_final: 0.0844 (ppp) REVERT: B 995 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8298 (ttp-110) REVERT: C 179 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8894 (mtmt) REVERT: C 722 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8810 (t80) REVERT: C 920 TYR cc_start: 0.8116 (t80) cc_final: 0.7858 (t80) REVERT: C 930 MET cc_start: 0.7385 (mmp) cc_final: 0.7086 (mmm) REVERT: C 963 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8188 (p0) REVERT: D 190 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7839 (t80) REVERT: D 582 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8824 (mt) REVERT: D 812 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5152 (tm-30) REVERT: D 930 MET cc_start: 0.8218 (pmm) cc_final: 0.7859 (pmm) REVERT: D 936 MET cc_start: 0.2446 (OUTLIER) cc_final: 0.0239 (tpt) REVERT: E 112 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (mt) REVERT: F 40 ASN cc_start: 0.8164 (m-40) cc_final: 0.7695 (t0) REVERT: F 69 GLU cc_start: 0.8636 (mp0) cc_final: 0.8323 (mp0) outliers start: 138 outliers final: 89 residues processed: 355 average time/residue: 0.2071 time to fit residues: 124.7985 Evaluate side-chains 321 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 874 ILE Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 705 ASN Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 218 optimal weight: 0.5980 chunk 393 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 197 optimal weight: 0.2980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.110556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.070308 restraints weight = 91340.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072410 restraints weight = 48666.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073715 restraints weight = 33599.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074545 restraints weight = 26989.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074964 restraints weight = 23735.216| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34830 Z= 0.106 Angle : 0.530 11.722 46938 Z= 0.269 Chirality : 0.039 0.234 5011 Planarity : 0.003 0.051 5988 Dihedral : 4.523 56.468 4532 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Rotamer: Outliers : 2.59 % Allowed : 26.42 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 4074 helix: 1.26 (0.11), residues: 2430 sheet: -1.65 (0.35), residues: 199 loop : -0.97 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.017 0.001 TYR D 888 PHE 0.027 0.001 PHE A 839 TRP 0.014 0.001 TRP A 958 HIS 0.013 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00237 (34830) covalent geometry : angle 0.53041 (46938) hydrogen bonds : bond 0.03199 ( 1722) hydrogen bonds : angle 3.99344 ( 4935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 237 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8180 (p90) REVERT: A 190 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 421 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7076 (tpp) REVERT: A 441 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 586 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 766 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5474 (tm-30) REVERT: A 778 PHE cc_start: 0.7433 (t80) cc_final: 0.7116 (t80) REVERT: A 866 MET cc_start: -0.1270 (ptp) cc_final: -0.1588 (mtt) REVERT: A 936 MET cc_start: 0.3156 (ptm) cc_final: -0.1296 (mmt) REVERT: B 134 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8511 (p90) REVERT: B 348 ARG cc_start: 0.8807 (tmm-80) cc_final: 0.8602 (ptm-80) REVERT: B 511 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6764 (t80) REVERT: B 647 MET cc_start: 0.8368 (mmm) cc_final: 0.7622 (tpp) REVERT: B 708 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5540 (m-10) REVERT: B 800 TYR cc_start: 0.6890 (m-10) cc_final: 0.6666 (m-10) REVERT: B 803 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7580 (p0) REVERT: B 929 LYS cc_start: 0.8497 (mttm) cc_final: 0.8282 (tmtt) REVERT: B 976 MET cc_start: 0.1778 (pmm) cc_final: 0.0699 (ppp) REVERT: C 722 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8791 (t80) REVERT: C 963 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8166 (p0) REVERT: D 582 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8456 (mt) REVERT: D 771 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7895 (pt) REVERT: D 812 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4964 (tm-30) REVERT: D 930 MET cc_start: 0.8074 (pmm) cc_final: 0.7788 (pmm) REVERT: D 936 MET cc_start: 0.2200 (OUTLIER) cc_final: 0.0040 (tpt) REVERT: E 112 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7890 (mt) REVERT: F 40 ASN cc_start: 0.8107 (m-40) cc_final: 0.7621 (t0) REVERT: F 69 GLU cc_start: 0.8602 (mp0) cc_final: 0.8280 (mp0) outliers start: 97 outliers final: 59 residues processed: 319 average time/residue: 0.2003 time to fit residues: 109.8239 Evaluate side-chains 299 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 223 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 705 ASN Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 771 ILE Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 6.9990 chunk 200 optimal weight: 0.0870 chunk 152 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 131 optimal weight: 0.0010 chunk 322 optimal weight: 0.9980 chunk 409 optimal weight: 0.0170 chunk 375 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 overall best weight: 0.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN C 881 HIS ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070708 restraints weight = 91057.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072763 restraints weight = 48504.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074074 restraints weight = 33477.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074799 restraints weight = 26857.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075338 restraints weight = 23870.486| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34830 Z= 0.106 Angle : 0.530 11.231 46938 Z= 0.268 Chirality : 0.039 0.230 5011 Planarity : 0.003 0.050 5988 Dihedral : 4.387 58.610 4529 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 2.38 % Allowed : 26.58 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.14), residues: 4074 helix: 1.30 (0.11), residues: 2440 sheet: -1.58 (0.35), residues: 195 loop : -0.97 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 447 TYR 0.027 0.001 TYR A 743 PHE 0.022 0.001 PHE D 533 TRP 0.013 0.001 TRP D 919 HIS 0.008 0.001 HIS C 975 Details of bonding type rmsd covalent geometry : bond 0.00240 (34830) covalent geometry : angle 0.53034 (46938) hydrogen bonds : bond 0.03184 ( 1722) hydrogen bonds : angle 3.93915 ( 4935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 242 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8165 (p90) REVERT: A 190 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8223 (t80) REVERT: A 421 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.6969 (tpp) REVERT: A 441 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 586 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8687 (mp) REVERT: A 766 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5404 (tm-30) REVERT: A 778 PHE cc_start: 0.7384 (t80) cc_final: 0.7080 (t80) REVERT: A 866 MET cc_start: -0.1374 (ptp) cc_final: -0.1653 (mtt) REVERT: A 936 MET cc_start: 0.3189 (ptm) cc_final: -0.1247 (mmt) REVERT: B 348 ARG cc_start: 0.8804 (tmm-80) cc_final: 0.8597 (ptm-80) REVERT: B 445 LEU cc_start: 0.8628 (mt) cc_final: 0.8420 (tp) REVERT: B 511 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6702 (t80) REVERT: B 560 GLU cc_start: 0.7984 (mp0) cc_final: 0.7783 (mp0) REVERT: B 647 MET cc_start: 0.8347 (mmm) cc_final: 0.7639 (tpp) REVERT: B 708 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5542 (m-10) REVERT: B 800 TYR cc_start: 0.6894 (m-10) cc_final: 0.6671 (m-10) REVERT: B 803 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7585 (p0) REVERT: B 929 LYS cc_start: 0.8522 (mttm) cc_final: 0.8200 (pttp) REVERT: B 976 MET cc_start: 0.1801 (pmm) cc_final: 0.0750 (ppp) REVERT: C 712 PHE cc_start: 0.9043 (t80) cc_final: 0.8573 (t80) REVERT: C 722 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8750 (t80) REVERT: C 963 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8129 (p0) REVERT: D 812 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.4959 (tt0) REVERT: D 930 MET cc_start: 0.8077 (pmm) cc_final: 0.7819 (pmm) REVERT: D 936 MET cc_start: 0.2174 (OUTLIER) cc_final: 0.0029 (tpt) REVERT: E 112 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7918 (mt) outliers start: 89 outliers final: 62 residues processed: 320 average time/residue: 0.1849 time to fit residues: 101.3918 Evaluate side-chains 302 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 226 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 705 ASN Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1002 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.0040 chunk 332 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 396 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN C 503 HIS ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.109371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068810 restraints weight = 91777.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070827 restraints weight = 49599.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072094 restraints weight = 34471.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072581 restraints weight = 27876.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073267 restraints weight = 25158.744| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34830 Z= 0.177 Angle : 0.573 12.255 46938 Z= 0.291 Chirality : 0.041 0.265 5011 Planarity : 0.003 0.049 5988 Dihedral : 4.396 56.959 4525 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.41 % Allowed : 26.66 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.14), residues: 4074 helix: 1.25 (0.11), residues: 2437 sheet: -1.61 (0.35), residues: 195 loop : -0.99 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 348 TYR 0.038 0.001 TYR C 888 PHE 0.038 0.001 PHE A 839 TRP 0.014 0.001 TRP D 919 HIS 0.009 0.001 HIS C 975 Details of bonding type rmsd covalent geometry : bond 0.00416 (34830) covalent geometry : angle 0.57282 (46938) hydrogen bonds : bond 0.03665 ( 1722) hydrogen bonds : angle 4.05740 ( 4935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 229 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8272 (t80) REVERT: A 319 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9387 (mm) REVERT: A 421 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7021 (tpp) REVERT: A 441 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8325 (t80) REVERT: A 586 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8734 (mp) REVERT: A 766 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5512 (tm-30) REVERT: A 778 PHE cc_start: 0.7371 (t80) cc_final: 0.7057 (t80) REVERT: A 866 MET cc_start: -0.1157 (ptp) cc_final: -0.1424 (mtt) REVERT: A 936 MET cc_start: 0.3075 (ptm) cc_final: -0.1436 (mmt) REVERT: B 348 ARG cc_start: 0.8836 (tmm-80) cc_final: 0.8619 (ptm-80) REVERT: B 421 MET cc_start: 0.8665 (tpt) cc_final: 0.8436 (tpt) REVERT: B 511 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6705 (t80) REVERT: B 560 GLU cc_start: 0.7990 (mp0) cc_final: 0.7760 (mp0) REVERT: B 614 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8215 (m110) REVERT: B 647 MET cc_start: 0.8329 (mmm) cc_final: 0.7689 (tpp) REVERT: B 708 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: B 929 LYS cc_start: 0.8499 (mttm) cc_final: 0.8194 (pttp) REVERT: B 976 MET cc_start: 0.1758 (pmm) cc_final: 0.0794 (ppp) REVERT: C 712 PHE cc_start: 0.9065 (t80) cc_final: 0.8565 (t80) REVERT: C 722 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8745 (t80) REVERT: C 862 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.6805 (mm) REVERT: C 963 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8173 (p0) REVERT: D 227 MET cc_start: 0.7435 (ttm) cc_final: 0.7216 (ttt) REVERT: D 812 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5046 (tt0) REVERT: D 930 MET cc_start: 0.8141 (pmm) cc_final: 0.7829 (pmm) REVERT: E 12 HIS cc_start: 0.8826 (p-80) cc_final: 0.8616 (p90) REVERT: E 112 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7860 (mt) REVERT: F 40 ASN cc_start: 0.8066 (m-40) cc_final: 0.7527 (t0) outliers start: 90 outliers final: 68 residues processed: 307 average time/residue: 0.1977 time to fit residues: 104.5435 Evaluate side-chains 306 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 224 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 915 THR Chi-restraints excluded: chain C residue 963 ASN Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 705 ASN Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 938 ASP Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1002 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 275 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 335 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 376 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.109341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068625 restraints weight = 91585.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070614 restraints weight = 49888.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071884 restraints weight = 34979.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072595 restraints weight = 28306.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073082 restraints weight = 25182.067| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 34830 Z= 0.208 Angle : 0.671 59.157 46938 Z= 0.368 Chirality : 0.043 0.960 5011 Planarity : 0.003 0.054 5988 Dihedral : 4.373 56.949 4523 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 2.49 % Allowed : 26.58 % Favored : 70.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 4074 helix: 1.23 (0.11), residues: 2437 sheet: -1.62 (0.35), residues: 195 loop : -0.99 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 348 TYR 0.037 0.001 TYR C 888 PHE 0.027 0.001 PHE A 839 TRP 0.013 0.001 TRP A 958 HIS 0.010 0.001 HIS C 975 Details of bonding type rmsd covalent geometry : bond 0.00467 (34830) covalent geometry : angle 0.67087 (46938) hydrogen bonds : bond 0.03712 ( 1722) hydrogen bonds : angle 4.06395 ( 4935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6223.98 seconds wall clock time: 108 minutes 38.68 seconds (6518.68 seconds total)