Starting phenix.real_space_refine on Mon Sep 30 02:05:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl6_40574/09_2024/8sl6_40574.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 67 5.16 5 C 15329 2.51 5 N 4219 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 5867 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 35, 'TRANS': 857} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1411 Unresolved non-hydrogen angles: 1771 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 8, 'TYR:plan': 9, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 22, 'PHE:plan': 27, 'GLU:plan': 41, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 834 Chain: "B" Number of atoms: 5976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 5976 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 363} Link IDs: {'PTRANS': 35, 'TRANS': 872} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1424 Unresolved non-hydrogen angles: 1789 Unresolved non-hydrogen dihedrals: 1181 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 9, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 24, 'PHE:plan': 28, 'GLU:plan': 44, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 837 Chain: "C" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 6032 Classifications: {'peptide': 920} Incomplete info: {'truncation_to_alanine': 372} Link IDs: {'PTRANS': 35, 'TRANS': 884} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1455 Unresolved non-hydrogen angles: 1822 Unresolved non-hydrogen dihedrals: 1197 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 9, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 26, 'GLU:plan': 46, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 849 Chain: "D" Number of atoms: 6079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 6079 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 353} Link IDs: {'PTRANS': 35, 'TRANS': 877} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1358 Unresolved non-hydrogen angles: 1710 Unresolved non-hydrogen dihedrals: 1116 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 25, 'GLU:plan': 42, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 782 Time building chain proxies: 15.58, per 1000 atoms: 0.65 Number of scatterers: 23954 At special positions: 0 Unit cell: (150.12, 150.12, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 4339 8.00 N 4219 7.00 C 15329 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: 6.75 Conformation dependent library (CDL) restraints added in 3.5 seconds 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6942 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 9 sheets defined 74.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.995A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.925A pdb=" N LEU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.695A pdb=" N ALA A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'A' and resid 347 through 362 removed outlier: 4.433A pdb=" N ALA A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.368A pdb=" N SER A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 394 Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.818A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.549A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.543A pdb=" N ALA A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 590 removed outlier: 4.020A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.534A pdb=" N VAL A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 removed outlier: 3.528A pdb=" N SER A 606 " --> pdb=" O HIS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.816A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.794A pdb=" N TRP A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 719 through 729 removed outlier: 3.577A pdb=" N ALA A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 756 Processing helix chain 'A' and resid 763 through 787 removed outlier: 3.610A pdb=" N GLU A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 4.007A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 825 Processing helix chain 'A' and resid 829 through 851 removed outlier: 4.334A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 895 removed outlier: 4.506A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.600A pdb=" N ARG A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 959 through 984 Processing helix chain 'A' and resid 984 through 1006 removed outlier: 4.148A pdb=" N ALA A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 993 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 removed outlier: 4.192A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.917A pdb=" N SER B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.873A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 236 through 248 removed outlier: 4.100A pdb=" N LEU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 330 through 345 Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.597A pdb=" N ALA B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 393 Processing helix chain 'B' and resid 395 through 404 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.796A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.968A pdb=" N TYR B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 561 removed outlier: 3.794A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 574 through 591 Processing helix chain 'B' and resid 592 through 599 removed outlier: 3.854A pdb=" N VAL B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.526A pdb=" N LEU B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.534A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.749A pdb=" N GLN B 629 " --> pdb=" O HIS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 655 removed outlier: 3.875A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.619A pdb=" N ALA B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 756 removed outlier: 3.707A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 787 removed outlier: 3.698A pdb=" N GLU B 767 " --> pdb=" O PRO B 763 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 770 " --> pdb=" O SER B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 803 Processing helix chain 'B' and resid 804 through 824 removed outlier: 3.526A pdb=" N CYS B 823 " --> pdb=" O VAL B 819 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 849 Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.920A pdb=" N HIS B 855 " --> pdb=" O PHE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 895 removed outlier: 3.742A pdb=" N ARG B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 removed outlier: 4.960A pdb=" N ARG B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 959 through 984 removed outlier: 3.589A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1006 removed outlier: 3.659A pdb=" N MET B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1027 Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1090 Processing helix chain 'B' and resid 1090 through 1095 Processing helix chain 'B' and resid 1097 through 1106 removed outlier: 4.354A pdb=" N ILE B1101 " --> pdb=" O GLN B1097 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B1102 " --> pdb=" O GLU B1098 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B1106 " --> pdb=" O LYS B1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 61 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.535A pdb=" N LEU C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.845A pdb=" N LEU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.633A pdb=" N ALA C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.625A pdb=" N ALA C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'C' and resid 347 through 360 removed outlier: 3.622A pdb=" N TYR C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 removed outlier: 3.868A pdb=" N ASN C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 5.068A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.657A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 429 through 446 removed outlier: 3.643A pdb=" N GLU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 478 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.981A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 543 through 559 removed outlier: 4.139A pdb=" N ALA C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 Processing helix chain 'C' and resid 574 through 591 removed outlier: 4.051A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 590 " --> pdb=" O CYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 600 removed outlier: 3.939A pdb=" N ALA C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 606 Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 removed outlier: 4.184A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 638 Processing helix chain 'C' and resid 645 through 653 Processing helix chain 'C' and resid 656 through 662 removed outlier: 3.983A pdb=" N TYR C 660 " --> pdb=" O PRO C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 729 removed outlier: 3.881A pdb=" N ALA C 729 " --> pdb=" O LYS C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 756 removed outlier: 3.817A pdb=" N VAL C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 787 Processing helix chain 'C' and resid 793 through 803 removed outlier: 3.605A pdb=" N LYS C 797 " --> pdb=" O ARG C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 removed outlier: 3.572A pdb=" N MET C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 853 removed outlier: 4.038A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 848 " --> pdb=" O PHE C 844 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 849 " --> pdb=" O THR C 845 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 895 removed outlier: 4.234A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 866 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 917 removed outlier: 4.846A pdb=" N ARG C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 959 through 985 Processing helix chain 'C' and resid 987 through 1006 Processing helix chain 'C' and resid 1010 through 1027 removed outlier: 3.834A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1115 removed outlier: 3.767A pdb=" N LEU C1113 " --> pdb=" O ASN C1109 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU C1114 " --> pdb=" O TYR C1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.545A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.729A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.838A pdb=" N LEU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 241 " --> pdb=" O PRO D 237 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.566A pdb=" N ALA D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 295 through 310 Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.540A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 4.050A pdb=" N TYR D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 379 through 392 removed outlier: 4.378A pdb=" N VAL D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 404 Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.729A pdb=" N LEU D 413 " --> pdb=" O MET D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 429 through 446 Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 527 removed outlier: 4.016A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 527 " --> pdb=" O TRP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.923A pdb=" N MET D 539 " --> pdb=" O TYR D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 561 removed outlier: 3.767A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 574 through 591 removed outlier: 4.073A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 590 " --> pdb=" O CYS D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 598 Processing helix chain 'D' and resid 610 through 618 Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.923A pdb=" N PHE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 624 " --> pdb=" O LYS D 620 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 625' Processing helix chain 'D' and resid 625 through 638 removed outlier: 3.545A pdb=" N GLN D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'D' and resid 719 through 729 Processing helix chain 'D' and resid 729 through 757 removed outlier: 4.262A pdb=" N LEU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 754 " --> pdb=" O TYR D 750 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 787 removed outlier: 3.638A pdb=" N THR D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 771 " --> pdb=" O GLU D 767 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE D 775 " --> pdb=" O TYR D 771 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR D 776 " --> pdb=" O PHE D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 803 Processing helix chain 'D' and resid 804 through 826 Processing helix chain 'D' and resid 830 through 851 removed outlier: 4.461A pdb=" N LEU D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR D 845 " --> pdb=" O PHE D 841 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 846 " --> pdb=" O MET D 842 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 847 " --> pdb=" O VAL D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 895 removed outlier: 4.129A pdb=" N ASP D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 895 " --> pdb=" O GLN D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 916 removed outlier: 3.570A pdb=" N ILE D 904 " --> pdb=" O ARG D 900 " (cutoff:3.500A) Proline residue: D 912 - end of helix removed outlier: 3.741A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 959 through 1006 removed outlier: 3.801A pdb=" N PHE D 981 " --> pdb=" O PHE D 977 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 984 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLY D 986 " --> pdb=" O GLN D 982 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 993 " --> pdb=" O ASP D 989 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 994 " --> pdb=" O MET D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1027 removed outlier: 4.396A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1108 removed outlier: 3.936A pdb=" N ALA D1108 " --> pdb=" O LEU D1104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 188 removed outlier: 5.753A pdb=" N GLY A 138 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 188 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 140 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 103 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N MET A 139 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 105 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER A 141 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N SER A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 68 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 231 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 70 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 256 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP A 253 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR A 319 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 255 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 188 removed outlier: 6.736A pdb=" N ALA B 136 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 186 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 138 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 188 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 140 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 105 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N SER B 141 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 71 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 256 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP B 253 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR B 319 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 255 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 28 Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.964A pdb=" N ALA C 136 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE C 186 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY C 138 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 188 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA C 140 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 101 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 137 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE C 103 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET C 139 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 105 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N SER C 141 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 71 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER C 106 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 256 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 253 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TYR C 319 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 255 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 188 removed outlier: 6.929A pdb=" N ALA D 136 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE D 186 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY D 138 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL D 188 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D 140 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE D 103 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N MET D 139 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 256 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 253 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N TYR D 319 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 255 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 601 through 602 removed outlier: 3.638A pdb=" N THR D 608 " --> pdb=" O ASN D 602 " (cutoff:3.500A) 1859 hydrogen bonds defined for protein. 5544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.49 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4015 1.32 - 1.44: 6511 1.44 - 1.57: 13829 1.57 - 1.69: 0 1.69 - 1.82: 96 Bond restraints: 24451 Sorted by residual: bond pdb=" CA TRP D 537 " pdb=" C TRP D 537 " ideal model delta sigma weight residual 1.522 1.434 0.088 1.40e-02 5.10e+03 3.99e+01 bond pdb=" C TYR D 910 " pdb=" O TYR D 910 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.28e+01 bond pdb=" C PHE D 536 " pdb=" N TRP D 537 " ideal model delta sigma weight residual 1.335 1.299 0.036 1.38e-02 5.25e+03 6.69e+00 bond pdb=" C GLY D 859 " pdb=" N PRO D 860 " ideal model delta sigma weight residual 1.336 1.314 0.022 9.80e-03 1.04e+04 5.06e+00 bond pdb=" CB TRP D 605 " pdb=" CG TRP D 605 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.07e+00 ... (remaining 24446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 32673 1.79 - 3.57: 829 3.57 - 5.36: 135 5.36 - 7.14: 28 7.14 - 8.93: 4 Bond angle restraints: 33669 Sorted by residual: angle pdb=" N LEU D 914 " pdb=" CA LEU D 914 " pdb=" C LEU D 914 " ideal model delta sigma weight residual 112.04 119.71 -7.67 1.44e+00 4.82e-01 2.83e+01 angle pdb=" C LEU D 914 " pdb=" N GLN D 915 " pdb=" CA GLN D 915 " ideal model delta sigma weight residual 120.29 112.76 7.53 1.42e+00 4.96e-01 2.81e+01 angle pdb=" CA ARG D 911 " pdb=" C ARG D 911 " pdb=" N PRO D 912 " ideal model delta sigma weight residual 120.77 116.47 4.30 9.70e-01 1.06e+00 1.97e+01 angle pdb=" N LEU D 901 " pdb=" CA LEU D 901 " pdb=" C LEU D 901 " ideal model delta sigma weight residual 111.14 115.51 -4.37 1.08e+00 8.57e-01 1.64e+01 angle pdb=" CA LEU D 914 " pdb=" C LEU D 914 " pdb=" O LEU D 914 " ideal model delta sigma weight residual 120.31 115.52 4.79 1.25e+00 6.40e-01 1.47e+01 ... (remaining 33664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 13198 17.65 - 35.29: 762 35.29 - 52.94: 94 52.94 - 70.58: 12 70.58 - 88.22: 13 Dihedral angle restraints: 14079 sinusoidal: 3510 harmonic: 10569 Sorted by residual: dihedral pdb=" CA ALA D 348 " pdb=" C ALA D 348 " pdb=" N GLN D 349 " pdb=" CA GLN D 349 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE B 412 " pdb=" C PHE B 412 " pdb=" N LEU B 413 " pdb=" CA LEU B 413 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 856 " pdb=" C LYS A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3955 0.080 - 0.159: 212 0.159 - 0.239: 1 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 4169 Sorted by residual: chirality pdb=" CA LEU D 914 " pdb=" N LEU D 914 " pdb=" C LEU D 914 " pdb=" CB LEU D 914 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA TRP D 537 " pdb=" N TRP D 537 " pdb=" C TRP D 537 " pdb=" CB TRP D 537 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CG LEU C 522 " pdb=" CB LEU C 522 " pdb=" CD1 LEU C 522 " pdb=" CD2 LEU C 522 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 4166 not shown) Planarity restraints: 4347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 904 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ILE D 904 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE D 904 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D 905 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS D 655 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO D 656 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 656 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 656 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 176 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO C 177 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " 0.031 5.00e-02 4.00e+02 ... (remaining 4344 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 486 2.68 - 3.24: 27194 3.24 - 3.79: 38560 3.79 - 4.35: 43428 4.35 - 4.90: 69531 Nonbonded interactions: 179199 Sorted by model distance: nonbonded pdb=" NH1 ARG B 482 " pdb=" O GLY B 483 " model vdw 2.128 3.120 nonbonded pdb=" O PHE D 402 " pdb=" OG SER D 405 " model vdw 2.149 3.040 nonbonded pdb=" O PHE B 476 " pdb=" NZ LYS B 552 " model vdw 2.151 3.120 nonbonded pdb=" O SER B 426 " pdb=" OG SER B 429 " model vdw 2.153 3.040 nonbonded pdb=" O PHE A 746 " pdb=" OG SER A 749 " model vdw 2.161 3.040 ... (remaining 179194 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 24 through 376 or (resid 377 through 379 and (name N or na \ me CA or name C or name O or name CB )) or resid 380 through 382 or (resid 383 a \ nd (name N or name CA or name C or name O or name CB )) or resid 384 through 386 \ or (resid 387 and (name N or name CA or name C or name O or name CB )) or resid \ 388 or (resid 389 through 390 and (name N or name CA or name C or name O or nam \ e CB )) or resid 391 through 394 or (resid 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 or (resid 400 and (name N o \ r name CA or name C or name O or name CB )) or resid 401 through 403 or (resid 4 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 405 through \ 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 481 or (resid 482 and (name N or name CA or name C or name O or \ name CB )) or resid 483 through 514 or (resid 515 and (name N or name CA or nam \ e C or name O or name CB )) or resid 516 through 541 or (resid 542 and (name N o \ r name CA or name C or name O or name CB )) or resid 543 through 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) or r \ esid 602 through 607 or (resid 608 and (name N or name CA or name C or name O or \ name CB )) or resid 609 through 615 or (resid 616 through 621 and (name N or na \ me CA or name C or name O or name CB )) or resid 622 through 652 or (resid 653 t \ hrough 655 and (name N or name CA or name C or name O or name CB )) or resid 656 \ through 659 or (resid 660 through 720 and (name N or name CA or name C or name \ O or name CB )) or resid 721 through 769 or (resid 770 through 772 and (name N o \ r name CA or name C or name O or name CB )) or resid 773 through 873 or (resid 8 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 875 through \ 896 or (resid 898 and (name N or name CA or name C or name O or name CB )) or r \ esid 899 through 1089 or (resid 1090 through 1091 and (name N or name CA or name \ C or name O or name CB )) or resid 1092)) selection = (chain 'B' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or resid 347 through 360 or (resid 361 through 3 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 369 through \ 376 or (resid 377 through 379 and (name N or name CA or name C or name O or nam \ e CB )) or resid 380 through 382 or (resid 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 through 403 \ or (resid 404 and (name N or name CA or name C or name O or name CB )) or resid \ 405 through 408 or (resid 409 through 410 and (name N or name CA or name C or n \ ame O or name CB )) or resid 411 through 414 or (resid 415 and (name N or name C \ A or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or na \ me CA or name C or name O or name CB )) or resid 418 through 446 or (resid 464 a \ nd (name N or name CA or name C or name O or name CB )) or resid 465 through 481 \ or (resid 482 and (name N or name CA or name C or name O or name CB )) or resid \ 483 through 517 or (resid 518 and (name N or name CA or name C or name O or nam \ e CB )) or resid 519 through 538 or (resid 539 and (name N or name CA or name C \ or name O or name CB )) or resid 540 or (resid 541 through 542 and (name N or na \ me CA or name C or name O or name CB )) or resid 543 through 555 or (resid 556 a \ nd (name N or name CA or name C or name O or name CB )) or resid 557 through 600 \ or (resid 601 and (name N or name CA or name C or name O or name CB )) or resid \ 602 through 606 or (resid 607 through 608 and (name N or name CA or name C or n \ ame O or name CB )) or resid 609 through 615 or (resid 616 through 621 and (name \ N or name CA or name C or name O or name CB )) or resid 622 through 652 or (res \ id 653 through 655 and (name N or name CA or name C or name O or name CB )) or r \ esid 656 through 659 or (resid 660 through 720 and (name N or name CA or name C \ or name O or name CB )) or resid 721 through 769 or (resid 770 through 772 and ( \ name N or name CA or name C or name O or name CB )) or resid 773 through 846 or \ (resid 847 through 854 and (name N or name CA or name C or name O or name CB )) \ or resid 855 through 1082 or (resid 1083 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1084 through 1086 or (resid 1087 through 1091 and (na \ me N or name CA or name C or name O or name CB )) or resid 1092)) selection = (chain 'C' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 through 360 or (resid 361 through 368 a \ nd (name N or name CA or name C or name O or name CB )) or resid 369 through 377 \ or (resid 378 through 379 and (name N or name CA or name C or name O or name CB \ )) or resid 380 through 382 or (resid 383 and (name N or name CA or name C or n \ ame O or name CB )) or resid 384 through 386 or (resid 387 and (name N or name C \ A or name C or name O or name CB )) or resid 388 or (resid 389 through 390 and ( \ name N or name CA or name C or name O or name CB )) or resid 391 through 393 or \ (resid 394 through 395 and (name N or name CA or name C or name O or name CB )) \ or resid 396 through 397 or (resid 398 and (name N or name CA or name C or name \ O or name CB )) or resid 399 or (resid 400 and (name N or name CA or name C or n \ ame O or name CB )) or resid 401 through 408 or (resid 409 through 410 and (name \ N or name CA or name C or name O or name CB )) or resid 411 through 414 or (res \ id 415 and (name N or name CA or name C or name O or name CB )) or resid 416 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 446 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 514 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 517 or (resid 518 and (name \ N or name CA or name C or name O or name CB )) or resid 519 through 526 or (res \ id 527 and (name N or name CA or name C or name O or name CB )) or resid 528 thr \ ough 652 or (resid 653 through 655 and (name N or name CA or name C or name O or \ name CB )) or resid 656 through 659 or (resid 660 through 720 and (name N or na \ me CA or name C or name O or name CB )) or resid 721 through 769 or (resid 770 t \ hrough 772 and (name N or name CA or name C or name O or name CB )) or resid 773 \ through 846 or (resid 847 through 854 and (name N or name CA or name C or name \ O or name CB )) or resid 855 through 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 through 1077 or (resid 1078 through \ 1079 and (name N or name CA or name C or name O or name CB )) or resid 1080 thr \ ough 1089 or (resid 1090 through 1091 and (name N or name CA or name C or name O \ or name CB )) or resid 1092)) selection = (chain 'D' and (resid 24 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or resid 347 through 360 or (resid 361 through 3 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 369 through \ 376 or (resid 377 through 379 and (name N or name CA or name C or name O or nam \ e CB )) or resid 380 through 397 or (resid 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 or (resid 400 and (name N or name CA or nam \ e C or name O or name CB )) or resid 401 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 408 or (resid 4 \ 09 through 410 and (name N or name CA or name C or name O or name CB )) or resid \ 411 through 414 or (resid 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or \ name CB )) or resid 418 through 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 446 or (resid 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 481 or (resid 4 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 483 through \ 484 or resid 509 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 516 through 517 or (resid 518 and (name N or name \ CA or name C or name O or name CB )) or resid 519 through 526 or (resid 527 and \ (name N or name CA or name C or name O or name CB )) or resid 528 or (resid 529 \ and (name N or name CA or name C or name O or name CB )) or resid 530 through 53 \ 8 or (resid 539 and (name N or name CA or name C or name O or name CB )) or (res \ id 540 through 542 and (name N or name CA or name C or name O or name CB )) or r \ esid 543 through 554 or (resid 555 through 556 and (name N or name CA or name C \ or name O or name CB )) or resid 557 through 584 or (resid 585 and (name N or na \ me CA or name C or name O or name CB )) or resid 586 through 592 or (resid 593 t \ hrough 594 and (name N or name CA or name C or name O or name CB )) or resid 595 \ through 599 or (resid 600 through 601 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 606 or (resid 607 through 608 and (name N o \ r name CA or name C or name O or name CB )) or resid 609 through 615 or (resid 6 \ 16 through 621 and (name N or name CA or name C or name O or name CB )) or resid \ 622 through 721 or (resid 722 and (name N or name CA or name C or name O or nam \ e CB )) or resid 723 through 816 or (resid 817 and (name N or name CA or name C \ or name O or name CB )) or resid 818 through 830 or (resid 831 through 832 and ( \ name N or name CA or name C or name O or name CB )) or resid 833 through 843 or \ (resid 844 and (name N or name CA or name C or name O or name CB )) or resid 845 \ through 846 or (resid 847 through 854 and (name N or name CA or name C or name \ O or name CB )) or resid 855 through 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 through 1082 or (resid 1083 and (na \ me N or name CA or name C or name O or name CB )) or resid 1084 through 1089 or \ (resid 1090 through 1091 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1092)) } 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: 3.820 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: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 55.340 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.100 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24451 Z= 0.366 Angle : 0.710 8.928 33669 Z= 0.428 Chirality : 0.039 0.398 4169 Planarity : 0.004 0.065 4347 Dihedral : 11.903 88.225 7137 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3522 helix: -0.37 (0.09), residues: 2441 sheet: -0.61 (0.33), residues: 208 loop : -2.24 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 302 HIS 0.010 0.001 HIS C 998 PHE 0.029 0.002 PHE C 476 TYR 0.018 0.002 TYR D 535 ARG 0.011 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8905 (tp) cc_final: 0.8527 (pp) REVERT: A 752 LEU cc_start: 0.9152 (tp) cc_final: 0.8890 (pp) REVERT: B 243 MET cc_start: 0.8916 (tmm) cc_final: 0.8566 (tmm) REVERT: B 254 LEU cc_start: 0.9181 (tp) cc_final: 0.8465 (pp) REVERT: B 882 TRP cc_start: 0.9029 (t-100) cc_final: 0.8807 (t-100) REVERT: B 1000 ILE cc_start: 0.9723 (mt) cc_final: 0.9426 (tt) REVERT: C 135 VAL cc_start: 0.9255 (m) cc_final: 0.8998 (p) REVERT: C 806 TRP cc_start: 0.8542 (m100) cc_final: 0.8099 (m100) REVERT: C 972 LEU cc_start: 0.9279 (mm) cc_final: 0.8980 (pp) REVERT: D 232 LEU cc_start: 0.8987 (tp) cc_final: 0.8778 (tt) REVERT: D 882 TRP cc_start: 0.8867 (t-100) cc_final: 0.8559 (t-100) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2936 time to fit residues: 117.1557 Evaluate side-chains 180 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.3980 chunk 274 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 93 optimal weight: 0.0060 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 283 optimal weight: 0.0980 chunk 109 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 328 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 118 GLN B 123 HIS B 204 GLN B 602 ASN B 603 HIS B1060 ASN C 204 GLN C 439 HIS C 527 GLN C 528 ASN C 603 HIS C 737 ASN C1060 ASN D 344 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24451 Z= 0.174 Angle : 0.532 6.642 33669 Z= 0.285 Chirality : 0.036 0.138 4169 Planarity : 0.004 0.052 4347 Dihedral : 4.094 21.359 3703 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3522 helix: 1.53 (0.10), residues: 2517 sheet: 0.11 (0.34), residues: 198 loop : -1.94 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 253 HIS 0.008 0.001 HIS B 603 PHE 0.029 0.001 PHE A1061 TYR 0.012 0.001 TYR A 535 ARG 0.029 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.7350 (mtt) cc_final: 0.7127 (mtt) REVERT: A 752 LEU cc_start: 0.9168 (tp) cc_final: 0.8870 (pp) REVERT: B 557 MET cc_start: 0.8612 (tmm) cc_final: 0.8308 (tmm) REVERT: B 581 ASP cc_start: 0.8511 (m-30) cc_final: 0.8255 (m-30) REVERT: C 135 VAL cc_start: 0.9062 (m) cc_final: 0.8858 (p) REVERT: C 387 MET cc_start: 0.8407 (tmm) cc_final: 0.8156 (tmm) REVERT: C 972 LEU cc_start: 0.9234 (mm) cc_final: 0.8945 (pp) REVERT: D 254 LEU cc_start: 0.9222 (tp) cc_final: 0.8794 (pp) REVERT: D 882 TRP cc_start: 0.8809 (t-100) cc_final: 0.8407 (t60) outliers start: 3 outliers final: 0 residues processed: 243 average time/residue: 0.2765 time to fit residues: 116.6187 Evaluate side-chains 178 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 273 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 329 optimal weight: 9.9990 chunk 355 optimal weight: 0.7980 chunk 293 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 264 optimal weight: 0.8980 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 225 GLN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS C 123 HIS C 394 ASN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN C 998 HIS D 184 HIS ** D 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24451 Z= 0.367 Angle : 0.627 9.151 33669 Z= 0.344 Chirality : 0.039 0.155 4169 Planarity : 0.005 0.052 4347 Dihedral : 4.344 21.741 3703 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3522 helix: 1.37 (0.10), residues: 2515 sheet: 0.30 (0.34), residues: 211 loop : -1.78 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 302 HIS 0.009 0.001 HIS D 612 PHE 0.030 0.002 PHE D 476 TYR 0.020 0.002 TYR A 535 ARG 0.008 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8925 (tp) cc_final: 0.8708 (tp) REVERT: A 840 ASP cc_start: 0.8917 (t0) cc_final: 0.8499 (m-30) REVERT: B 253 TRP cc_start: 0.7982 (m100) cc_final: 0.6962 (m100) REVERT: C 387 MET cc_start: 0.8665 (tmm) cc_final: 0.8269 (tmm) REVERT: C 581 ASP cc_start: 0.8182 (m-30) cc_final: 0.7934 (m-30) REVERT: C 972 LEU cc_start: 0.9301 (mm) cc_final: 0.9014 (pp) REVERT: D 882 TRP cc_start: 0.8872 (t-100) cc_final: 0.8453 (t-100) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2794 time to fit residues: 102.7492 Evaluate side-chains 165 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN B 603 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN D 528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24451 Z= 0.184 Angle : 0.497 6.553 33669 Z= 0.267 Chirality : 0.036 0.140 4169 Planarity : 0.004 0.048 4347 Dihedral : 3.957 19.235 3703 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3522 helix: 1.96 (0.10), residues: 2527 sheet: 0.51 (0.35), residues: 204 loop : -1.72 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 302 HIS 0.007 0.001 HIS D 123 PHE 0.023 0.001 PHE D 476 TYR 0.012 0.001 TYR D 535 ARG 0.007 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 ASP cc_start: 0.8900 (t0) cc_final: 0.8433 (m-30) REVERT: B 253 TRP cc_start: 0.7926 (m100) cc_final: 0.7014 (m100) REVERT: C 387 MET cc_start: 0.8553 (tmm) cc_final: 0.8179 (tmm) REVERT: C 581 ASP cc_start: 0.8028 (m-30) cc_final: 0.7764 (m-30) REVERT: C 972 LEU cc_start: 0.9300 (mm) cc_final: 0.9061 (pp) REVERT: D 413 LEU cc_start: 0.8785 (tp) cc_final: 0.8557 (tt) REVERT: D 882 TRP cc_start: 0.8851 (t-100) cc_final: 0.8462 (t-100) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.2617 time to fit residues: 98.6532 Evaluate side-chains 175 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 0 optimal weight: 60.0000 chunk 178 optimal weight: 20.0000 chunk 314 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 394 ASN C 527 GLN C 528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24451 Z= 0.422 Angle : 0.671 10.764 33669 Z= 0.365 Chirality : 0.040 0.188 4169 Planarity : 0.005 0.061 4347 Dihedral : 4.443 23.209 3703 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3522 helix: 1.40 (0.10), residues: 2515 sheet: 0.07 (0.34), residues: 219 loop : -1.75 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP D 302 HIS 0.008 0.002 HIS D 123 PHE 0.035 0.002 PHE D 398 TYR 0.022 0.002 TYR C 535 ARG 0.012 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 ASP cc_start: 0.8975 (t0) cc_final: 0.8598 (m-30) REVERT: B 253 TRP cc_start: 0.7839 (m100) cc_final: 0.6995 (m100) REVERT: C 581 ASP cc_start: 0.8115 (m-30) cc_final: 0.7874 (m-30) REVERT: C 806 TRP cc_start: 0.8391 (m100) cc_final: 0.7981 (m100) REVERT: C 972 LEU cc_start: 0.9289 (mm) cc_final: 0.9003 (pp) REVERT: D 882 TRP cc_start: 0.8900 (t-100) cc_final: 0.8576 (t-100) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2823 time to fit residues: 96.4652 Evaluate side-chains 157 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 6.9990 chunk 315 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 350 optimal weight: 0.5980 chunk 290 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24451 Z= 0.190 Angle : 0.515 13.999 33669 Z= 0.273 Chirality : 0.036 0.164 4169 Planarity : 0.004 0.078 4347 Dihedral : 4.014 24.224 3703 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.15), residues: 3522 helix: 2.01 (0.10), residues: 2515 sheet: 0.30 (0.36), residues: 202 loop : -1.64 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 302 HIS 0.007 0.001 HIS D 123 PHE 0.016 0.001 PHE C 412 TYR 0.013 0.001 TYR D 535 ARG 0.005 0.000 ARG D 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8526 (tmm) cc_final: 0.8197 (tmm) REVERT: A 581 ASP cc_start: 0.8702 (m-30) cc_final: 0.8475 (m-30) REVERT: A 840 ASP cc_start: 0.8943 (t0) cc_final: 0.8546 (m-30) REVERT: B 254 LEU cc_start: 0.9472 (tp) cc_final: 0.9094 (mm) REVERT: C 581 ASP cc_start: 0.7889 (m-30) cc_final: 0.7640 (m-30) REVERT: C 806 TRP cc_start: 0.8335 (m100) cc_final: 0.7930 (m100) REVERT: D 842 MET cc_start: 0.9308 (mmt) cc_final: 0.9002 (mmm) REVERT: D 882 TRP cc_start: 0.8825 (t-100) cc_final: 0.8407 (t-100) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2901 time to fit residues: 102.4773 Evaluate side-chains 168 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 255 optimal weight: 30.0000 chunk 198 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 348 optimal weight: 40.0000 chunk 218 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN C 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24451 Z= 0.302 Angle : 0.585 11.678 33669 Z= 0.313 Chirality : 0.038 0.169 4169 Planarity : 0.004 0.088 4347 Dihedral : 4.173 20.688 3703 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3522 helix: 1.82 (0.10), residues: 2519 sheet: 0.08 (0.35), residues: 208 loop : -1.75 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 378 HIS 0.006 0.001 HIS B 612 PHE 0.028 0.002 PHE C 476 TYR 0.020 0.002 TYR D 535 ARG 0.010 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8580 (tmm) cc_final: 0.8343 (tmm) REVERT: A 581 ASP cc_start: 0.8728 (m-30) cc_final: 0.8499 (m-30) REVERT: A 840 ASP cc_start: 0.8946 (t0) cc_final: 0.8592 (m-30) REVERT: B 253 TRP cc_start: 0.7633 (m100) cc_final: 0.6924 (m100) REVERT: C 581 ASP cc_start: 0.8061 (m-30) cc_final: 0.7831 (m-30) REVERT: C 806 TRP cc_start: 0.8345 (m100) cc_final: 0.7945 (m100) REVERT: D 413 LEU cc_start: 0.8955 (tp) cc_final: 0.8585 (tt) REVERT: D 842 MET cc_start: 0.9353 (mmt) cc_final: 0.9021 (mmm) REVERT: D 882 TRP cc_start: 0.8884 (t-100) cc_final: 0.8495 (t-100) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2730 time to fit residues: 92.6247 Evaluate side-chains 164 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 274 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24451 Z= 0.148 Angle : 0.493 8.644 33669 Z= 0.257 Chirality : 0.035 0.142 4169 Planarity : 0.004 0.050 4347 Dihedral : 3.791 20.111 3703 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 0.92 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3522 helix: 2.27 (0.10), residues: 2531 sheet: 0.08 (0.36), residues: 199 loop : -1.65 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP D 302 HIS 0.007 0.001 HIS D 301 PHE 0.016 0.001 PHE C 412 TYR 0.016 0.001 TYR A 164 ARG 0.003 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8629 (tmm) cc_final: 0.8398 (tmm) REVERT: A 581 ASP cc_start: 0.8686 (m-30) cc_final: 0.8413 (m-30) REVERT: A 840 ASP cc_start: 0.8947 (t0) cc_final: 0.8638 (m-30) REVERT: A 893 LEU cc_start: 0.8760 (tp) cc_final: 0.8559 (pp) REVERT: B 253 TRP cc_start: 0.7625 (m100) cc_final: 0.7125 (m100) REVERT: B 254 LEU cc_start: 0.9391 (tp) cc_final: 0.8916 (mm) REVERT: B 610 CYS cc_start: 0.8990 (m) cc_final: 0.8773 (m) REVERT: C 806 TRP cc_start: 0.8314 (m100) cc_final: 0.7892 (m100) REVERT: D 842 MET cc_start: 0.9341 (mmt) cc_final: 0.8938 (mmp) REVERT: D 882 TRP cc_start: 0.8829 (t-100) cc_final: 0.8437 (t-100) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2789 time to fit residues: 102.8700 Evaluate side-chains 172 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 10.0000 chunk 334 optimal weight: 0.3980 chunk 304 optimal weight: 5.9990 chunk 325 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 255 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 293 optimal weight: 9.9990 chunk 307 optimal weight: 0.7980 chunk 324 optimal weight: 5.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24451 Z= 0.232 Angle : 0.523 8.463 33669 Z= 0.277 Chirality : 0.036 0.147 4169 Planarity : 0.004 0.059 4347 Dihedral : 3.828 19.625 3703 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3522 helix: 2.22 (0.10), residues: 2538 sheet: 0.05 (0.34), residues: 210 loop : -1.66 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 302 HIS 0.007 0.001 HIS C 301 PHE 0.044 0.001 PHE D 476 TYR 0.017 0.001 TYR A 164 ARG 0.006 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8615 (tmm) cc_final: 0.8387 (tmm) REVERT: A 581 ASP cc_start: 0.8705 (m-30) cc_final: 0.8444 (m-30) REVERT: A 840 ASP cc_start: 0.8913 (t0) cc_final: 0.8606 (m-30) REVERT: A 893 LEU cc_start: 0.8773 (tp) cc_final: 0.8558 (pp) REVERT: A 1085 ASP cc_start: 0.8547 (t0) cc_final: 0.8239 (t0) REVERT: B 253 TRP cc_start: 0.7691 (m100) cc_final: 0.7006 (m100) REVERT: B 610 CYS cc_start: 0.9011 (m) cc_final: 0.8808 (m) REVERT: C 806 TRP cc_start: 0.8326 (m100) cc_final: 0.7893 (m100) REVERT: D 413 LEU cc_start: 0.8909 (tp) cc_final: 0.8650 (tt) REVERT: D 842 MET cc_start: 0.9361 (mmt) cc_final: 0.9046 (mmp) REVERT: D 882 TRP cc_start: 0.8877 (t-100) cc_final: 0.8600 (t-100) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2717 time to fit residues: 98.5096 Evaluate side-chains 170 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 163 optimal weight: 40.0000 chunk 239 optimal weight: 20.0000 chunk 360 optimal weight: 1.9990 chunk 331 optimal weight: 0.4980 chunk 287 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24451 Z= 0.173 Angle : 0.501 11.037 33669 Z= 0.261 Chirality : 0.036 0.136 4169 Planarity : 0.004 0.050 4347 Dihedral : 3.715 20.523 3703 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.15), residues: 3522 helix: 2.35 (0.10), residues: 2527 sheet: 0.05 (0.34), residues: 210 loop : -1.60 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 302 HIS 0.007 0.001 HIS A 301 PHE 0.038 0.001 PHE D 476 TYR 0.019 0.001 TYR A 164 ARG 0.004 0.000 ARG C 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8630 (tmm) cc_final: 0.8408 (tmm) REVERT: A 581 ASP cc_start: 0.8637 (m-30) cc_final: 0.8411 (m-30) REVERT: A 840 ASP cc_start: 0.8950 (t0) cc_final: 0.8660 (m-30) REVERT: A 842 MET cc_start: 0.8703 (mmp) cc_final: 0.8486 (mmp) REVERT: A 893 LEU cc_start: 0.8743 (tp) cc_final: 0.8484 (pp) REVERT: A 1085 ASP cc_start: 0.8515 (t0) cc_final: 0.8218 (t0) REVERT: B 253 TRP cc_start: 0.7694 (m100) cc_final: 0.7194 (m100) REVERT: B 254 LEU cc_start: 0.9346 (tp) cc_final: 0.8884 (mm) REVERT: B 610 CYS cc_start: 0.8994 (m) cc_final: 0.8767 (m) REVERT: C 806 TRP cc_start: 0.8338 (m100) cc_final: 0.7949 (m100) REVERT: D 882 TRP cc_start: 0.8855 (t-100) cc_final: 0.8554 (t60) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2615 time to fit residues: 95.3262 Evaluate side-chains 173 residues out of total 3182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 0.9990 chunk 305 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 287 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063805 restraints weight = 162805.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062102 restraints weight = 117513.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062348 restraints weight = 124478.911| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24451 Z= 0.145 Angle : 0.485 9.903 33669 Z= 0.250 Chirality : 0.035 0.145 4169 Planarity : 0.004 0.050 4347 Dihedral : 3.562 18.551 3703 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.15), residues: 3522 helix: 2.43 (0.10), residues: 2530 sheet: 0.17 (0.35), residues: 210 loop : -1.59 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 302 HIS 0.004 0.001 HIS C 314 PHE 0.023 0.001 PHE D 398 TYR 0.019 0.001 TYR A 164 ARG 0.004 0.000 ARG C 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.69 seconds wall clock time: 75 minutes 2.84 seconds (4502.84 seconds total)