Starting phenix.real_space_refine on Mon Sep 14 07:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.map" model { file = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o77_0639/09_2026/6o77_0639.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 18884 2.51 5 N 4688 2.21 5 O 5168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7115 Classifications: {'peptide': 872} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 849} Chain breaks: 11 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 8.32, per 1000 atoms: 0.29 Number of scatterers: 28884 At special positions: 0 Unit cell: (126.021, 126.021, 153.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5168 8.00 N 4688 7.00 C 18884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 930 " distance=2.03 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 930 " distance=2.03 Simple disulfide: pdb=" SG CYS D 919 " - pdb=" SG CYS D 930 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 8 sheets defined 65.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 348 " --> pdb=" O CYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.995A pdb=" N PHE A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.555A pdb=" N THR A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 459 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA A 554 " --> pdb=" O HIS A 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.639A pdb=" N ALA A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.921A pdb=" N ILE A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR A 723 " --> pdb=" O SER A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE A 735 " --> pdb=" O TRP A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 959 removed outlier: 3.630A pdb=" N ASN A 958 " --> pdb=" O MET A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA A 967 " --> pdb=" O ASN A 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 972 " --> pdb=" O MET A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP A1076 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1077 " --> pdb=" O ARG A1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A1078 " --> pdb=" O GLN A1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.580A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.603A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL B 334 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 348 " --> pdb=" O CYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.845A pdb=" N GLU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.995A pdb=" N PHE B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.621A pdb=" N ALA B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.641A pdb=" N ALA B 554 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.640A pdb=" N ALA B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.801A pdb=" N ALA B 651 " --> pdb=" O CYS B 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE B 686 " --> pdb=" O LYS B 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR B 723 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE B 735 " --> pdb=" O TRP B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS B 846 " --> pdb=" O ASN B 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.562A pdb=" N ALA B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN B 958 " --> pdb=" O MET B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA B 967 " --> pdb=" O ASN B 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 972 " --> pdb=" O MET B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 994 removed outlier: 4.208A pdb=" N GLN B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 989 " --> pdb=" O LYS B 985 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'B' and resid 1041 through 1061 removed outlier: 3.858A pdb=" N ALA B1061 " --> pdb=" O ILE B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP B1076 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B1077 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS B1078 " --> pdb=" O GLN B1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP B1081 " --> pdb=" O ALA B1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.707A pdb=" N SER C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.690A pdb=" N LYS C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 348 " --> pdb=" O CYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.995A pdb=" N PHE C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.736A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 459 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 524 removed outlier: 3.970A pdb=" N LYS C 517 " --> pdb=" O THR C 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 518 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA C 651 " --> pdb=" O CYS C 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR C 723 " --> pdb=" O SER C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE C 735 " --> pdb=" O TRP C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE C 760 " --> pdb=" O THR C 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 787 Processing helix chain 'C' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 831 removed outlier: 3.607A pdb=" N TYR C 816 " --> pdb=" O GLU C 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 837 removed outlier: 4.156A pdb=" N HIS C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 removed outlier: 4.367A pdb=" N LYS C 846 " --> pdb=" O ASN C 842 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 851 " --> pdb=" O ILE C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 875 removed outlier: 3.534A pdb=" N ALA C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN C 958 " --> pdb=" O MET C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 976 removed outlier: 3.582A pdb=" N ALA C 967 " --> pdb=" O ASN C 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 989 " --> pdb=" O LYS C 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'C' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA C1061 " --> pdb=" O ILE C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP C1076 " --> pdb=" O PHE C1072 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C1077 " --> pdb=" O ARG C1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C1078 " --> pdb=" O GLN C1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C1080 " --> pdb=" O ASP C1076 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C1081 " --> pdb=" O ALA C1077 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C1091 " --> pdb=" O LYS C1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.579A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 3.604A pdb=" N PHE D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 267 through 279 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.708A pdb=" N SER D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.633A pdb=" N VAL D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.691A pdb=" N LYS D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 348 " --> pdb=" O CYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 376 removed outlier: 3.846A pdb=" N GLU D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.995A pdb=" N PHE D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.735A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 438 removed outlier: 3.534A pdb=" N ALA D 433 " --> pdb=" O GLN D 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 removed outlier: 3.554A pdb=" N THR D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 459 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.622A pdb=" N ALA D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.969A pdb=" N LYS D 517 " --> pdb=" O THR D 513 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 518 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.640A pdb=" N ALA D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.665A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.638A pdb=" N ALA D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 626 removed outlier: 3.799A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.509A pdb=" N LEU D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.800A pdb=" N ALA D 651 " --> pdb=" O CYS D 647 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 682 through 689 removed outlier: 3.920A pdb=" N ILE D 686 " --> pdb=" O LYS D 682 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 723 removed outlier: 3.644A pdb=" N THR D 723 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 749 removed outlier: 3.810A pdb=" N PHE D 735 " --> pdb=" O TRP D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 776 removed outlier: 3.513A pdb=" N ILE D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 761 " --> pdb=" O ALA D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 787 Processing helix chain 'D' and resid 788 through 808 removed outlier: 3.666A pdb=" N MET D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 831 removed outlier: 3.606A pdb=" N TYR D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 837 removed outlier: 4.157A pdb=" N HIS D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 851 removed outlier: 4.366A pdb=" N LYS D 846 " --> pdb=" O ASN D 842 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 851 " --> pdb=" O ILE D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 875 removed outlier: 3.535A pdb=" N ALA D 874 " --> pdb=" O ALA D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 887 Processing helix chain 'D' and resid 894 through 900 removed outlier: 3.561A pdb=" N ALA D 900 " --> pdb=" O GLU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 959 removed outlier: 3.631A pdb=" N ASN D 958 " --> pdb=" O MET D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 976 removed outlier: 3.583A pdb=" N ALA D 967 " --> pdb=" O ASN D 963 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 994 removed outlier: 4.209A pdb=" N GLN D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1041 through 1061 removed outlier: 3.857A pdb=" N ALA D1061 " --> pdb=" O ILE D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.588A pdb=" N ASP D1076 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D1077 " --> pdb=" O ARG D1073 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS D1078 " --> pdb=" O GLN D1074 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1079 " --> pdb=" O LEU D1075 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D1080 " --> pdb=" O ASP D1076 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP D1081 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.792A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.791A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.793A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4644 1.31 - 1.43: 8156 1.43 - 1.56: 16412 1.56 - 1.69: 88 1.69 - 1.82: 252 Bond restraints: 29552 Sorted by residual: bond pdb=" CAI Y01 C1403 " pdb=" CAZ Y01 C1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1403 " pdb=" CAZ Y01 D1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 A1403 " pdb=" CAZ Y01 A1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 B1403 " pdb=" CAZ Y01 B1403 " ideal model delta sigma weight residual 1.332 1.696 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAI Y01 D1402 " pdb=" CAZ Y01 D1402 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 ... (remaining 29547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 39359 3.34 - 6.67: 574 6.67 - 10.01: 87 10.01 - 13.34: 4 13.34 - 16.68: 8 Bond angle restraints: 40032 Sorted by residual: angle pdb=" C ASP D 907 " pdb=" N ASP D 908 " pdb=" CA ASP D 908 " ideal model delta sigma weight residual 121.83 112.81 9.02 1.48e+00 4.57e-01 3.71e+01 angle pdb=" C ASP A 907 " pdb=" N ASP A 908 " pdb=" CA ASP A 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP C 907 " pdb=" N ASP C 908 " pdb=" CA ASP C 908 " ideal model delta sigma weight residual 121.83 112.82 9.01 1.48e+00 4.57e-01 3.70e+01 angle pdb=" C ASP B 907 " pdb=" N ASP B 908 " pdb=" CA ASP B 908 " ideal model delta sigma weight residual 121.83 112.83 9.00 1.48e+00 4.57e-01 3.70e+01 angle pdb=" N ASP A 907 " pdb=" CA ASP A 907 " pdb=" C ASP A 907 " ideal model delta sigma weight residual 111.33 118.07 -6.74 1.21e+00 6.83e-01 3.10e+01 ... (remaining 40027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15345 17.97 - 35.94: 1623 35.94 - 53.91: 252 53.91 - 71.88: 64 71.88 - 89.85: 28 Dihedral angle restraints: 17312 sinusoidal: 7108 harmonic: 10204 Sorted by residual: dihedral pdb=" CA GLN C 876 " pdb=" C GLN C 876 " pdb=" N GLY C 877 " pdb=" CA GLY C 877 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN D 876 " pdb=" C GLN D 876 " pdb=" N GLY D 877 " pdb=" CA GLY D 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN B 876 " pdb=" C GLN B 876 " pdb=" N GLY B 877 " pdb=" CA GLY B 877 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 17309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4285 0.114 - 0.228: 155 0.228 - 0.342: 24 0.342 - 0.456: 8 0.456 - 0.571: 12 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CBI Y01 B1404 " pdb=" CAU Y01 B1404 " pdb=" CBE Y01 B1404 " pdb=" CBG Y01 B1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CBI Y01 D1404 " pdb=" CAU Y01 D1404 " pdb=" CBE Y01 D1404 " pdb=" CBG Y01 D1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CBI Y01 A1404 " pdb=" CAU Y01 A1404 " pdb=" CBE Y01 A1404 " pdb=" CBG Y01 A1404 " both_signs ideal model delta sigma weight residual False 2.94 2.37 0.57 2.00e-01 2.50e+01 8.08e+00 ... (remaining 4481 not shown) Planarity restraints: 4928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 905 " 0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO B 906 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 906 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 906 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.33e+01 pdb=" N PRO C 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 906 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 905 " -0.108 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO D 906 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO D 906 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO D 906 " -0.080 5.00e-02 4.00e+02 ... (remaining 4925 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 20 2.26 - 2.92: 11749 2.92 - 3.58: 40812 3.58 - 4.24: 69088 4.24 - 4.90: 113633 Nonbonded interactions: 235302 Sorted by model distance: nonbonded pdb=" CH2 TRP A 888 " pdb=" O SER A 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP D 888 " pdb=" O SER D 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP B 888 " pdb=" O SER B 926 " model vdw 1.604 3.340 nonbonded pdb=" CH2 TRP C 888 " pdb=" O SER C 926 " model vdw 1.604 3.340 nonbonded pdb=" CZ3 TRP D 888 " pdb=" O SER D 926 " model vdw 2.016 3.340 ... (remaining 235297 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.350 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.013 0.364 29556 Z= 0.609 Angle : 1.006 16.675 40040 Z= 0.517 Chirality : 0.063 0.571 4484 Planarity : 0.007 0.164 4928 Dihedral : 15.242 89.851 10668 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.77 (0.10), residues: 3392 helix: -4.01 (0.05), residues: 2156 sheet: -2.45 (0.33), residues: 208 loop : -3.09 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 655 TYR 0.016 0.002 TYR C 971 PHE 0.021 0.002 PHE B 806 TRP 0.023 0.003 TRP D 516 HIS 0.009 0.002 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.01251 / 0.61 (29552) covalent geometry : angle 1.00618 / 0.52 (40032) SS BOND : bond 0.00425 / 0.26 ( 4) SS BOND : angle 1.70704 / 1.00 ( 8) hydrogen bonds : bond 0.27470 / 18.17 ( 1340) hydrogen bonds : angle 9.61019 / 6.58 ( 3984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 953 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.8035 (ttt180) cc_final: 0.6296 (ptp-170) REVERT: A 149 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8587 (mtmt) REVERT: A 323 SER cc_start: 0.8416 (m) cc_final: 0.7928 (m) REVERT: A 592 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (mmp) REVERT: A 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7845 (pp20) REVERT: A 611 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 649 GLU cc_start: 0.8034 (mp0) cc_final: 0.7663 (pm20) REVERT: A 672 GLN cc_start: 0.8006 (tt0) cc_final: 0.7768 (tt0) REVERT: A 674 TYR cc_start: 0.8270 (m-80) cc_final: 0.7896 (m-10) REVERT: A 688 MET cc_start: 0.7379 (mtp) cc_final: 0.6331 (ppp) REVERT: A 775 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7544 (ttt180) REVERT: A 789 TRP cc_start: 0.8714 (m100) cc_final: 0.8308 (m100) REVERT: A 790 ASN cc_start: 0.9162 (m-40) cc_final: 0.8789 (t0) REVERT: A 798 PHE cc_start: 0.8640 (t80) cc_final: 0.8414 (t80) REVERT: A 825 ASP cc_start: 0.8431 (t0) cc_final: 0.8190 (t0) REVERT: A 841 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6726 (ttp80) REVERT: A 887 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 955 LEU cc_start: 0.9183 (tp) cc_final: 0.8925 (tp) REVERT: A 1056 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8762 (ttpp) REVERT: B 110 ARG cc_start: 0.8070 (ttt180) cc_final: 0.6282 (ptp-170) REVERT: B 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: B 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: B 606 GLU cc_start: 0.8296 (pp20) cc_final: 0.7853 (pp20) REVERT: B 649 GLU cc_start: 0.8049 (mp0) cc_final: 0.7666 (pm20) REVERT: B 672 GLN cc_start: 0.8008 (tt0) cc_final: 0.7772 (tt0) REVERT: B 674 TYR cc_start: 0.8269 (m-80) cc_final: 0.7901 (m-10) REVERT: B 688 MET cc_start: 0.7370 (mtp) cc_final: 0.6334 (ppp) REVERT: B 775 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7573 (ttt180) REVERT: B 789 TRP cc_start: 0.8719 (m100) cc_final: 0.8313 (m100) REVERT: B 790 ASN cc_start: 0.9163 (m-40) cc_final: 0.8792 (t0) REVERT: B 798 PHE cc_start: 0.8638 (t80) cc_final: 0.8390 (t80) REVERT: B 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8152 (t0) REVERT: B 841 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6744 (ttp80) REVERT: B 887 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 955 LEU cc_start: 0.9186 (tp) cc_final: 0.8940 (tp) REVERT: C 110 ARG cc_start: 0.8071 (ttt180) cc_final: 0.6281 (ptp-170) REVERT: C 149 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8571 (mtmt) REVERT: C 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8174 (mmp) REVERT: C 606 GLU cc_start: 0.8299 (pp20) cc_final: 0.7856 (pp20) REVERT: C 649 GLU cc_start: 0.8046 (mp0) cc_final: 0.7661 (pm20) REVERT: C 672 GLN cc_start: 0.8007 (tt0) cc_final: 0.7772 (tt0) REVERT: C 674 TYR cc_start: 0.8270 (m-80) cc_final: 0.7899 (m-10) REVERT: C 688 MET cc_start: 0.7367 (mtp) cc_final: 0.6332 (ppp) REVERT: C 775 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7566 (ttt180) REVERT: C 789 TRP cc_start: 0.8720 (m100) cc_final: 0.8324 (m100) REVERT: C 790 ASN cc_start: 0.9164 (m-40) cc_final: 0.8785 (t0) REVERT: C 798 PHE cc_start: 0.8636 (t80) cc_final: 0.8388 (t80) REVERT: C 825 ASP cc_start: 0.8398 (t0) cc_final: 0.8147 (t0) REVERT: C 841 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6743 (ttp80) REVERT: C 887 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 955 LEU cc_start: 0.9184 (tp) cc_final: 0.8939 (tp) REVERT: D 110 ARG cc_start: 0.8069 (ttt180) cc_final: 0.6288 (ptp-170) REVERT: D 149 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8573 (mtmt) REVERT: D 592 MET cc_start: 0.8454 (mmm) cc_final: 0.8173 (mmp) REVERT: D 606 GLU cc_start: 0.8298 (pp20) cc_final: 0.7858 (pp20) REVERT: D 649 GLU cc_start: 0.8048 (mp0) cc_final: 0.7664 (pm20) REVERT: D 672 GLN cc_start: 0.8007 (tt0) cc_final: 0.7773 (tt0) REVERT: D 674 TYR cc_start: 0.8267 (m-80) cc_final: 0.7896 (m-10) REVERT: D 688 MET cc_start: 0.7368 (mtp) cc_final: 0.6332 (ppp) REVERT: D 775 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7565 (ttt180) REVERT: D 789 TRP cc_start: 0.8719 (m100) cc_final: 0.8324 (m100) REVERT: D 790 ASN cc_start: 0.9163 (m-40) cc_final: 0.8789 (t0) REVERT: D 798 PHE cc_start: 0.8637 (t80) cc_final: 0.8389 (t80) REVERT: D 825 ASP cc_start: 0.8401 (t0) cc_final: 0.8148 (t0) REVERT: D 841 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6746 (ttp80) REVERT: D 887 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7392 (mt-10) REVERT: D 955 LEU cc_start: 0.9185 (tp) cc_final: 0.8937 (tp) outliers start: 0 outliers final: 0 residues processed: 953 average time/residue: 0.1998 time to fit residues: 294.9999 Evaluate side-chains 770 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 770 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 213 ASN A 248 HIS A 308 ASN A 380 HIS A 440 ASN A 662 GLN A 666 GLN A 683 ASN A 882 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 GLN B 145 ASN B 213 ASN B 248 HIS B 308 ASN B 440 ASN B 662 GLN B 666 GLN B 683 ASN B 882 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 GLN C 145 ASN C 213 ASN C 248 HIS C 308 ASN C 440 ASN C 662 GLN C 666 GLN C 683 ASN C 882 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 GLN D 145 ASN D 213 ASN D 248 HIS D 308 ASN D 440 ASN D 662 GLN D 666 GLN D 683 ASN D 882 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125337 restraints weight = 44505.466| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.64 r_work: 0.3333 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 29556 Z= 0.153 Angle : 0.683 12.328 40040 Z= 0.357 Chirality : 0.043 0.223 4484 Planarity : 0.006 0.149 4928 Dihedral : 7.646 58.161 3892 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 1.22 % Allowed : 13.91 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.12), residues: 3392 helix: -1.91 (0.09), residues: 2208 sheet: -2.20 (0.35), residues: 196 loop : -2.94 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 875 TYR 0.017 0.001 TYR D 905 PHE 0.026 0.001 PHE D 921 TRP 0.018 0.001 TRP D 444 HIS 0.004 0.001 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (29552) covalent geometry : angle 0.68278 / 0.36 (40032) SS BOND : bond 0.00626 / 0.38 ( 4) SS BOND : angle 1.44485 / 0.83 ( 8) hydrogen bonds : bond 0.05478 / 3.61 ( 1340) hydrogen bonds : angle 4.87745 / 3.31 ( 3984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 806 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 SER cc_start: 0.8499 (m) cc_final: 0.8110 (m) REVERT: A 592 MET cc_start: 0.8504 (mmm) cc_final: 0.8178 (mmp) REVERT: A 611 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8316 (mm-30) REVERT: A 632 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 649 GLU cc_start: 0.8541 (mp0) cc_final: 0.8161 (pm20) REVERT: A 671 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8563 (mtpt) REVERT: A 672 GLN cc_start: 0.8216 (tt0) cc_final: 0.7928 (tt0) REVERT: A 674 TYR cc_start: 0.8657 (m-80) cc_final: 0.8381 (m-10) REVERT: A 688 MET cc_start: 0.7756 (mtp) cc_final: 0.6549 (tmm) REVERT: A 775 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7461 (ttt180) REVERT: A 789 TRP cc_start: 0.8625 (m100) cc_final: 0.8291 (m100) REVERT: A 790 ASN cc_start: 0.9269 (m-40) cc_final: 0.8760 (t0) REVERT: A 798 PHE cc_start: 0.8923 (t80) cc_final: 0.8691 (t80) REVERT: A 832 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8677 (mtp85) REVERT: A 841 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7380 (ttp80) REVERT: A 955 LEU cc_start: 0.9297 (tp) cc_final: 0.8987 (tp) REVERT: B 323 SER cc_start: 0.8578 (m) cc_final: 0.8159 (m) REVERT: B 592 MET cc_start: 0.8504 (mmm) cc_final: 0.8183 (mmp) REVERT: B 632 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 649 GLU cc_start: 0.8523 (mp0) cc_final: 0.8133 (pm20) REVERT: B 671 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8562 (mtpt) REVERT: B 672 GLN cc_start: 0.8202 (tt0) cc_final: 0.7904 (tt0) REVERT: B 674 TYR cc_start: 0.8677 (m-80) cc_final: 0.8393 (m-10) REVERT: B 688 MET cc_start: 0.7743 (mtp) cc_final: 0.6539 (tmm) REVERT: B 775 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7460 (ttt180) REVERT: B 789 TRP cc_start: 0.8625 (m100) cc_final: 0.8291 (m100) REVERT: B 790 ASN cc_start: 0.9275 (m-40) cc_final: 0.8868 (m-40) REVERT: B 798 PHE cc_start: 0.8919 (t80) cc_final: 0.8695 (t80) REVERT: B 841 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7437 (ttp80) REVERT: B 853 MET cc_start: 0.8689 (mmt) cc_final: 0.8393 (mmt) REVERT: B 955 LEU cc_start: 0.9298 (tp) cc_final: 0.8984 (tp) REVERT: C 323 SER cc_start: 0.8569 (m) cc_final: 0.8151 (m) REVERT: C 592 MET cc_start: 0.8513 (mmm) cc_final: 0.8191 (mmp) REVERT: C 632 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8124 (mt-10) REVERT: C 649 GLU cc_start: 0.8527 (mp0) cc_final: 0.8130 (pm20) REVERT: C 671 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8579 (mtpt) REVERT: C 672 GLN cc_start: 0.8239 (tt0) cc_final: 0.7950 (tt0) REVERT: C 674 TYR cc_start: 0.8656 (m-80) cc_final: 0.8373 (m-10) REVERT: C 688 MET cc_start: 0.7749 (mtp) cc_final: 0.6542 (tmm) REVERT: C 775 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7466 (ttt180) REVERT: C 789 TRP cc_start: 0.8645 (m100) cc_final: 0.8313 (m100) REVERT: C 790 ASN cc_start: 0.9270 (m-40) cc_final: 0.8758 (t0) REVERT: C 798 PHE cc_start: 0.8923 (t80) cc_final: 0.8703 (t80) REVERT: C 841 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7379 (ttp80) REVERT: C 853 MET cc_start: 0.8688 (mmt) cc_final: 0.8391 (mmt) REVERT: C 1068 MET cc_start: 0.4549 (ttt) cc_final: 0.4186 (pmm) REVERT: D 323 SER cc_start: 0.8571 (m) cc_final: 0.8152 (m) REVERT: D 592 MET cc_start: 0.8506 (mmm) cc_final: 0.8185 (mmp) REVERT: D 632 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8102 (mt-10) REVERT: D 649 GLU cc_start: 0.8521 (mp0) cc_final: 0.8130 (pm20) REVERT: D 671 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8571 (mtpt) REVERT: D 672 GLN cc_start: 0.8229 (tt0) cc_final: 0.7935 (tt0) REVERT: D 674 TYR cc_start: 0.8659 (m-80) cc_final: 0.8376 (m-10) REVERT: D 688 MET cc_start: 0.7737 (mtp) cc_final: 0.6538 (tmm) REVERT: D 775 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7474 (ttt180) REVERT: D 789 TRP cc_start: 0.8638 (m100) cc_final: 0.8304 (m100) REVERT: D 790 ASN cc_start: 0.9270 (m-40) cc_final: 0.8754 (t0) REVERT: D 798 PHE cc_start: 0.8928 (t80) cc_final: 0.8710 (t80) REVERT: D 841 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7428 (ttp80) outliers start: 38 outliers final: 20 residues processed: 818 average time/residue: 0.1808 time to fit residues: 235.3593 Evaluate side-chains 735 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 715 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 774 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 188 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 835 HIS ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123987 restraints weight = 44518.514| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.88 r_work: 0.3294 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29556 Z= 0.145 Angle : 0.611 11.391 40040 Z= 0.316 Chirality : 0.042 0.189 4484 Planarity : 0.005 0.138 4928 Dihedral : 7.148 59.832 3892 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 2.38 % Allowed : 14.75 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.14), residues: 3392 helix: -0.76 (0.10), residues: 2220 sheet: -2.13 (0.35), residues: 196 loop : -2.88 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 875 TYR 0.013 0.001 TYR D 905 PHE 0.014 0.001 PHE B 921 TRP 0.015 0.001 TRP D 444 HIS 0.004 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (29552) covalent geometry : angle 0.61083 / 0.32 (40032) SS BOND : bond 0.00664 / 0.40 ( 4) SS BOND : angle 1.87977 / 1.07 ( 8) hydrogen bonds : bond 0.04014 / 2.64 ( 1340) hydrogen bonds : angle 4.26945 / 2.90 ( 3984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 782 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 SER cc_start: 0.8279 (m) cc_final: 0.7830 (m) REVERT: A 592 MET cc_start: 0.8426 (mmm) cc_final: 0.8034 (mmp) REVERT: A 606 GLU cc_start: 0.8541 (pp20) cc_final: 0.8120 (pp20) REVERT: A 611 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 645 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.6652 (t) REVERT: A 649 GLU cc_start: 0.8781 (mp0) cc_final: 0.8101 (mp0) REVERT: A 674 TYR cc_start: 0.8686 (m-80) cc_final: 0.8336 (m-80) REVERT: A 688 MET cc_start: 0.7640 (mtp) cc_final: 0.6351 (tmm) REVERT: A 785 PHE cc_start: 0.8571 (m-10) cc_final: 0.8231 (m-10) REVERT: A 790 ASN cc_start: 0.9245 (m-40) cc_final: 0.8796 (t0) REVERT: A 798 PHE cc_start: 0.8784 (t80) cc_final: 0.8553 (t80) REVERT: A 841 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7523 (ttp80) REVERT: A 955 LEU cc_start: 0.9339 (tp) cc_final: 0.9061 (tp) REVERT: B 323 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8069 (m) REVERT: B 592 MET cc_start: 0.8417 (mmm) cc_final: 0.8037 (mmp) REVERT: B 606 GLU cc_start: 0.8540 (pp20) cc_final: 0.8135 (pp20) REVERT: B 607 GLU cc_start: 0.8845 (tp30) cc_final: 0.8265 (tp30) REVERT: B 645 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.6648 (t) REVERT: B 649 GLU cc_start: 0.8779 (mp0) cc_final: 0.8071 (mp0) REVERT: B 674 TYR cc_start: 0.8689 (m-80) cc_final: 0.8333 (m-80) REVERT: B 688 MET cc_start: 0.7588 (mtp) cc_final: 0.6339 (tmm) REVERT: B 785 PHE cc_start: 0.8555 (m-10) cc_final: 0.8234 (m-10) REVERT: B 798 PHE cc_start: 0.8781 (t80) cc_final: 0.8523 (t80) REVERT: B 841 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7596 (ttp80) REVERT: B 898 TYR cc_start: 0.9342 (t80) cc_final: 0.8750 (t80) REVERT: B 955 LEU cc_start: 0.9337 (tp) cc_final: 0.9055 (tp) REVERT: B 1068 MET cc_start: 0.4490 (pmm) cc_final: 0.4002 (mtt) REVERT: C 323 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8072 (m) REVERT: C 592 MET cc_start: 0.8423 (mmm) cc_final: 0.7979 (mmp) REVERT: C 606 GLU cc_start: 0.8547 (pp20) cc_final: 0.8139 (pp20) REVERT: C 607 GLU cc_start: 0.8852 (tp30) cc_final: 0.8275 (tp30) REVERT: C 645 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.6656 (t) REVERT: C 649 GLU cc_start: 0.8775 (mp0) cc_final: 0.8073 (mp0) REVERT: C 672 GLN cc_start: 0.8344 (tt0) cc_final: 0.8140 (tt0) REVERT: C 674 TYR cc_start: 0.8685 (m-80) cc_final: 0.8327 (m-80) REVERT: C 688 MET cc_start: 0.7638 (mtp) cc_final: 0.6355 (tmm) REVERT: C 785 PHE cc_start: 0.8591 (m-10) cc_final: 0.8289 (m-10) REVERT: C 798 PHE cc_start: 0.8783 (t80) cc_final: 0.8528 (t80) REVERT: C 841 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7505 (ttp80) REVERT: C 898 TYR cc_start: 0.9343 (t80) cc_final: 0.8752 (t80) REVERT: C 955 LEU cc_start: 0.9335 (tp) cc_final: 0.9053 (tp) REVERT: C 1068 MET cc_start: 0.4469 (ttt) cc_final: 0.3647 (pmm) REVERT: D 323 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8064 (m) REVERT: D 592 MET cc_start: 0.8424 (mmm) cc_final: 0.7981 (mmp) REVERT: D 606 GLU cc_start: 0.8536 (pp20) cc_final: 0.8132 (pp20) REVERT: D 607 GLU cc_start: 0.8852 (tp30) cc_final: 0.8270 (tp30) REVERT: D 645 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.6666 (t) REVERT: D 649 GLU cc_start: 0.8782 (mp0) cc_final: 0.8075 (mp0) REVERT: D 672 GLN cc_start: 0.8365 (tt0) cc_final: 0.8163 (tt0) REVERT: D 674 TYR cc_start: 0.8684 (m-80) cc_final: 0.8322 (m-80) REVERT: D 688 MET cc_start: 0.7602 (mtp) cc_final: 0.6345 (tmm) REVERT: D 785 PHE cc_start: 0.8572 (m-10) cc_final: 0.8250 (m-10) REVERT: D 798 PHE cc_start: 0.8788 (t80) cc_final: 0.8531 (t80) REVERT: D 841 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7580 (ttp80) REVERT: D 898 TYR cc_start: 0.9343 (t80) cc_final: 0.8748 (t80) outliers start: 74 outliers final: 27 residues processed: 812 average time/residue: 0.1711 time to fit residues: 224.7018 Evaluate side-chains 757 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 723 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 905 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 222 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124910 restraints weight = 44087.363| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.85 r_work: 0.3304 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 29556 Z= 0.137 Angle : 0.594 11.239 40040 Z= 0.308 Chirality : 0.042 0.184 4484 Planarity : 0.005 0.129 4928 Dihedral : 6.886 59.328 3892 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.60 % Allowed : 17.29 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3392 helix: -0.27 (0.11), residues: 2208 sheet: -2.18 (0.35), residues: 196 loop : -2.83 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 875 TYR 0.011 0.001 TYR A 905 PHE 0.015 0.001 PHE A 921 TRP 0.032 0.002 TRP A 516 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (29552) covalent geometry : angle 0.59331 / 0.31 (40032) SS BOND : bond 0.00775 / 0.47 ( 4) SS BOND : angle 1.97499 / 1.11 ( 8) hydrogen bonds : bond 0.03669 / 2.40 ( 1340) hydrogen bonds : angle 4.13709 / 2.81 ( 3984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 753 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.9234 (mmm) cc_final: 0.9002 (tpp) REVERT: A 323 SER cc_start: 0.8305 (m) cc_final: 0.7880 (m) REVERT: A 592 MET cc_start: 0.8368 (mmm) cc_final: 0.8097 (mmp) REVERT: A 606 GLU cc_start: 0.8542 (pp20) cc_final: 0.8121 (pp20) REVERT: A 607 GLU cc_start: 0.8858 (tp30) cc_final: 0.8656 (tp30) REVERT: A 645 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.6532 (t) REVERT: A 649 GLU cc_start: 0.8785 (mp0) cc_final: 0.8058 (mp0) REVERT: A 674 TYR cc_start: 0.8694 (m-80) cc_final: 0.8332 (m-80) REVERT: A 688 MET cc_start: 0.7626 (mtp) cc_final: 0.6405 (tmm) REVERT: A 785 PHE cc_start: 0.8573 (m-10) cc_final: 0.8339 (m-80) REVERT: A 789 TRP cc_start: 0.8760 (m100) cc_final: 0.8464 (m100) REVERT: A 798 PHE cc_start: 0.8717 (t80) cc_final: 0.8477 (t80) REVERT: A 841 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7463 (ttp80) REVERT: B 152 MET cc_start: 0.9228 (mmm) cc_final: 0.8987 (tpp) REVERT: B 323 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8160 (m) REVERT: B 389 GLU cc_start: 0.8095 (tp30) cc_final: 0.7889 (tp30) REVERT: B 592 MET cc_start: 0.8355 (mmm) cc_final: 0.7910 (mmp) REVERT: B 606 GLU cc_start: 0.8529 (pp20) cc_final: 0.8113 (pp20) REVERT: B 607 GLU cc_start: 0.8881 (tp30) cc_final: 0.8326 (tp30) REVERT: B 645 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.6545 (t) REVERT: B 649 GLU cc_start: 0.8795 (mp0) cc_final: 0.8046 (mp0) REVERT: B 674 TYR cc_start: 0.8698 (m-80) cc_final: 0.8339 (m-80) REVERT: B 688 MET cc_start: 0.7632 (mtp) cc_final: 0.6430 (tmm) REVERT: B 785 PHE cc_start: 0.8544 (m-10) cc_final: 0.8199 (m-10) REVERT: B 789 TRP cc_start: 0.8773 (m100) cc_final: 0.8478 (m100) REVERT: B 798 PHE cc_start: 0.8720 (t80) cc_final: 0.8484 (t80) REVERT: B 841 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7528 (ttp80) REVERT: B 898 TYR cc_start: 0.9382 (t80) cc_final: 0.8683 (t80) REVERT: B 1068 MET cc_start: 0.4502 (pmm) cc_final: 0.3883 (mtt) REVERT: C 152 MET cc_start: 0.9221 (mmm) cc_final: 0.8984 (tpp) REVERT: C 323 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 389 GLU cc_start: 0.8139 (tp30) cc_final: 0.7921 (tp30) REVERT: C 592 MET cc_start: 0.8350 (mmm) cc_final: 0.7916 (mmp) REVERT: C 606 GLU cc_start: 0.8523 (pp20) cc_final: 0.8106 (pp20) REVERT: C 607 GLU cc_start: 0.8881 (tp30) cc_final: 0.8326 (tp30) REVERT: C 645 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.6442 (t) REVERT: C 649 GLU cc_start: 0.8803 (mp0) cc_final: 0.8054 (mp0) REVERT: C 674 TYR cc_start: 0.8692 (m-80) cc_final: 0.8330 (m-80) REVERT: C 688 MET cc_start: 0.7615 (mtp) cc_final: 0.6402 (tmm) REVERT: C 785 PHE cc_start: 0.8551 (m-10) cc_final: 0.8207 (m-10) REVERT: C 789 TRP cc_start: 0.8781 (m100) cc_final: 0.8438 (m100) REVERT: C 798 PHE cc_start: 0.8715 (t80) cc_final: 0.8471 (t80) REVERT: C 841 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7488 (ttp80) REVERT: C 898 TYR cc_start: 0.9376 (t80) cc_final: 0.8679 (t80) REVERT: C 977 GLN cc_start: 0.8569 (tp40) cc_final: 0.8108 (tp40) REVERT: C 1068 MET cc_start: 0.4479 (ttt) cc_final: 0.3505 (pmm) REVERT: D 152 MET cc_start: 0.9241 (mmm) cc_final: 0.9001 (tpp) REVERT: D 323 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8138 (m) REVERT: D 389 GLU cc_start: 0.8132 (tp30) cc_final: 0.7916 (tp30) REVERT: D 592 MET cc_start: 0.8350 (mmm) cc_final: 0.7919 (mmp) REVERT: D 606 GLU cc_start: 0.8523 (pp20) cc_final: 0.8107 (pp20) REVERT: D 607 GLU cc_start: 0.8894 (tp30) cc_final: 0.8340 (tp30) REVERT: D 645 SER cc_start: 0.7685 (OUTLIER) cc_final: 0.6553 (t) REVERT: D 649 GLU cc_start: 0.8801 (mp0) cc_final: 0.8046 (mp0) REVERT: D 674 TYR cc_start: 0.8684 (m-80) cc_final: 0.8318 (m-80) REVERT: D 688 MET cc_start: 0.7643 (mtp) cc_final: 0.6432 (tmm) REVERT: D 785 PHE cc_start: 0.8557 (m-10) cc_final: 0.8209 (m-10) REVERT: D 789 TRP cc_start: 0.8754 (m100) cc_final: 0.8511 (m100) REVERT: D 798 PHE cc_start: 0.8710 (t80) cc_final: 0.8465 (t80) REVERT: D 841 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7526 (ttp80) REVERT: D 898 TYR cc_start: 0.9374 (t80) cc_final: 0.8678 (t80) REVERT: D 955 LEU cc_start: 0.9265 (tp) cc_final: 0.9029 (tp) REVERT: D 977 GLN cc_start: 0.8566 (tp40) cc_final: 0.8103 (tp40) outliers start: 81 outliers final: 45 residues processed: 785 average time/residue: 0.1726 time to fit residues: 219.9134 Evaluate side-chains 756 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 704 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 905 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 54 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 204 optimal weight: 0.1980 chunk 214 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 201 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125890 restraints weight = 44085.896| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.87 r_work: 0.3317 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 29556 Z= 0.124 Angle : 0.575 10.801 40040 Z= 0.298 Chirality : 0.042 0.182 4484 Planarity : 0.005 0.122 4928 Dihedral : 6.668 58.612 3892 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.84 % Favored : 93.04 % Rotamer: Outliers : 2.51 % Allowed : 18.96 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3392 helix: 0.07 (0.11), residues: 2192 sheet: -2.05 (0.35), residues: 196 loop : -2.66 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 875 TYR 0.012 0.001 TYR B 905 PHE 0.019 0.001 PHE A 921 TRP 0.037 0.002 TRP A 516 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (29552) covalent geometry : angle 0.57345 / 0.30 (40032) SS BOND : bond 0.01309 / 0.79 ( 4) SS BOND : angle 3.05469 / 1.72 ( 8) hydrogen bonds : bond 0.03500 / 2.30 ( 1340) hydrogen bonds : angle 4.02093 / 2.73 ( 3984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 770 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.9200 (mmm) cc_final: 0.8966 (tpp) REVERT: A 306 SER cc_start: 0.9089 (t) cc_final: 0.8506 (p) REVERT: A 323 SER cc_start: 0.8330 (m) cc_final: 0.7912 (m) REVERT: A 592 MET cc_start: 0.8248 (mmm) cc_final: 0.7867 (mmp) REVERT: A 606 GLU cc_start: 0.8528 (pp20) cc_final: 0.8102 (pp20) REVERT: A 628 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8415 (mt-10) REVERT: A 645 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.6432 (t) REVERT: A 649 GLU cc_start: 0.8802 (mp0) cc_final: 0.8053 (mp0) REVERT: A 674 TYR cc_start: 0.8682 (m-80) cc_final: 0.8360 (m-80) REVERT: A 688 MET cc_start: 0.7619 (mtp) cc_final: 0.6401 (tmm) REVERT: A 785 PHE cc_start: 0.8573 (m-10) cc_final: 0.8369 (m-80) REVERT: A 789 TRP cc_start: 0.8751 (m100) cc_final: 0.8535 (m100) REVERT: A 798 PHE cc_start: 0.8688 (t80) cc_final: 0.8423 (t80) REVERT: A 841 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7576 (ttp80) REVERT: A 955 LEU cc_start: 0.9287 (tp) cc_final: 0.9067 (tp) REVERT: A 977 GLN cc_start: 0.8582 (tp40) cc_final: 0.8105 (tp40) REVERT: B 152 MET cc_start: 0.9210 (mmm) cc_final: 0.8968 (tpp) REVERT: B 306 SER cc_start: 0.9098 (t) cc_final: 0.8511 (p) REVERT: B 323 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8181 (m) REVERT: B 592 MET cc_start: 0.8304 (mmm) cc_final: 0.7930 (mmp) REVERT: B 606 GLU cc_start: 0.8517 (pp20) cc_final: 0.8092 (pp20) REVERT: B 607 GLU cc_start: 0.8860 (tp30) cc_final: 0.8385 (tp30) REVERT: B 628 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 645 SER cc_start: 0.7611 (OUTLIER) cc_final: 0.6406 (t) REVERT: B 649 GLU cc_start: 0.8794 (mp0) cc_final: 0.8040 (mp0) REVERT: B 674 TYR cc_start: 0.8679 (m-80) cc_final: 0.8357 (m-80) REVERT: B 688 MET cc_start: 0.7606 (mtp) cc_final: 0.6371 (tmm) REVERT: B 785 PHE cc_start: 0.8550 (m-10) cc_final: 0.8321 (m-80) REVERT: B 789 TRP cc_start: 0.8745 (m100) cc_final: 0.8538 (m100) REVERT: B 798 PHE cc_start: 0.8689 (t80) cc_final: 0.8421 (t80) REVERT: B 841 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7496 (ttp80) REVERT: B 898 TYR cc_start: 0.9367 (t80) cc_final: 0.8721 (t80) REVERT: B 955 LEU cc_start: 0.9276 (tp) cc_final: 0.9054 (tp) REVERT: B 977 GLN cc_start: 0.8594 (tp40) cc_final: 0.8165 (tp40) REVERT: B 1049 MET cc_start: 0.7888 (ptm) cc_final: 0.7683 (ttp) REVERT: C 152 MET cc_start: 0.9201 (mmm) cc_final: 0.8958 (tpp) REVERT: C 306 SER cc_start: 0.9097 (t) cc_final: 0.8510 (p) REVERT: C 323 SER cc_start: 0.8559 (m) cc_final: 0.8170 (m) REVERT: C 592 MET cc_start: 0.8309 (mmm) cc_final: 0.7932 (mmp) REVERT: C 606 GLU cc_start: 0.8519 (pp20) cc_final: 0.8092 (pp20) REVERT: C 607 GLU cc_start: 0.8840 (tp30) cc_final: 0.8369 (tp30) REVERT: C 628 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8432 (mt-10) REVERT: C 645 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.6421 (t) REVERT: C 649 GLU cc_start: 0.8813 (mp0) cc_final: 0.8071 (mp0) REVERT: C 674 TYR cc_start: 0.8672 (m-80) cc_final: 0.8348 (m-80) REVERT: C 688 MET cc_start: 0.7611 (mtp) cc_final: 0.6393 (tmm) REVERT: C 785 PHE cc_start: 0.8542 (m-10) cc_final: 0.8196 (m-10) REVERT: C 789 TRP cc_start: 0.8788 (m100) cc_final: 0.8492 (m100) REVERT: C 841 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7616 (ttp80) REVERT: C 898 TYR cc_start: 0.9365 (t80) cc_final: 0.8719 (t80) REVERT: C 955 LEU cc_start: 0.9275 (tp) cc_final: 0.9055 (tp) REVERT: C 977 GLN cc_start: 0.8588 (tp40) cc_final: 0.8160 (tp40) REVERT: C 1068 MET cc_start: 0.4504 (ttt) cc_final: 0.3902 (pmm) REVERT: D 152 MET cc_start: 0.9203 (mmm) cc_final: 0.8959 (tpp) REVERT: D 306 SER cc_start: 0.9098 (t) cc_final: 0.8517 (p) REVERT: D 323 SER cc_start: 0.8559 (m) cc_final: 0.8174 (m) REVERT: D 592 MET cc_start: 0.8310 (mmm) cc_final: 0.7932 (mmp) REVERT: D 606 GLU cc_start: 0.8517 (pp20) cc_final: 0.8094 (pp20) REVERT: D 607 GLU cc_start: 0.8848 (tp30) cc_final: 0.8374 (tp30) REVERT: D 628 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8442 (mt-10) REVERT: D 645 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.6420 (t) REVERT: D 649 GLU cc_start: 0.8807 (mp0) cc_final: 0.8059 (mp0) REVERT: D 674 TYR cc_start: 0.8667 (m-80) cc_final: 0.8341 (m-80) REVERT: D 688 MET cc_start: 0.7614 (mtp) cc_final: 0.6373 (tmm) REVERT: D 785 PHE cc_start: 0.8574 (m-10) cc_final: 0.8339 (m-80) REVERT: D 789 TRP cc_start: 0.8733 (m100) cc_final: 0.8435 (m100) REVERT: D 798 PHE cc_start: 0.8675 (t80) cc_final: 0.8411 (t80) REVERT: D 841 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7529 (ttp80) REVERT: D 898 TYR cc_start: 0.9368 (t80) cc_final: 0.8721 (t80) REVERT: D 953 TYR cc_start: 0.9506 (t80) cc_final: 0.9129 (t80) REVERT: D 955 LEU cc_start: 0.9293 (tp) cc_final: 0.9054 (tp) REVERT: D 977 GLN cc_start: 0.8595 (tp40) cc_final: 0.8169 (tp40) outliers start: 78 outliers final: 46 residues processed: 798 average time/residue: 0.1691 time to fit residues: 219.9629 Evaluate side-chains 770 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 719 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 905 TYR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 905 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 1068 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 331 optimal weight: 0.0070 chunk 205 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 272 optimal weight: 0.0070 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN A 646 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 646 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 646 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126644 restraints weight = 43874.831| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.87 r_work: 0.3328 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 29556 Z= 0.118 Angle : 0.574 10.370 40040 Z= 0.298 Chirality : 0.041 0.180 4484 Planarity : 0.005 0.117 4928 Dihedral : 6.518 58.653 3892 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 2.09 % Allowed : 20.28 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3392 helix: 0.19 (0.11), residues: 2212 sheet: -1.95 (0.36), residues: 196 loop : -2.62 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 832 TYR 0.011 0.001 TYR B 905 PHE 0.013 0.001 PHE B 921 TRP 0.041 0.002 TRP C 516 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (29552) covalent geometry : angle 0.57277 / 0.30 (40032) SS BOND : bond 0.00429 / 0.26 ( 4) SS BOND : angle 2.57790 / 1.45 ( 8) hydrogen bonds : bond 0.03397 / 2.23 ( 1340) hydrogen bonds : angle 3.97658 / 2.71 ( 3984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 765 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8682 (pp30) cc_final: 0.8337 (pp30) REVERT: A 306 SER cc_start: 0.9043 (t) cc_final: 0.8437 (p) REVERT: A 435 ASP cc_start: 0.8650 (m-30) cc_final: 0.8224 (m-30) REVERT: A 606 GLU cc_start: 0.8545 (pp20) cc_final: 0.8112 (pp20) REVERT: A 607 GLU cc_start: 0.8882 (tp30) cc_final: 0.8377 (tp30) REVERT: A 628 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8380 (mt-10) REVERT: A 645 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.6222 (t) REVERT: A 646 ASN cc_start: 0.7634 (m-40) cc_final: 0.6951 (m110) REVERT: A 649 GLU cc_start: 0.8796 (mp0) cc_final: 0.7956 (mp0) REVERT: A 674 TYR cc_start: 0.8677 (m-80) cc_final: 0.8346 (m-80) REVERT: A 688 MET cc_start: 0.7613 (mtp) cc_final: 0.6367 (tmm) REVERT: A 785 PHE cc_start: 0.8579 (m-10) cc_final: 0.8373 (m-80) REVERT: A 789 TRP cc_start: 0.8728 (m100) cc_final: 0.8447 (m100) REVERT: A 790 ASN cc_start: 0.9026 (m-40) cc_final: 0.8541 (t0) REVERT: A 798 PHE cc_start: 0.8704 (t80) cc_final: 0.8439 (t80) REVERT: A 841 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7579 (ttp80) REVERT: A 955 LEU cc_start: 0.9314 (tp) cc_final: 0.9095 (tp) REVERT: A 977 GLN cc_start: 0.8608 (tp40) cc_final: 0.8096 (tp40) REVERT: B 297 GLN cc_start: 0.8700 (pp30) cc_final: 0.8326 (pp30) REVERT: B 306 SER cc_start: 0.9052 (t) cc_final: 0.8435 (p) REVERT: B 323 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8176 (m) REVERT: B 435 ASP cc_start: 0.8651 (m-30) cc_final: 0.8223 (m-30) REVERT: B 592 MET cc_start: 0.8279 (mmm) cc_final: 0.7898 (mmp) REVERT: B 606 GLU cc_start: 0.8536 (pp20) cc_final: 0.8088 (pp20) REVERT: B 607 GLU cc_start: 0.8867 (tp30) cc_final: 0.8357 (tp30) REVERT: B 628 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8404 (mt-10) REVERT: B 645 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.6258 (t) REVERT: B 646 ASN cc_start: 0.7632 (m-40) cc_final: 0.7013 (m110) REVERT: B 649 GLU cc_start: 0.8813 (mp0) cc_final: 0.7990 (mp0) REVERT: B 674 TYR cc_start: 0.8673 (m-80) cc_final: 0.8343 (m-80) REVERT: B 688 MET cc_start: 0.7607 (mtp) cc_final: 0.6364 (tmm) REVERT: B 785 PHE cc_start: 0.8573 (m-10) cc_final: 0.8372 (m-80) REVERT: B 832 ARG cc_start: 0.8968 (tpp80) cc_final: 0.8601 (mtp85) REVERT: B 841 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7600 (ttp80) REVERT: B 898 TYR cc_start: 0.9356 (t80) cc_final: 0.8707 (t80) REVERT: B 955 LEU cc_start: 0.9309 (tp) cc_final: 0.9089 (tp) REVERT: B 977 GLN cc_start: 0.8614 (tp40) cc_final: 0.8099 (tp40) REVERT: C 297 GLN cc_start: 0.8690 (pp30) cc_final: 0.8364 (pp30) REVERT: C 306 SER cc_start: 0.9056 (t) cc_final: 0.8441 (p) REVERT: C 592 MET cc_start: 0.8279 (mmm) cc_final: 0.7897 (mmp) REVERT: C 606 GLU cc_start: 0.8540 (pp20) cc_final: 0.8092 (pp20) REVERT: C 607 GLU cc_start: 0.8873 (tp30) cc_final: 0.8360 (tp30) REVERT: C 628 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8407 (mt-10) REVERT: C 645 SER cc_start: 0.7569 (OUTLIER) cc_final: 0.6308 (t) REVERT: C 649 GLU cc_start: 0.8824 (mp0) cc_final: 0.8056 (mp0) REVERT: C 674 TYR cc_start: 0.8653 (m-80) cc_final: 0.8367 (m-80) REVERT: C 688 MET cc_start: 0.7608 (mtp) cc_final: 0.6360 (tmm) REVERT: C 785 PHE cc_start: 0.8569 (m-10) cc_final: 0.8337 (m-80) REVERT: C 789 TRP cc_start: 0.8726 (m100) cc_final: 0.8480 (m100) REVERT: C 841 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7607 (ttp80) REVERT: C 898 TYR cc_start: 0.9357 (t80) cc_final: 0.8710 (t80) REVERT: C 955 LEU cc_start: 0.9308 (tp) cc_final: 0.9088 (tp) REVERT: C 977 GLN cc_start: 0.8614 (tp40) cc_final: 0.8101 (tp40) REVERT: C 1068 MET cc_start: 0.4346 (ttt) cc_final: 0.3872 (pmm) REVERT: D 297 GLN cc_start: 0.8686 (pp30) cc_final: 0.8357 (pp30) REVERT: D 306 SER cc_start: 0.9047 (t) cc_final: 0.8439 (p) REVERT: D 323 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8176 (m) REVERT: D 592 MET cc_start: 0.8276 (mmm) cc_final: 0.7896 (mmp) REVERT: D 606 GLU cc_start: 0.8534 (pp20) cc_final: 0.8087 (pp20) REVERT: D 607 GLU cc_start: 0.8877 (tp30) cc_final: 0.8363 (tp30) REVERT: D 628 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8410 (mt-10) REVERT: D 645 SER cc_start: 0.7574 (OUTLIER) cc_final: 0.6251 (t) REVERT: D 646 ASN cc_start: 0.7623 (m-40) cc_final: 0.7008 (m110) REVERT: D 649 GLU cc_start: 0.8812 (mp0) cc_final: 0.7990 (mp0) REVERT: D 674 TYR cc_start: 0.8664 (m-80) cc_final: 0.8374 (m-80) REVERT: D 688 MET cc_start: 0.7615 (mtp) cc_final: 0.6366 (tmm) REVERT: D 785 PHE cc_start: 0.8581 (m-10) cc_final: 0.8374 (m-80) REVERT: D 789 TRP cc_start: 0.8724 (m100) cc_final: 0.8394 (m100) REVERT: D 841 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7620 (ttp80) REVERT: D 898 TYR cc_start: 0.9354 (t80) cc_final: 0.8701 (t80) REVERT: D 955 LEU cc_start: 0.9306 (tp) cc_final: 0.9061 (tp) REVERT: D 977 GLN cc_start: 0.8609 (tp40) cc_final: 0.8093 (tp40) outliers start: 65 outliers final: 43 residues processed: 798 average time/residue: 0.1625 time to fit residues: 213.3597 Evaluate side-chains 803 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 754 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 1068 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 138 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 298 optimal weight: 0.0070 chunk 222 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 226 optimal weight: 0.0030 chunk 254 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 127 optimal weight: 1.9990 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN A 915 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128243 restraints weight = 43848.204| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.87 r_work: 0.3338 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29556 Z= 0.110 Angle : 0.567 9.936 40040 Z= 0.294 Chirality : 0.041 0.181 4484 Planarity : 0.005 0.111 4928 Dihedral : 6.356 59.022 3892 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 2.47 % Allowed : 20.76 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3392 helix: 0.39 (0.11), residues: 2188 sheet: -1.79 (0.37), residues: 196 loop : -2.49 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 355 TYR 0.015 0.001 TYR A 905 PHE 0.013 0.001 PHE B 921 TRP 0.046 0.002 TRP C 516 HIS 0.003 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (29552) covalent geometry : angle 0.56574 / 0.29 (40032) SS BOND : bond 0.00548 / 0.33 ( 4) SS BOND : angle 2.19362 / 1.23 ( 8) hydrogen bonds : bond 0.03282 / 2.15 ( 1340) hydrogen bonds : angle 3.92870 / 2.69 ( 3984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 801 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8695 (pp30) cc_final: 0.8336 (pp30) REVERT: A 306 SER cc_start: 0.9038 (t) cc_final: 0.8435 (p) REVERT: A 606 GLU cc_start: 0.8523 (pp20) cc_final: 0.8076 (pp20) REVERT: A 607 GLU cc_start: 0.8895 (tp30) cc_final: 0.8393 (tp30) REVERT: A 628 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8394 (mt-10) REVERT: A 645 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.6168 (t) REVERT: A 646 ASN cc_start: 0.7424 (m-40) cc_final: 0.6854 (m110) REVERT: A 649 GLU cc_start: 0.8771 (mp0) cc_final: 0.7971 (mp0) REVERT: A 674 TYR cc_start: 0.8648 (m-80) cc_final: 0.8443 (m-10) REVERT: A 688 MET cc_start: 0.7596 (mtp) cc_final: 0.6349 (tmm) REVERT: A 789 TRP cc_start: 0.8707 (m100) cc_final: 0.8426 (m100) REVERT: A 808 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 854 MET cc_start: 0.7889 (mmp) cc_final: 0.7588 (ptt) REVERT: A 955 LEU cc_start: 0.9316 (tp) cc_final: 0.9076 (tp) REVERT: A 977 GLN cc_start: 0.8642 (tp40) cc_final: 0.8152 (tp40) REVERT: B 297 GLN cc_start: 0.8706 (pp30) cc_final: 0.8285 (pp30) REVERT: B 306 SER cc_start: 0.9045 (t) cc_final: 0.8427 (p) REVERT: B 323 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8169 (m) REVERT: B 592 MET cc_start: 0.8257 (mmm) cc_final: 0.7789 (mmp) REVERT: B 606 GLU cc_start: 0.8525 (pp20) cc_final: 0.8063 (pp20) REVERT: B 608 LEU cc_start: 0.8863 (tp) cc_final: 0.8093 (tp) REVERT: B 628 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8374 (mt-10) REVERT: B 645 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.6214 (t) REVERT: B 646 ASN cc_start: 0.7423 (m-40) cc_final: 0.6924 (m110) REVERT: B 649 GLU cc_start: 0.8768 (mp0) cc_final: 0.7988 (mp0) REVERT: B 674 TYR cc_start: 0.8650 (m-80) cc_final: 0.8359 (m-80) REVERT: B 688 MET cc_start: 0.7591 (mtp) cc_final: 0.6342 (tmm) REVERT: B 779 MET cc_start: 0.8207 (tpp) cc_final: 0.7537 (ttm) REVERT: B 785 PHE cc_start: 0.8594 (m-10) cc_final: 0.8384 (m-80) REVERT: B 832 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8627 (mtp85) REVERT: B 854 MET cc_start: 0.7895 (mmp) cc_final: 0.7584 (ptt) REVERT: B 898 TYR cc_start: 0.9359 (t80) cc_final: 0.8808 (t80) REVERT: B 955 LEU cc_start: 0.9318 (tp) cc_final: 0.9073 (tp) REVERT: B 977 GLN cc_start: 0.8634 (tp40) cc_final: 0.8151 (tp40) REVERT: C 297 GLN cc_start: 0.8704 (pp30) cc_final: 0.8276 (pp30) REVERT: C 306 SER cc_start: 0.9043 (t) cc_final: 0.8420 (p) REVERT: C 323 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8171 (m) REVERT: C 592 MET cc_start: 0.8286 (mmm) cc_final: 0.7820 (mmp) REVERT: C 606 GLU cc_start: 0.8526 (pp20) cc_final: 0.8064 (pp20) REVERT: C 608 LEU cc_start: 0.8867 (tp) cc_final: 0.8101 (tp) REVERT: C 628 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8417 (mt-10) REVERT: C 645 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.6252 (t) REVERT: C 649 GLU cc_start: 0.8769 (mp0) cc_final: 0.8001 (mp0) REVERT: C 688 MET cc_start: 0.7581 (mtp) cc_final: 0.6338 (tmm) REVERT: C 779 MET cc_start: 0.8156 (tpp) cc_final: 0.7473 (ttm) REVERT: C 785 PHE cc_start: 0.8590 (m-10) cc_final: 0.8350 (m-80) REVERT: C 789 TRP cc_start: 0.8685 (m100) cc_final: 0.8485 (m100) REVERT: C 854 MET cc_start: 0.7884 (mmp) cc_final: 0.7586 (ptt) REVERT: C 898 TYR cc_start: 0.9359 (t80) cc_final: 0.8810 (t80) REVERT: C 955 LEU cc_start: 0.9318 (tp) cc_final: 0.9074 (tp) REVERT: C 977 GLN cc_start: 0.8616 (tp40) cc_final: 0.8131 (tp40) REVERT: C 1049 MET cc_start: 0.7863 (ptm) cc_final: 0.7559 (ttp) REVERT: C 1068 MET cc_start: 0.4240 (ttt) cc_final: 0.3952 (pmm) REVERT: D 297 GLN cc_start: 0.8699 (pp30) cc_final: 0.8270 (pp30) REVERT: D 306 SER cc_start: 0.9042 (t) cc_final: 0.8424 (p) REVERT: D 323 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8158 (m) REVERT: D 592 MET cc_start: 0.8288 (mmm) cc_final: 0.7820 (mmp) REVERT: D 606 GLU cc_start: 0.8526 (pp20) cc_final: 0.8061 (pp20) REVERT: D 608 LEU cc_start: 0.8867 (tp) cc_final: 0.8102 (tp) REVERT: D 628 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8418 (mt-10) REVERT: D 645 SER cc_start: 0.7533 (OUTLIER) cc_final: 0.6191 (t) REVERT: D 646 ASN cc_start: 0.7424 (m-40) cc_final: 0.6922 (m110) REVERT: D 649 GLU cc_start: 0.8784 (mp0) cc_final: 0.7998 (mp0) REVERT: D 688 MET cc_start: 0.7596 (mtp) cc_final: 0.6355 (tmm) REVERT: D 779 MET cc_start: 0.8196 (tpp) cc_final: 0.7518 (ttm) REVERT: D 785 PHE cc_start: 0.8598 (m-10) cc_final: 0.8381 (m-80) REVERT: D 789 TRP cc_start: 0.8701 (m100) cc_final: 0.8344 (m100) REVERT: D 854 MET cc_start: 0.7880 (mmp) cc_final: 0.7592 (ptt) REVERT: D 898 TYR cc_start: 0.9343 (t80) cc_final: 0.8747 (t80) REVERT: D 955 LEU cc_start: 0.9312 (tp) cc_final: 0.9039 (tp) REVERT: D 977 GLN cc_start: 0.8622 (tp40) cc_final: 0.8136 (tp40) REVERT: D 1049 MET cc_start: 0.7849 (ptm) cc_final: 0.7549 (ttp) outliers start: 77 outliers final: 48 residues processed: 847 average time/residue: 0.1628 time to fit residues: 226.5415 Evaluate side-chains 813 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 757 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 915 ASN Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 268 optimal weight: 1.9990 chunk 328 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN A 915 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 732 ASN D 915 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125532 restraints weight = 44065.366| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.85 r_work: 0.3299 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29556 Z= 0.158 Angle : 0.615 11.308 40040 Z= 0.315 Chirality : 0.043 0.182 4484 Planarity : 0.005 0.107 4928 Dihedral : 6.363 59.953 3892 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 2.54 % Allowed : 21.63 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3392 helix: 0.45 (0.11), residues: 2208 sheet: -1.86 (0.36), residues: 196 loop : -2.49 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 832 TYR 0.015 0.001 TYR A 905 PHE 0.012 0.001 PHE A 620 TRP 0.049 0.002 TRP B 516 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (29552) covalent geometry : angle 0.61485 / 0.32 (40032) SS BOND : bond 0.00457 / 0.28 ( 4) SS BOND : angle 2.01546 / 1.14 ( 8) hydrogen bonds : bond 0.03478 / 2.27 ( 1340) hydrogen bonds : angle 3.93663 / 2.69 ( 3984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 776 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8748 (pp30) cc_final: 0.8382 (pp30) REVERT: A 323 SER cc_start: 0.8232 (m) cc_final: 0.7861 (m) REVERT: A 435 ASP cc_start: 0.8663 (m-30) cc_final: 0.8251 (m-30) REVERT: A 486 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8278 (mm-30) REVERT: A 606 GLU cc_start: 0.8524 (pp20) cc_final: 0.8072 (pp20) REVERT: A 607 GLU cc_start: 0.8891 (tp30) cc_final: 0.8405 (tp30) REVERT: A 613 GLU cc_start: 0.8075 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 628 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 645 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.6215 (t) REVERT: A 646 ASN cc_start: 0.7432 (m-40) cc_final: 0.7025 (m110) REVERT: A 649 GLU cc_start: 0.8807 (mp0) cc_final: 0.7963 (mp0) REVERT: A 674 TYR cc_start: 0.8675 (m-80) cc_final: 0.8342 (m-80) REVERT: A 688 MET cc_start: 0.7611 (mtp) cc_final: 0.6349 (tmm) REVERT: A 789 TRP cc_start: 0.8690 (m100) cc_final: 0.8438 (m100) REVERT: A 798 PHE cc_start: 0.8780 (t80) cc_final: 0.8483 (t80) REVERT: A 808 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 841 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7685 (ttp80) REVERT: A 854 MET cc_start: 0.7914 (mmp) cc_final: 0.7627 (ptt) REVERT: B 297 GLN cc_start: 0.8683 (pp30) cc_final: 0.8323 (pp30) REVERT: B 323 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8347 (m) REVERT: B 435 ASP cc_start: 0.8654 (m-30) cc_final: 0.8260 (m-30) REVERT: B 486 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 592 MET cc_start: 0.8296 (mmm) cc_final: 0.7938 (mmp) REVERT: B 606 GLU cc_start: 0.8460 (pp20) cc_final: 0.7953 (pp20) REVERT: B 613 GLU cc_start: 0.8020 (tt0) cc_final: 0.7705 (tm-30) REVERT: B 628 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 645 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.6198 (t) REVERT: B 646 ASN cc_start: 0.7426 (m-40) cc_final: 0.6996 (m110) REVERT: B 649 GLU cc_start: 0.8816 (mp0) cc_final: 0.7952 (mp0) REVERT: B 674 TYR cc_start: 0.8674 (m-80) cc_final: 0.8385 (m-80) REVERT: B 688 MET cc_start: 0.7611 (mtp) cc_final: 0.6346 (tmm) REVERT: B 798 PHE cc_start: 0.8731 (t80) cc_final: 0.8438 (t80) REVERT: B 841 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7681 (ttp80) REVERT: B 854 MET cc_start: 0.7896 (mmp) cc_final: 0.7615 (ptt) REVERT: B 898 TYR cc_start: 0.9387 (t80) cc_final: 0.8699 (t80) REVERT: B 977 GLN cc_start: 0.8714 (tp40) cc_final: 0.8138 (tp40) REVERT: C 297 GLN cc_start: 0.8683 (pp30) cc_final: 0.8320 (pp30) REVERT: C 323 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8346 (m) REVERT: C 435 ASP cc_start: 0.8646 (m-30) cc_final: 0.8248 (m-30) REVERT: C 592 MET cc_start: 0.8301 (mmm) cc_final: 0.7950 (mmp) REVERT: C 606 GLU cc_start: 0.8459 (pp20) cc_final: 0.7954 (pp20) REVERT: C 613 GLU cc_start: 0.8033 (tt0) cc_final: 0.7723 (tm-30) REVERT: C 628 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 645 SER cc_start: 0.7535 (OUTLIER) cc_final: 0.6213 (t) REVERT: C 649 GLU cc_start: 0.8852 (mp0) cc_final: 0.8074 (mp0) REVERT: C 688 MET cc_start: 0.7606 (mtp) cc_final: 0.6346 (tmm) REVERT: C 841 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7626 (ttp80) REVERT: C 854 MET cc_start: 0.7892 (mmp) cc_final: 0.7620 (ptt) REVERT: C 898 TYR cc_start: 0.9381 (t80) cc_final: 0.8696 (t80) REVERT: C 977 GLN cc_start: 0.8696 (tp40) cc_final: 0.8119 (tp40) REVERT: C 1068 MET cc_start: 0.4278 (ttt) cc_final: 0.3950 (pmm) REVERT: D 297 GLN cc_start: 0.8671 (pp30) cc_final: 0.8316 (pp30) REVERT: D 323 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (m) REVERT: D 435 ASP cc_start: 0.8662 (m-30) cc_final: 0.8266 (m-30) REVERT: D 486 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8293 (mm-30) REVERT: D 592 MET cc_start: 0.8295 (mmm) cc_final: 0.7944 (mmp) REVERT: D 606 GLU cc_start: 0.8463 (pp20) cc_final: 0.7958 (pp20) REVERT: D 613 GLU cc_start: 0.8026 (tt0) cc_final: 0.7715 (tm-30) REVERT: D 628 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8384 (mt-10) REVERT: D 645 SER cc_start: 0.7555 (OUTLIER) cc_final: 0.6189 (t) REVERT: D 646 ASN cc_start: 0.7431 (m-40) cc_final: 0.7022 (m110) REVERT: D 649 GLU cc_start: 0.8815 (mp0) cc_final: 0.7965 (mp0) REVERT: D 688 MET cc_start: 0.7616 (mtp) cc_final: 0.6358 (tmm) REVERT: D 789 TRP cc_start: 0.8695 (m100) cc_final: 0.8439 (m100) REVERT: D 841 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7635 (ttp80) REVERT: D 854 MET cc_start: 0.7893 (mmp) cc_final: 0.7624 (ptt) REVERT: D 898 TYR cc_start: 0.9383 (t80) cc_final: 0.8699 (t80) REVERT: D 977 GLN cc_start: 0.8690 (tp40) cc_final: 0.8115 (tp40) outliers start: 79 outliers final: 60 residues processed: 821 average time/residue: 0.1655 time to fit residues: 221.2322 Evaluate side-chains 814 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 746 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 TRP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 342 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 220 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 HIS A 499 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124071 restraints weight = 44301.259| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.86 r_work: 0.3279 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29556 Z= 0.183 Angle : 0.625 11.354 40040 Z= 0.323 Chirality : 0.044 0.284 4484 Planarity : 0.005 0.104 4928 Dihedral : 6.442 59.767 3892 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 2.54 % Allowed : 21.66 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 3392 helix: 0.48 (0.11), residues: 2196 sheet: -1.94 (0.35), residues: 196 loop : -2.45 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 832 TYR 0.016 0.001 TYR D 905 PHE 0.021 0.001 PHE B 921 TRP 0.051 0.002 TRP D 516 HIS 0.004 0.001 HIS C 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (29552) covalent geometry : angle 0.62413 / 0.32 (40032) SS BOND : bond 0.00505 / 0.30 ( 4) SS BOND : angle 2.02696 / 1.14 ( 8) hydrogen bonds : bond 0.03582 / 2.34 ( 1340) hydrogen bonds : angle 3.95616 / 2.70 ( 3984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 763 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8749 (pp30) cc_final: 0.8354 (pp30) REVERT: A 323 SER cc_start: 0.8235 (m) cc_final: 0.7901 (m) REVERT: A 435 ASP cc_start: 0.8678 (m-30) cc_final: 0.8270 (m-30) REVERT: A 486 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 607 GLU cc_start: 0.8908 (tp30) cc_final: 0.8407 (tp30) REVERT: A 628 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 645 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.6353 (t) REVERT: A 646 ASN cc_start: 0.7442 (m-40) cc_final: 0.7003 (m110) REVERT: A 649 GLU cc_start: 0.8807 (mp0) cc_final: 0.7902 (mp0) REVERT: A 674 TYR cc_start: 0.8707 (m-80) cc_final: 0.8379 (m-80) REVERT: A 688 MET cc_start: 0.7630 (mtp) cc_final: 0.6342 (tmm) REVERT: A 789 TRP cc_start: 0.8740 (m100) cc_final: 0.8489 (m100) REVERT: A 798 PHE cc_start: 0.8793 (t80) cc_final: 0.8482 (t80) REVERT: A 808 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 854 MET cc_start: 0.7919 (mmp) cc_final: 0.7635 (ptt) REVERT: B 297 GLN cc_start: 0.8713 (pp30) cc_final: 0.8366 (pp30) REVERT: B 435 ASP cc_start: 0.8669 (m-30) cc_final: 0.8276 (m-30) REVERT: B 486 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 592 MET cc_start: 0.8189 (mmm) cc_final: 0.7887 (mmp) REVERT: B 606 GLU cc_start: 0.8466 (pp20) cc_final: 0.7969 (pp20) REVERT: B 613 GLU cc_start: 0.7986 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 628 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 645 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.6325 (t) REVERT: B 646 ASN cc_start: 0.7441 (m-40) cc_final: 0.7066 (m110) REVERT: B 649 GLU cc_start: 0.8814 (mp0) cc_final: 0.7928 (mp0) REVERT: B 674 TYR cc_start: 0.8702 (m-80) cc_final: 0.8361 (m-80) REVERT: B 688 MET cc_start: 0.7634 (mtp) cc_final: 0.6345 (tmm) REVERT: B 798 PHE cc_start: 0.8777 (t80) cc_final: 0.8487 (t80) REVERT: B 854 MET cc_start: 0.7914 (mmp) cc_final: 0.7633 (ptt) REVERT: B 898 TYR cc_start: 0.9399 (t80) cc_final: 0.8720 (t80) REVERT: C 158 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8732 (tpp80) REVERT: C 181 LYS cc_start: 0.9204 (tttt) cc_final: 0.8906 (ttpt) REVERT: C 297 GLN cc_start: 0.8713 (pp30) cc_final: 0.8362 (pp30) REVERT: C 323 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8378 (m) REVERT: C 435 ASP cc_start: 0.8657 (m-30) cc_final: 0.8260 (m-30) REVERT: C 486 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8261 (mm-30) REVERT: C 592 MET cc_start: 0.8181 (mmm) cc_final: 0.7882 (mmp) REVERT: C 606 GLU cc_start: 0.8472 (pp20) cc_final: 0.7978 (pp20) REVERT: C 613 GLU cc_start: 0.7996 (tt0) cc_final: 0.7661 (tm-30) REVERT: C 628 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8439 (mt-10) REVERT: C 645 SER cc_start: 0.7648 (OUTLIER) cc_final: 0.6303 (t) REVERT: C 649 GLU cc_start: 0.8889 (mp0) cc_final: 0.8111 (mp0) REVERT: C 688 MET cc_start: 0.7627 (mtp) cc_final: 0.6345 (tmm) REVERT: C 785 PHE cc_start: 0.8526 (m-80) cc_final: 0.8229 (m-10) REVERT: C 798 PHE cc_start: 0.8741 (t80) cc_final: 0.8439 (t80) REVERT: C 854 MET cc_start: 0.7918 (mmp) cc_final: 0.7633 (ptt) REVERT: C 898 TYR cc_start: 0.9395 (t80) cc_final: 0.8716 (t80) REVERT: C 1068 MET cc_start: 0.4321 (ttt) cc_final: 0.3928 (pmm) REVERT: D 181 LYS cc_start: 0.9192 (tttt) cc_final: 0.8899 (ttpt) REVERT: D 297 GLN cc_start: 0.8709 (pp30) cc_final: 0.8365 (pp30) REVERT: D 323 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8352 (m) REVERT: D 435 ASP cc_start: 0.8675 (m-30) cc_final: 0.8282 (m-30) REVERT: D 486 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 592 MET cc_start: 0.8193 (mmm) cc_final: 0.7885 (mmp) REVERT: D 606 GLU cc_start: 0.8467 (pp20) cc_final: 0.7974 (pp20) REVERT: D 613 GLU cc_start: 0.7989 (tt0) cc_final: 0.7649 (tm-30) REVERT: D 628 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8438 (mt-10) REVERT: D 645 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.6306 (t) REVERT: D 646 ASN cc_start: 0.7447 (m-40) cc_final: 0.7066 (m110) REVERT: D 649 GLU cc_start: 0.8811 (mp0) cc_final: 0.7928 (mp0) REVERT: D 688 MET cc_start: 0.7638 (mtp) cc_final: 0.6357 (tmm) REVERT: D 789 TRP cc_start: 0.8740 (m100) cc_final: 0.8490 (m100) REVERT: D 798 PHE cc_start: 0.8737 (t80) cc_final: 0.8434 (t80) REVERT: D 854 MET cc_start: 0.7902 (mmp) cc_final: 0.7632 (ptt) REVERT: D 898 TYR cc_start: 0.9387 (t80) cc_final: 0.8704 (t80) outliers start: 79 outliers final: 71 residues processed: 800 average time/residue: 0.1603 time to fit residues: 209.7821 Evaluate side-chains 826 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 748 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 TRP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 TRP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 417 TRP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 417 TRP Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 612 TYR Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 97 optimal weight: 0.0000 chunk 246 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 158 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 258 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN A 600 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN B 499 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127007 restraints weight = 43776.461| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.86 r_work: 0.3326 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29556 Z= 0.122 Angle : 0.600 11.153 40040 Z= 0.309 Chirality : 0.042 0.255 4484 Planarity : 0.004 0.101 4928 Dihedral : 6.353 59.963 3892 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 2.22 % Allowed : 22.27 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3392 helix: 0.52 (0.11), residues: 2180 sheet: -1.88 (0.36), residues: 196 loop : -2.28 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 832 TYR 0.018 0.001 TYR D 905 PHE 0.012 0.001 PHE C 921 TRP 0.047 0.002 TRP A 516 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (29552) covalent geometry : angle 0.59961 / 0.31 (40032) SS BOND : bond 0.00466 / 0.28 ( 4) SS BOND : angle 1.92652 / 1.09 ( 8) hydrogen bonds : bond 0.03441 / 2.23 ( 1340) hydrogen bonds : angle 3.89587 / 2.67 ( 3984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 777 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8687 (pp30) cc_final: 0.8358 (pp30) REVERT: A 435 ASP cc_start: 0.8630 (m-30) cc_final: 0.8242 (m-30) REVERT: A 486 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 607 GLU cc_start: 0.8891 (tp30) cc_final: 0.8336 (tp30) REVERT: A 613 GLU cc_start: 0.7829 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 628 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8377 (mt-10) REVERT: A 645 SER cc_start: 0.7575 (OUTLIER) cc_final: 0.6553 (t) REVERT: A 649 GLU cc_start: 0.8773 (mp0) cc_final: 0.7999 (mp0) REVERT: A 674 TYR cc_start: 0.8651 (m-80) cc_final: 0.8446 (m-10) REVERT: A 688 MET cc_start: 0.7617 (mtp) cc_final: 0.6332 (tmm) REVERT: A 777 TRP cc_start: 0.7674 (t-100) cc_final: 0.7110 (t-100) REVERT: A 779 MET cc_start: 0.8043 (tpp) cc_final: 0.7234 (ttm) REVERT: A 785 PHE cc_start: 0.8438 (m-80) cc_final: 0.7756 (m-10) REVERT: A 789 TRP cc_start: 0.8754 (m100) cc_final: 0.8519 (m100) REVERT: A 790 ASN cc_start: 0.8956 (m-40) cc_final: 0.8472 (t0) REVERT: A 798 PHE cc_start: 0.8744 (t80) cc_final: 0.8428 (t80) REVERT: A 808 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 841 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7712 (ttp80) REVERT: A 854 MET cc_start: 0.7921 (mmp) cc_final: 0.7653 (ptt) REVERT: A 977 GLN cc_start: 0.8710 (tp40) cc_final: 0.8072 (tp40) REVERT: B 297 GLN cc_start: 0.8653 (pp30) cc_final: 0.8313 (pp30) REVERT: B 435 ASP cc_start: 0.8627 (m-30) cc_final: 0.8237 (m-30) REVERT: B 486 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 592 MET cc_start: 0.8154 (mmm) cc_final: 0.7804 (mmp) REVERT: B 606 GLU cc_start: 0.8433 (pp20) cc_final: 0.7939 (pp20) REVERT: B 613 GLU cc_start: 0.7927 (tt0) cc_final: 0.7601 (tm-30) REVERT: B 628 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 645 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.6536 (t) REVERT: B 649 GLU cc_start: 0.8778 (mp0) cc_final: 0.8000 (mp0) REVERT: B 674 TYR cc_start: 0.8644 (m-80) cc_final: 0.8352 (m-80) REVERT: B 688 MET cc_start: 0.7620 (mtp) cc_final: 0.6330 (tmm) REVERT: B 785 PHE cc_start: 0.8491 (m-80) cc_final: 0.8196 (m-10) REVERT: B 790 ASN cc_start: 0.8889 (m-40) cc_final: 0.8341 (t0) REVERT: B 832 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8654 (mtp85) REVERT: B 841 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7704 (ttp80) REVERT: B 854 MET cc_start: 0.7914 (mmp) cc_final: 0.7638 (ptt) REVERT: B 898 TYR cc_start: 0.9353 (t80) cc_final: 0.8756 (t80) REVERT: B 977 GLN cc_start: 0.8657 (tp40) cc_final: 0.8144 (tp40) REVERT: C 297 GLN cc_start: 0.8656 (pp30) cc_final: 0.8307 (pp30) REVERT: C 323 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8197 (m) REVERT: C 435 ASP cc_start: 0.8609 (m-30) cc_final: 0.8209 (m-30) REVERT: C 486 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8223 (mm-30) REVERT: C 592 MET cc_start: 0.8152 (mmm) cc_final: 0.7802 (mmp) REVERT: C 606 GLU cc_start: 0.8445 (pp20) cc_final: 0.7956 (pp20) REVERT: C 613 GLU cc_start: 0.7905 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 628 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8397 (mt-10) REVERT: C 645 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.6284 (t) REVERT: C 649 GLU cc_start: 0.8818 (mp0) cc_final: 0.8054 (mp0) REVERT: C 688 MET cc_start: 0.7615 (mtp) cc_final: 0.6331 (tmm) REVERT: C 785 PHE cc_start: 0.8538 (m-80) cc_final: 0.8213 (m-10) REVERT: C 841 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7653 (ttp80) REVERT: C 854 MET cc_start: 0.7916 (mmp) cc_final: 0.7637 (ptt) REVERT: C 898 TYR cc_start: 0.9341 (t80) cc_final: 0.8707 (t80) REVERT: C 977 GLN cc_start: 0.8661 (tp40) cc_final: 0.8148 (tp40) REVERT: C 1049 MET cc_start: 0.7954 (ptm) cc_final: 0.7748 (ttp) REVERT: D 297 GLN cc_start: 0.8656 (pp30) cc_final: 0.8369 (pp30) REVERT: D 323 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8178 (m) REVERT: D 435 ASP cc_start: 0.8629 (m-30) cc_final: 0.8232 (m-30) REVERT: D 486 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8230 (mm-30) REVERT: D 566 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8707 (mm-30) REVERT: D 592 MET cc_start: 0.8154 (mmm) cc_final: 0.7807 (mmp) REVERT: D 606 GLU cc_start: 0.8440 (pp20) cc_final: 0.7951 (pp20) REVERT: D 613 GLU cc_start: 0.7923 (tt0) cc_final: 0.7597 (tm-30) REVERT: D 628 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8387 (mt-10) REVERT: D 645 SER cc_start: 0.7560 (OUTLIER) cc_final: 0.6535 (t) REVERT: D 649 GLU cc_start: 0.8764 (mp0) cc_final: 0.7988 (mp0) REVERT: D 688 MET cc_start: 0.7623 (mtp) cc_final: 0.6345 (tmm) REVERT: D 785 PHE cc_start: 0.8496 (m-80) cc_final: 0.8226 (m-10) REVERT: D 789 TRP cc_start: 0.8731 (m100) cc_final: 0.8481 (m100) REVERT: D 854 MET cc_start: 0.7906 (mmp) cc_final: 0.7646 (ptt) REVERT: D 898 TYR cc_start: 0.9348 (t80) cc_final: 0.8808 (t80) REVERT: D 955 LEU cc_start: 0.9311 (tp) cc_final: 0.9102 (tp) REVERT: D 977 GLN cc_start: 0.8668 (tp40) cc_final: 0.8155 (tp40) REVERT: D 1049 MET cc_start: 0.7957 (ptm) cc_final: 0.7743 (ttp) REVERT: D 1068 MET cc_start: 0.4758 (ttt) cc_final: 0.3779 (mtt) outliers start: 69 outliers final: 55 residues processed: 814 average time/residue: 0.1714 time to fit residues: 228.0912 Evaluate side-chains 823 residues out of total 3112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 761 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 1073 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 888 TRP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 888 TRP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 732 ASN Chi-restraints excluded: chain D residue 774 VAL Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 888 TRP Chi-restraints excluded: chain D residue 1073 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 270 optimal weight: 2.9990 chunk 240 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 285 optimal weight: 0.0370 chunk 231 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 266 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 ASN ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126913 restraints weight = 44193.505| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.87 r_work: 0.3325 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 29556 Z= 0.152 Angle : 0.731 59.199 40040 Z= 0.407 Chirality : 0.042 0.221 4484 Planarity : 0.005 0.099 4928 Dihedral : 6.345 59.962 3892 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 2.02 % Allowed : 22.49 % Favored : 75.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 3392 helix: 0.53 (0.11), residues: 2180 sheet: -1.88 (0.36), residues: 196 loop : -2.28 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 832 TYR 0.016 0.001 TYR D 905 PHE 0.010 0.001 PHE A 620 TRP 0.042 0.002 TRP A 516 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (29552) covalent geometry : angle 0.73028 / 0.41 (40032) SS BOND : bond 0.00567 / 0.34 ( 4) SS BOND : angle 1.90975 / 1.08 ( 8) hydrogen bonds : bond 0.03448 / 2.24 ( 1340) hydrogen bonds : angle 3.90246 / 2.67 ( 3984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6784.44 seconds wall clock time: 117 minutes 3.68 seconds (7023.68 seconds total)