Starting phenix.real_space_refine on Mon Sep 30 11:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm0_22253/09_2024/6xm0_22253.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16037 2.51 5 N 4118 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25201 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8109 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 bond proxies already assigned to first conformer: 8280 Chain: "B" Number of atoms: 8242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8242 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8066 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 19.41, per 1000 atoms: 0.77 Number of scatterers: 25201 At special positions: 0 Unit cell: (139.4, 136, 198.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4938 8.00 N 4118 7.00 C 16037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 6.32 Conformation dependent library (CDL) restraints added in 4.2 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 23.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.548A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.794A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.668A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.960A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.738A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.739A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.894A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.547A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.523A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.526A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.698A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.212A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.676A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.576A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.641A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.640A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.509A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.521A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.521A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.978A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.560A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.326A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.544A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.802A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.702A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.917A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 632 through 636 removed outlier: 4.053A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.551A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.512A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.562A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.510A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.030A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.641A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.717A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.299A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.547A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.961A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.973A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.621A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.560A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.710A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.537A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.790A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.422A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.597A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.722A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.837A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.512A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.529A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.708A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.615A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.515A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.521A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.523A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.534A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.766A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.041A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.577A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.167A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.727A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.487A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.409A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.450A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2370 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: 10.92 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7024 1.33 - 1.47: 7519 1.47 - 1.60: 11084 1.60 - 1.74: 2 1.74 - 1.87: 130 Bond restraints: 25759 Sorted by residual: bond pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" N ALA B 520 " pdb=" CA ALA B 520 " ideal model delta sigma weight residual 1.456 1.489 -0.032 9.40e-03 1.13e+04 1.19e+01 bond pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N HIS B 245 " pdb=" CA HIS B 245 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N VAL C 320 " pdb=" CA VAL C 320 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.27e-02 6.20e+03 1.01e+01 ... (remaining 25754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 34094 2.89 - 5.77: 851 5.77 - 8.66: 94 8.66 - 11.54: 24 11.54 - 14.43: 5 Bond angle restraints: 35068 Sorted by residual: angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 134.02 -12.48 1.91e+00 2.74e-01 4.27e+01 angle pdb=" C GLN C 321 " pdb=" CA GLN C 321 " pdb=" CB GLN C 321 " ideal model delta sigma weight residual 108.86 118.00 -9.14 1.44e+00 4.82e-01 4.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.88 -7.18 1.22e+00 6.72e-01 3.47e+01 angle pdb=" C ALA A 522 " pdb=" N THR A 523 " pdb=" CA THR A 523 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" CA TYR B 904 " pdb=" CB TYR B 904 " pdb=" CG TYR B 904 " ideal model delta sigma weight residual 113.90 123.98 -10.08 1.80e+00 3.09e-01 3.13e+01 ... (remaining 35063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14342 17.77 - 35.53: 1375 35.53 - 53.30: 268 53.30 - 71.07: 57 71.07 - 88.84: 29 Dihedral angle restraints: 16071 sinusoidal: 6960 harmonic: 9111 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 11.96 81.04 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 165.65 -72.65 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -155.37 69.37 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 16068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3543 0.096 - 0.192: 568 0.192 - 0.287: 38 0.287 - 0.383: 9 0.383 - 0.479: 4 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CB THR A 95 " pdb=" CA THR A 95 " pdb=" OG1 THR A 95 " pdb=" CG2 THR A 95 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 4159 not shown) Planarity restraints: 4506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.338 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG B1307 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.323 2.00e-02 2.50e+03 2.75e-01 9.42e+02 pdb=" C7 NAG A1305 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.315 2.00e-02 2.50e+03 2.62e-01 8.57e+02 pdb=" C7 NAG A1306 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.202 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.442 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.014 2.00e-02 2.50e+03 ... (remaining 4503 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4006 2.76 - 3.30: 20382 3.30 - 3.83: 39468 3.83 - 4.37: 47055 4.37 - 4.90: 81810 Nonbonded interactions: 192721 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 449 " pdb=" O PHE B 497 " model vdw 2.281 3.040 nonbonded pdb=" O GLN C 134 " pdb=" OH TYR C 160 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR C1138 " pdb=" OE2 GLU C1144 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 619 " pdb=" NH2 ARG B 847 " model vdw 2.326 3.120 ... (remaining 192716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 612 or resid 614 through 827 or resid 853 through 1147 or resid 1301 through \ 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 827 or resid 853 through 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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=0.50 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: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.810 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.160 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.010 0.112 25759 Z= 0.666 Angle : 1.116 14.429 35068 Z= 0.599 Chirality : 0.070 0.479 4162 Planarity : 0.011 0.288 4464 Dihedral : 14.511 88.835 10086 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.25 % Favored : 91.52 % Rotamer: Outliers : 0.55 % Allowed : 5.85 % Favored : 93.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.12), residues: 3080 helix: -4.44 (0.08), residues: 681 sheet: -1.13 (0.20), residues: 621 loop : -2.89 (0.11), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 886 HIS 0.016 0.002 HIS C 625 PHE 0.051 0.004 PHE B 559 TYR 0.040 0.004 TYR A 873 ARG 0.011 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7913 (ptp-170) REVERT: B 271 GLN cc_start: 0.7455 (mt0) cc_final: 0.7015 (mp10) REVERT: B 616 ASN cc_start: 0.6899 (m-40) cc_final: 0.6631 (t0) REVERT: C 616 ASN cc_start: 0.8036 (t0) cc_final: 0.7707 (m-40) outliers start: 15 outliers final: 8 residues processed: 266 average time/residue: 1.1203 time to fit residues: 354.5915 Evaluate side-chains 215 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.0010 chunk 125 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 173 GLN A 207 HIS A 460 ASN A 544 ASN A 804 GLN A 901 GLN A 955 ASN B 66 HIS B 239 GLN B 245 HIS B 437 ASN B 474 GLN B 804 GLN B 853 GLN B 901 GLN C 49 HIS C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 804 GLN C 901 GLN C 935 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25759 Z= 0.180 Angle : 0.671 13.400 35068 Z= 0.347 Chirality : 0.047 0.515 4162 Planarity : 0.006 0.091 4464 Dihedral : 7.792 58.021 4531 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 1.43 % Allowed : 9.66 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3080 helix: -1.07 (0.18), residues: 677 sheet: -0.35 (0.20), residues: 645 loop : -2.51 (0.12), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.013 0.001 HIS A 207 PHE 0.022 0.001 PHE A 32 TYR 0.022 0.001 TYR B 904 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8642 (mptt) REVERT: B 271 GLN cc_start: 0.7408 (mt0) cc_final: 0.7035 (mp10) REVERT: B 309 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: C 52 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 616 ASN cc_start: 0.8001 (t0) cc_final: 0.7726 (m-40) REVERT: C 983 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6626 (ttp-110) outliers start: 39 outliers final: 21 residues processed: 250 average time/residue: 1.0955 time to fit residues: 329.1584 Evaluate side-chains 225 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 305 optimal weight: 0.5980 chunk 251 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN A1101 HIS B 125 ASN B 164 ASN B 613 GLN C 414 GLN C 540 ASN C 935 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25759 Z= 0.281 Angle : 0.700 13.401 35068 Z= 0.358 Chirality : 0.049 0.353 4162 Planarity : 0.005 0.082 4464 Dihedral : 7.371 58.346 4528 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 2.49 % Allowed : 10.68 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3080 helix: 0.26 (0.20), residues: 677 sheet: -0.11 (0.20), residues: 631 loop : -2.37 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.013 0.001 HIS A 207 PHE 0.025 0.002 PHE B 559 TYR 0.029 0.002 TYR B 904 ARG 0.005 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 206 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8633 (mptt) REVERT: B 271 GLN cc_start: 0.7384 (mt0) cc_final: 0.6956 (mp10) REVERT: B 500 THR cc_start: 0.3070 (OUTLIER) cc_final: 0.2851 (m) REVERT: B 747 THR cc_start: 0.8637 (m) cc_final: 0.8417 (m) REVERT: B 1017 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6178 (tp30) REVERT: C 52 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7421 (tm-30) REVERT: C 189 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.5933 (tt) REVERT: C 616 ASN cc_start: 0.8020 (t0) cc_final: 0.7740 (m-40) outliers start: 68 outliers final: 37 residues processed: 252 average time/residue: 1.0127 time to fit residues: 310.0770 Evaluate side-chains 234 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 0.0070 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 chunk 300 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 540 ASN A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 501 ASN C 540 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25759 Z= 0.234 Angle : 0.660 12.915 35068 Z= 0.337 Chirality : 0.048 0.445 4162 Planarity : 0.005 0.075 4464 Dihedral : 7.016 59.854 4527 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 2.74 % Allowed : 11.34 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3080 helix: 0.74 (0.21), residues: 678 sheet: 0.04 (0.20), residues: 644 loop : -2.27 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.013 0.001 HIS A 207 PHE 0.022 0.002 PHE A 592 TYR 0.026 0.002 TYR B 904 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 204 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1038 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8628 (mptt) REVERT: B 271 GLN cc_start: 0.7402 (mt0) cc_final: 0.6975 (mp10) REVERT: B 319 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7530 (ttm170) REVERT: B 425 LEU cc_start: 0.2078 (OUTLIER) cc_final: 0.1170 (mp) REVERT: B 500 THR cc_start: 0.3050 (OUTLIER) cc_final: 0.2836 (m) REVERT: B 531 THR cc_start: 0.7567 (m) cc_final: 0.7349 (p) REVERT: B 747 THR cc_start: 0.8623 (m) cc_final: 0.8414 (m) REVERT: B 1017 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: C 52 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 189 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.5890 (tt) REVERT: C 616 ASN cc_start: 0.8027 (t0) cc_final: 0.7766 (m-40) REVERT: C 983 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6596 (ttp-110) outliers start: 75 outliers final: 37 residues processed: 254 average time/residue: 0.9333 time to fit residues: 291.4770 Evaluate side-chains 237 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.0770 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 223 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 540 ASN A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 613 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25759 Z= 0.155 Angle : 0.596 12.042 35068 Z= 0.303 Chirality : 0.046 0.347 4162 Planarity : 0.004 0.073 4464 Dihedral : 6.427 59.787 4526 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 2.19 % Allowed : 12.58 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3080 helix: 1.23 (0.21), residues: 674 sheet: 0.21 (0.20), residues: 640 loop : -2.08 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.014 0.001 HIS A 207 PHE 0.020 0.001 PHE A 32 TYR 0.020 0.001 TYR B 904 ARG 0.006 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8123 (tt0) cc_final: 0.7756 (tm-30) REVERT: A 1038 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8653 (mptt) REVERT: B 271 GLN cc_start: 0.7346 (mt0) cc_final: 0.6904 (mp10) REVERT: B 319 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7443 (ttm170) REVERT: B 425 LEU cc_start: 0.2039 (OUTLIER) cc_final: 0.1288 (tp) REVERT: B 500 THR cc_start: 0.3217 (OUTLIER) cc_final: 0.3006 (m) REVERT: B 1017 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5934 (tp30) REVERT: C 52 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 117 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6093 (tt) REVERT: C 616 ASN cc_start: 0.8004 (t0) cc_final: 0.7766 (m-40) REVERT: C 661 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7139 (pt0) outliers start: 60 outliers final: 28 residues processed: 254 average time/residue: 0.9682 time to fit residues: 300.0700 Evaluate side-chains 235 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 501 ASN B 519 HIS B 607 GLN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25759 Z= 0.283 Angle : 0.670 12.693 35068 Z= 0.343 Chirality : 0.049 0.295 4162 Planarity : 0.005 0.078 4464 Dihedral : 6.524 59.234 4526 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.89 % Rotamer: Outliers : 2.63 % Allowed : 12.80 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3080 helix: 1.09 (0.21), residues: 673 sheet: 0.18 (0.20), residues: 616 loop : -2.09 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 64 HIS 0.012 0.001 HIS A 207 PHE 0.025 0.002 PHE A 855 TYR 0.032 0.002 TYR B 904 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 193 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8156 (tt0) cc_final: 0.7791 (tm-30) REVERT: A 1038 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8669 (mptt) REVERT: B 134 GLN cc_start: 0.3798 (OUTLIER) cc_final: 0.2808 (pp30) REVERT: B 271 GLN cc_start: 0.7413 (mt0) cc_final: 0.6969 (mp10) REVERT: B 319 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7465 (ttm170) REVERT: B 425 LEU cc_start: 0.2159 (OUTLIER) cc_final: 0.1349 (tp) REVERT: B 500 THR cc_start: 0.2984 (OUTLIER) cc_final: 0.2778 (m) REVERT: B 658 ASN cc_start: 0.7202 (m-40) cc_final: 0.6937 (m-40) REVERT: B 1017 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6120 (tp30) REVERT: C 52 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7493 (tm-30) REVERT: C 117 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6102 (tt) REVERT: C 189 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.5821 (tt) REVERT: C 616 ASN cc_start: 0.8013 (t0) cc_final: 0.7779 (m-40) REVERT: C 904 TYR cc_start: 0.7558 (p90) cc_final: 0.7142 (p90) outliers start: 72 outliers final: 48 residues processed: 244 average time/residue: 0.9168 time to fit residues: 274.2573 Evaluate side-chains 243 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 253 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25759 Z= 0.187 Angle : 0.617 12.284 35068 Z= 0.315 Chirality : 0.047 0.426 4162 Planarity : 0.004 0.075 4464 Dihedral : 6.221 57.290 4526 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 2.41 % Allowed : 13.31 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3080 helix: 1.22 (0.21), residues: 679 sheet: 0.29 (0.20), residues: 632 loop : -2.01 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 PHE 0.020 0.001 PHE A 32 TYR 0.024 0.001 TYR B 904 ARG 0.005 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 197 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8129 (tt0) cc_final: 0.7760 (tm-30) REVERT: A 360 ASN cc_start: 0.6173 (t0) cc_final: 0.5870 (m-40) REVERT: A 1038 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8661 (mptt) REVERT: B 271 GLN cc_start: 0.7390 (mt0) cc_final: 0.6948 (mp10) REVERT: B 319 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7415 (ttm170) REVERT: B 425 LEU cc_start: 0.2138 (OUTLIER) cc_final: 0.1338 (tp) REVERT: B 500 THR cc_start: 0.3135 (OUTLIER) cc_final: 0.2919 (m) REVERT: B 658 ASN cc_start: 0.7114 (m-40) cc_final: 0.6859 (m-40) REVERT: B 1017 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.5994 (tp30) REVERT: C 52 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 117 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6110 (tt) REVERT: C 189 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.5804 (tt) REVERT: C 616 ASN cc_start: 0.7983 (t0) cc_final: 0.7766 (m-40) outliers start: 66 outliers final: 41 residues processed: 245 average time/residue: 0.9798 time to fit residues: 293.6509 Evaluate side-chains 232 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 190 optimal weight: 0.0370 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25759 Z= 0.312 Angle : 0.689 13.036 35068 Z= 0.353 Chirality : 0.050 0.223 4162 Planarity : 0.005 0.078 4464 Dihedral : 6.454 58.213 4526 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 2.67 % Allowed : 13.50 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3080 helix: 1.01 (0.21), residues: 677 sheet: 0.20 (0.21), residues: 609 loop : -2.06 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 64 HIS 0.012 0.001 HIS A 207 PHE 0.033 0.002 PHE A 855 TYR 0.036 0.002 TYR B 904 ARG 0.007 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 191 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.6216 (t0) cc_final: 0.5913 (m-40) REVERT: A 1038 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8675 (mptt) REVERT: B 134 GLN cc_start: 0.3710 (OUTLIER) cc_final: 0.2744 (pp30) REVERT: B 271 GLN cc_start: 0.7387 (mt0) cc_final: 0.6939 (mp10) REVERT: B 319 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7465 (ttm170) REVERT: B 425 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1231 (tp) REVERT: B 500 THR cc_start: 0.3134 (OUTLIER) cc_final: 0.2902 (m) REVERT: B 1017 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: C 52 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 117 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6122 (tt) REVERT: C 189 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.5800 (tt) REVERT: C 616 ASN cc_start: 0.8021 (t0) cc_final: 0.7787 (m-40) REVERT: C 904 TYR cc_start: 0.7574 (p90) cc_final: 0.7058 (p90) outliers start: 73 outliers final: 51 residues processed: 242 average time/residue: 0.9841 time to fit residues: 291.8797 Evaluate side-chains 247 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 279 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 252 optimal weight: 0.4980 chunk 264 optimal weight: 2.9990 chunk 278 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A1101 HIS B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25759 Z= 0.164 Angle : 0.601 12.207 35068 Z= 0.306 Chirality : 0.046 0.225 4162 Planarity : 0.004 0.076 4464 Dihedral : 5.986 55.963 4526 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 2.05 % Allowed : 14.37 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3080 helix: 1.30 (0.21), residues: 679 sheet: 0.34 (0.20), residues: 632 loop : -1.96 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.013 0.001 HIS A 207 PHE 0.020 0.001 PHE A 32 TYR 0.021 0.001 TYR B 904 ARG 0.006 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8118 (tt0) cc_final: 0.7784 (tm-30) REVERT: A 360 ASN cc_start: 0.6126 (t0) cc_final: 0.5844 (m-40) REVERT: A 540 ASN cc_start: 0.7876 (m-40) cc_final: 0.7624 (m110) REVERT: A 1038 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8662 (mptt) REVERT: B 271 GLN cc_start: 0.7403 (mt0) cc_final: 0.6948 (mp10) REVERT: B 319 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7397 (ttm170) REVERT: B 425 LEU cc_start: 0.1807 (OUTLIER) cc_final: 0.1059 (mp) REVERT: B 658 ASN cc_start: 0.7109 (m-40) cc_final: 0.6853 (m-40) REVERT: B 1017 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6021 (tp30) REVERT: C 52 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 117 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6104 (tt) REVERT: C 189 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.5740 (tt) REVERT: C 616 ASN cc_start: 0.7979 (t0) cc_final: 0.7769 (m-40) outliers start: 56 outliers final: 40 residues processed: 231 average time/residue: 1.0022 time to fit residues: 283.6434 Evaluate side-chains 228 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 0.0470 chunk 180 optimal weight: 0.3980 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 0.1980 chunk 309 optimal weight: 1.9990 chunk 285 optimal weight: 0.0030 chunk 246 optimal weight: 0.0020 chunk 25 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS B 125 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 422 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25759 Z= 0.134 Angle : 0.562 11.190 35068 Z= 0.286 Chirality : 0.044 0.234 4162 Planarity : 0.004 0.073 4464 Dihedral : 5.431 55.495 4526 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 1.28 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3080 helix: 1.69 (0.21), residues: 682 sheet: 0.43 (0.20), residues: 629 loop : -1.79 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.014 0.001 HIS A 207 PHE 0.024 0.001 PHE C 32 TYR 0.018 0.001 TYR B 904 ARG 0.008 0.000 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.705 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8084 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 360 ASN cc_start: 0.6129 (t0) cc_final: 0.5873 (m-40) REVERT: A 540 ASN cc_start: 0.7804 (m-40) cc_final: 0.7539 (m110) REVERT: A 1038 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8635 (mptt) REVERT: B 134 GLN cc_start: 0.3579 (OUTLIER) cc_final: 0.2712 (pp30) REVERT: B 271 GLN cc_start: 0.7284 (mt0) cc_final: 0.6845 (mp10) REVERT: B 319 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7278 (ttm170) REVERT: B 425 LEU cc_start: 0.1988 (OUTLIER) cc_final: 0.1234 (mp) REVERT: B 500 THR cc_start: 0.3125 (OUTLIER) cc_final: 0.2893 (m) REVERT: C 52 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7390 (tm-30) REVERT: C 117 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6075 (tt) REVERT: C 616 ASN cc_start: 0.8014 (t0) cc_final: 0.7762 (m-40) outliers start: 35 outliers final: 18 residues processed: 233 average time/residue: 0.9794 time to fit residues: 275.7870 Evaluate side-chains 215 residues out of total 2732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 chunk 227 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 216 optimal weight: 0.2980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1101 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.203453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152383 restraints weight = 29749.480| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.08 r_work: 0.3393 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25759 Z= 0.169 Angle : 0.589 11.641 35068 Z= 0.300 Chirality : 0.046 0.235 4162 Planarity : 0.004 0.074 4464 Dihedral : 5.440 55.060 4523 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 1.28 % Allowed : 15.69 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3080 helix: 1.74 (0.21), residues: 674 sheet: 0.47 (0.20), residues: 638 loop : -1.77 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.011 0.001 HIS A 207 PHE 0.018 0.001 PHE A 32 TYR 0.025 0.001 TYR B 904 ARG 0.004 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7424.90 seconds wall clock time: 133 minutes 35.61 seconds (8015.61 seconds total)