Starting phenix.real_space_refine on Thu May 29 06:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsd_38616/05_2025/8xsd_38616.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2460 atoms to isotropic. 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 137 5.16 5 C 18933 2.51 5 N 4976 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29708 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8201 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 991} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8255 Classifications: {'peptide': 1055} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 998} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8215 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 863 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 863 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 863 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 14.97, per 1000 atoms: 0.50 Number of scatterers: 29708 At special positions: 0 Unit cell: (167.99, 162.64, 224.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 137 16.00 O 5662 8.00 N 4976 7.00 C 18933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.04 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.04 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.25 Conformation dependent library (CDL) restraints added in 3.6 seconds 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 59 sheets defined 21.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.857A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.510A pdb=" N LEU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 500 through 503 removed outlier: 3.921A pdb=" N HIS A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 755 removed outlier: 3.542A pdb=" N ASN A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.790A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.741A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 864 through 882 removed outlier: 4.218A pdb=" N GLN A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 871 " --> pdb=" O MET A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.928A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.644A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.777A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 4.074A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 986 Processing helix chain 'A' and resid 987 through 1028 removed outlier: 4.782A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1148 removed outlier: 4.335A pdb=" N GLU A1142 " --> pdb=" O PRO A1138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.695A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 403 through 409 removed outlier: 4.672A pdb=" N SER B 406 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 407 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 409 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.757A pdb=" N TYR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 503 removed outlier: 4.034A pdb=" N HIS B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 541 through 544 Processing helix chain 'B' and resid 735 through 741 removed outlier: 4.021A pdb=" N TYR B 739 " --> pdb=" O ASP B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.881A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 4.348A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR B 776 " --> pdb=" O GLN B 772 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN B 777 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.547A pdb=" N LEU B 819 " --> pdb=" O PRO B 815 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 820 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 852 removed outlier: 4.288A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 848 through 852' Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.509A pdb=" N GLY B 887 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.577A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 916 removed outlier: 4.007A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.545A pdb=" N GLY B 930 " --> pdb=" O ASN B 926 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 937 " --> pdb=" O GLN B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.566A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 966 Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.550A pdb=" N LEU B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 1030 removed outlier: 3.657A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B1001 " --> pdb=" O GLY B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 3.666A pdb=" N LEU B1143 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.678A pdb=" N VAL C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.138A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 367 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.199A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 409 removed outlier: 3.856A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER C 406 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 407 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 409 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 removed outlier: 4.173A pdb=" N LEU C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 751 " --> pdb=" O CYS C 747 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 758 through 781 removed outlier: 4.154A pdb=" N LEU C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 773 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 776 " --> pdb=" O GLN C 772 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 777 " --> pdb=" O ASP C 773 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 779 " --> pdb=" O ASN C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.708A pdb=" N THR C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.602A pdb=" N GLY C 887 " --> pdb=" O TRP C 884 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 888 " --> pdb=" O THR C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 884 through 888' Processing helix chain 'C' and resid 895 through 905 removed outlier: 3.825A pdb=" N ALA C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 905 " --> pdb=" O ALA C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 908 No H-bonds generated for 'chain 'C' and resid 906 through 908' Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.781A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.664A pdb=" N ILE C 932 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 965 removed outlier: 3.908A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.786A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1030 removed outlier: 4.269A pdb=" N GLU C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 996 " --> pdb=" O ASP C 992 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C1011 " --> pdb=" O THR C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1148 removed outlier: 3.667A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.726A pdb=" N THR H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.858A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.632A pdb=" N ALA G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 4.022A pdb=" N THR G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.740A pdb=" N THR I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.773A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.811A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 228 removed outlier: 6.019A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 225 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 201 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 208 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS A 185 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.504A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.652A pdb=" N PHE A 541 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.244A pdb=" N VAL A 393 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN A 392 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 514 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.818A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL A 654 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 689 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 673 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 710 through 720 removed outlier: 3.638A pdb=" N LYS A1071 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN A1069 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 716 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 718 " --> pdb=" O TYR A1065 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A1065 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 720 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A1063 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.632A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.367A pdb=" N ILE A 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1079 through 1080 Processing sheet with id=AB6, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.618A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.397A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.215A pdb=" N LEU B 274 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 286 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS B 276 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 127 removed outlier: 3.664A pdb=" N ASN B 119 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 239 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP B 102 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 237 " --> pdb=" O TRP B 102 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE B 104 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG B 235 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.596A pdb=" N LEU B 648 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 641 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 324 removed outlier: 4.122A pdb=" N GLU B 322 " --> pdb=" O CYS B 536 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.795A pdb=" N ASN B 352 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 397 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 356 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN B 392 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 514 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 434 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 430 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC6, first strand: chain 'B' and resid 563 through 565 removed outlier: 6.978A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 652 through 658 removed outlier: 5.176A pdb=" N THR B 694 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER B 656 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 689 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 673 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 691 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AC9, first strand: chain 'B' and resid 710 through 711 removed outlier: 3.565A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 720 removed outlier: 3.601A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B1063 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 726 Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 3.681A pdb=" N SER B1121 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.973A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 222 through 227 removed outlier: 5.972A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 201 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN C 186 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU C 94 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 124 through 127 Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.870A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 322 through 324 removed outlier: 3.896A pdb=" N GLU C 322 " --> pdb=" O CYS C 536 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 548 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 546 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 586 " --> pdb=" O VAL C 549 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.580A pdb=" N ALA C 395 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 356 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL C 393 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS C 430 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 658 removed outlier: 6.386A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL C 654 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 662 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 710 through 711 removed outlier: 3.685A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 720 removed outlier: 3.544A pdb=" N ASN C 715 " --> pdb=" O ALA C1068 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 734 Processing sheet with id=AE9, first strand: chain 'C' and resid 1051 through 1054 removed outlier: 3.688A pdb=" N ALA C1054 " --> pdb=" O GLY C1057 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 3.570A pdb=" N SER C1121 " --> pdb=" O ALA C1085 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.880A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.530A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.891A pdb=" N ALA L 19 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 54 through 55 removed outlier: 4.127A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR L 98 " --> pdb=" O TYR L 91 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.707A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.881A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'J' and resid 54 through 55 removed outlier: 4.027A pdb=" N SER J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'I' and resid 57 through 58 removed outlier: 5.651A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.694A pdb=" N PHE K 72 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 46 through 47 removed outlier: 4.022A pdb=" N TYR K 91 " --> pdb=" O THR K 98 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR K 98 " --> pdb=" O TYR K 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 49 through 50 removed outlier: 4.128A pdb=" N TYR K 50 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 932 hydrogen bonds defined for protein. 2493 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: 11.86 Time building geometry restraints manager: 7.38 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: 5958 1.33 - 1.45: 7799 1.45 - 1.58: 16467 1.58 - 1.70: 0 1.70 - 1.83: 179 Bond restraints: 30403 Sorted by residual: bond pdb=" C PRO A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.335 1.387 -0.052 1.28e-02 6.10e+03 1.66e+01 bond pdb=" N ARG A 344 " pdb=" CA ARG A 344 " ideal model delta sigma weight residual 1.454 1.502 -0.048 1.18e-02 7.18e+03 1.63e+01 bond pdb=" C GLN A1140 " pdb=" N PRO A1141 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.20e-02 6.94e+03 1.41e+01 bond pdb=" N ILE A 356 " pdb=" CA ILE A 356 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.20e-02 6.94e+03 1.35e+01 bond pdb=" N ASN A 332 " pdb=" CA ASN A 332 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.17e-02 7.31e+03 1.29e+01 ... (remaining 30398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 40774 2.91 - 5.81: 515 5.81 - 8.72: 65 8.72 - 11.63: 5 11.63 - 14.53: 3 Bond angle restraints: 41362 Sorted by residual: angle pdb=" N PRO B 328 " pdb=" CA PRO B 328 " pdb=" C PRO B 328 " ideal model delta sigma weight residual 111.77 123.42 -11.65 1.67e+00 3.59e-01 4.87e+01 angle pdb=" N PHE B 327 " pdb=" CA PHE B 327 " pdb=" C PHE B 327 " ideal model delta sigma weight residual 110.40 101.83 8.57 1.31e+00 5.83e-01 4.28e+01 angle pdb=" N TYR A 349 " pdb=" CA TYR A 349 " pdb=" C TYR A 349 " ideal model delta sigma weight residual 113.16 105.25 7.91 1.24e+00 6.50e-01 4.07e+01 angle pdb=" C PHE B 327 " pdb=" CA PHE B 327 " pdb=" CB PHE B 327 " ideal model delta sigma weight residual 109.09 117.72 -8.63 1.51e+00 4.39e-01 3.27e+01 angle pdb=" N ILE A 330 " pdb=" CA ILE A 330 " pdb=" C ILE A 330 " ideal model delta sigma weight residual 110.23 104.38 5.85 1.04e+00 9.25e-01 3.16e+01 ... (remaining 41357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.03: 16604 20.03 - 40.05: 1280 40.05 - 60.08: 157 60.08 - 80.11: 34 80.11 - 100.13: 20 Dihedral angle restraints: 18095 sinusoidal: 7038 harmonic: 11057 Sorted by residual: dihedral pdb=" CA ASN A 329 " pdb=" C ASN A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta harmonic sigma weight residual -180.00 -79.87 -100.13 0 5.00e+00 4.00e-02 4.01e+02 dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual -86.00 -176.11 90.11 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 -178.80 -88.20 1 1.00e+01 1.00e-02 9.30e+01 ... (remaining 18092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4244 0.094 - 0.189: 385 0.189 - 0.283: 14 0.283 - 0.377: 0 0.377 - 0.472: 2 Chirality restraints: 4645 Sorted by residual: chirality pdb=" CB ILE G 51 " pdb=" CA ILE G 51 " pdb=" CG1 ILE G 51 " pdb=" CG2 ILE G 51 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE C 567 " pdb=" CA ILE C 567 " pdb=" CG1 ILE C 567 " pdb=" CG2 ILE C 567 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CB ILE A 103 " pdb=" CA ILE A 103 " pdb=" CG1 ILE A 103 " pdb=" CG2 ILE A 103 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4642 not shown) Planarity restraints: 5373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 326 " 1.093 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG B 326 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 326 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 326 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 326 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 353 " -0.675 9.50e-02 1.11e+02 3.03e-01 5.59e+01 pdb=" NE ARG A 353 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 353 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 353 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 353 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 344 " -0.415 9.50e-02 1.11e+02 1.86e-01 2.15e+01 pdb=" NE ARG A 344 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 344 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 344 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 344 " -0.011 2.00e-02 2.50e+03 ... (remaining 5370 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1614 2.73 - 3.27: 28389 3.27 - 3.82: 46274 3.82 - 4.36: 53218 4.36 - 4.90: 92731 Nonbonded interactions: 222226 Sorted by model distance: nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 103 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR C 616 " pdb=" OE1 GLU C 617 " model vdw 2.239 3.040 nonbonded pdb=" OE1 GLN B 132 " pdb=" OG SER B 159 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 754 " pdb=" OD2 ASP C 992 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.255 3.040 ... (remaining 222221 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 29 through 620 or resid 638 through 824 or resid 852 throu \ gh 1148)) selection = (chain 'B' and (resid 29 through 175 or resid 184 through 620 or resid 638 throu \ gh 824 or resid 852 through 1148)) selection = (chain 'C' and (resid 29 through 175 or resid 184 through 243 or resid 262 throu \ gh 620 or resid 638 through 1148)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 60.490 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0094 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 : 0.004 0.055 30447 Z= 0.213 Angle : 0.808 14.533 41450 Z= 0.448 Chirality : 0.053 0.472 4645 Planarity : 0.010 0.490 5373 Dihedral : 13.967 100.134 10877 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.52 % Favored : 93.25 % Rotamer: Outliers : 0.27 % Allowed : 0.61 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.62 (0.12), residues: 3775 helix: -1.87 (0.16), residues: 587 sheet: -0.59 (0.18), residues: 827 loop : -2.25 (0.11), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 351 HIS 0.013 0.001 HIS B 503 PHE 0.038 0.002 PHE C 369 TYR 0.025 0.001 TYR J 37 ARG 0.010 0.001 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.26267 ( 932) hydrogen bonds : angle 9.18976 ( 2493) SS BOND : bond 0.00405 ( 44) SS BOND : angle 1.34292 ( 88) covalent geometry : bond 0.00374 (30403) covalent geometry : angle 0.80657 (41362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0911 (t-90) cc_final: -0.1744 (t-90) REVERT: A 58 PHE cc_start: 0.2120 (m-10) cc_final: 0.1241 (m-80) REVERT: A 79 ASN cc_start: 0.1844 (t0) cc_final: 0.1229 (m110) REVERT: A 533 LYS cc_start: 0.1087 (mmmm) cc_final: 0.0835 (ptmt) REVERT: A 649 ILE cc_start: -0.0682 (pt) cc_final: -0.1036 (tt) REVERT: B 175 MET cc_start: 0.0155 (tpp) cc_final: -0.0250 (ptt) REVERT: B 407 GLN cc_start: 0.2450 (pt0) cc_final: 0.2146 (pm20) REVERT: B 578 GLN cc_start: -0.1477 (OUTLIER) cc_final: -0.3290 (tt0) REVERT: B 695 MET cc_start: 0.2166 (ptm) cc_final: 0.1555 (ppp) REVERT: B 738 MET cc_start: -0.3257 (ttm) cc_final: -0.4964 (mmm) REVERT: B 933 GLN cc_start: 0.2640 (tt0) cc_final: 0.2312 (tp40) REVERT: C 64 TRP cc_start: -0.2912 (p90) cc_final: -0.4985 (p-90) REVERT: C 672 TYR cc_start: 0.2297 (t80) cc_final: 0.1612 (t80) REVERT: C 771 GLU cc_start: -0.0469 (tt0) cc_final: -0.1236 (mt-10) REVERT: H 82 MET cc_start: 0.1237 (mmp) cc_final: -0.0209 (pmm) REVERT: G 82 MET cc_start: 0.3296 (mpp) cc_final: 0.2520 (mpp) REVERT: I 82 MET cc_start: 0.2539 (mmt) cc_final: 0.1670 (ppp) outliers start: 9 outliers final: 4 residues processed: 232 average time/residue: 0.4068 time to fit residues: 150.6566 Evaluate side-chains 139 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 578 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 114 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 40.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 542 ASN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 753 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN B 52 GLN B 412 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 407 GLN C1099 HIS G 83 ASN K 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.363944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.356119 restraints weight = 92695.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.5546 r_free = 0.5546 target = 0.358367 restraints weight = 53953.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5559 r_free = 0.5559 target = 0.359694 restraints weight = 33214.155| |-----------------------------------------------------------------------------| r_work (final): 0.5556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0661 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30447 Z= 0.204 Angle : 0.738 10.601 41450 Z= 0.390 Chirality : 0.049 0.441 4645 Planarity : 0.006 0.130 5373 Dihedral : 5.268 59.468 4122 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.20 % Favored : 93.67 % Rotamer: Outliers : 1.00 % Allowed : 7.65 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.18 (0.12), residues: 3775 helix: -0.53 (0.19), residues: 611 sheet: -0.69 (0.18), residues: 822 loop : -2.09 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 884 HIS 0.007 0.002 HIS C1062 PHE 0.048 0.002 PHE C1101 TYR 0.028 0.002 TYR A 902 ARG 0.018 0.001 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 932) hydrogen bonds : angle 6.54035 ( 2493) SS BOND : bond 0.00895 ( 44) SS BOND : angle 1.45752 ( 88) covalent geometry : bond 0.00427 (30403) covalent geometry : angle 0.73533 (41362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 3.115 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0054 (t-90) cc_final: -0.1271 (t-90) REVERT: A 58 PHE cc_start: 0.2693 (m-10) cc_final: 0.2297 (m-80) REVERT: A 151 MET cc_start: -0.0909 (mpp) cc_final: -0.1238 (mpp) REVERT: A 533 LYS cc_start: 0.0637 (mmmm) cc_final: 0.0256 (pttp) REVERT: A 799 ASN cc_start: 0.4085 (t0) cc_final: 0.3686 (t0) REVERT: A 1017 ARG cc_start: 0.1572 (ttp80) cc_final: 0.1330 (ptt180) REVERT: B 175 MET cc_start: 0.0957 (tpp) cc_final: 0.0179 (ptt) REVERT: B 695 MET cc_start: 0.1850 (ptm) cc_final: 0.1439 (ppp) REVERT: B 738 MET cc_start: -0.2684 (ttm) cc_final: -0.4793 (mmm) REVERT: C 672 TYR cc_start: 0.3310 (t80) cc_final: 0.1708 (t80) REVERT: C 1027 MET cc_start: 0.4380 (ttm) cc_final: 0.3948 (ttm) REVERT: H 34 MET cc_start: 0.0139 (mmm) cc_final: -0.0110 (mmm) REVERT: H 82 MET cc_start: 0.2696 (mmp) cc_final: 0.0421 (pmm) REVERT: G 82 MET cc_start: 0.4068 (mpp) cc_final: 0.3234 (mpp) REVERT: I 57 THR cc_start: 0.4760 (OUTLIER) cc_final: 0.4533 (p) REVERT: I 82 MET cc_start: 0.2914 (mmt) cc_final: 0.2542 (ppp) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.3832 time to fit residues: 113.8129 Evaluate side-chains 155 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 212 optimal weight: 0.9990 chunk 315 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 208 optimal weight: 0.0980 chunk 127 optimal weight: 6.9990 chunk 353 optimal weight: 8.9990 chunk 345 optimal weight: 40.0000 chunk 341 optimal weight: 8.9990 chunk 306 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 194 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 933 GLN B 953 ASN ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.363803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.355473 restraints weight = 92894.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.357784 restraints weight = 54799.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5557 r_free = 0.5557 target = 0.359150 restraints weight = 33985.969| |-----------------------------------------------------------------------------| r_work (final): 0.5555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0673 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30447 Z= 0.118 Angle : 0.551 9.390 41450 Z= 0.291 Chirality : 0.043 0.191 4645 Planarity : 0.005 0.077 5373 Dihedral : 4.665 59.561 4114 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 1.06 % Allowed : 10.47 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.78 (0.13), residues: 3775 helix: 0.40 (0.20), residues: 603 sheet: -0.56 (0.18), residues: 825 loop : -1.95 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 884 HIS 0.017 0.001 HIS C1099 PHE 0.017 0.001 PHE C1119 TYR 0.017 0.001 TYR C1065 ARG 0.004 0.000 ARG A1017 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 932) hydrogen bonds : angle 5.94165 ( 2493) SS BOND : bond 0.00583 ( 44) SS BOND : angle 1.11166 ( 88) covalent geometry : bond 0.00244 (30403) covalent geometry : angle 0.54956 (41362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 2.895 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0644 (t-90) cc_final: -0.1782 (t-90) REVERT: A 58 PHE cc_start: 0.2732 (m-10) cc_final: 0.2331 (m-80) REVERT: A 151 MET cc_start: -0.0844 (mpp) cc_final: -0.1169 (mpp) REVERT: A 533 LYS cc_start: 0.0579 (mmmm) cc_final: 0.0051 (pttp) REVERT: A 695 MET cc_start: 0.2139 (mtp) cc_final: 0.1776 (mtt) REVERT: A 793 LYS cc_start: 0.3189 (mttp) cc_final: 0.1601 (pptt) REVERT: A 799 ASN cc_start: 0.3463 (t0) cc_final: 0.3092 (t0) REVERT: A 866 GLU cc_start: 0.2001 (OUTLIER) cc_final: -0.1018 (mt-10) REVERT: A 872 THR cc_start: -0.2740 (OUTLIER) cc_final: -0.4672 (t) REVERT: A 1017 ARG cc_start: 0.1641 (ttp80) cc_final: 0.1262 (ptp-170) REVERT: B 175 MET cc_start: 0.0456 (tpp) cc_final: -0.0252 (ptt) REVERT: B 695 MET cc_start: 0.2173 (ptm) cc_final: 0.1900 (ppp) REVERT: B 738 MET cc_start: -0.2488 (ttm) cc_final: -0.4802 (mmm) REVERT: C 672 TYR cc_start: 0.3435 (t80) cc_final: 0.2100 (t80) REVERT: C 1027 MET cc_start: 0.4647 (ttm) cc_final: 0.4171 (ttm) REVERT: C 1084 LYS cc_start: 0.4736 (tppt) cc_final: 0.4510 (tppp) REVERT: H 82 MET cc_start: 0.3115 (mmp) cc_final: 0.0443 (pmm) REVERT: G 82 MET cc_start: 0.2622 (mpp) cc_final: 0.2159 (mpp) REVERT: I 105 MET cc_start: 0.0981 (OUTLIER) cc_final: -0.0114 (ttp) outliers start: 35 outliers final: 17 residues processed: 159 average time/residue: 0.3932 time to fit residues: 105.1634 Evaluate side-chains 144 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 18 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 180 optimal weight: 0.0870 chunk 201 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 294 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 358 optimal weight: 30.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN A1034 GLN A1046 HIS A1104 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS C 205 HIS ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5632 r_free = 0.5632 target = 0.378895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5652 r_free = 0.5652 target = 0.370436 restraints weight = 96101.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5659 r_free = 0.5659 target = 0.371273 restraints weight = 56219.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5667 r_free = 0.5667 target = 0.371848 restraints weight = 35227.473| |-----------------------------------------------------------------------------| r_work (final): 0.5553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0873 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30447 Z= 0.161 Angle : 0.640 20.951 41450 Z= 0.337 Chirality : 0.046 0.264 4645 Planarity : 0.005 0.076 5373 Dihedral : 4.836 58.150 4114 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 2.22 % Allowed : 12.99 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.77 (0.13), residues: 3775 helix: 0.26 (0.20), residues: 616 sheet: -0.41 (0.18), residues: 822 loop : -1.97 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 884 HIS 0.008 0.001 HIS C1086 PHE 0.044 0.002 PHE C1101 TYR 0.019 0.001 TYR C1045 ARG 0.009 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 932) hydrogen bonds : angle 5.86788 ( 2493) SS BOND : bond 0.00475 ( 44) SS BOND : angle 1.24468 ( 88) covalent geometry : bond 0.00324 (30403) covalent geometry : angle 0.63814 (41362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 137 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0476 (t-90) cc_final: -0.1509 (t-90) REVERT: A 58 PHE cc_start: 0.3107 (m-10) cc_final: 0.2492 (m-80) REVERT: A 151 MET cc_start: -0.0331 (mpp) cc_final: -0.0731 (mpp) REVERT: A 318 VAL cc_start: -0.1834 (OUTLIER) cc_final: -0.2117 (m) REVERT: A 695 MET cc_start: 0.2323 (mtp) cc_final: 0.2054 (mpp) REVERT: A 771 GLU cc_start: -0.0317 (OUTLIER) cc_final: -0.4447 (mm-30) REVERT: A 793 LYS cc_start: 0.3624 (mttp) cc_final: 0.1318 (pptt) REVERT: A 866 GLU cc_start: 0.1733 (OUTLIER) cc_final: -0.1988 (pt0) REVERT: A 872 THR cc_start: -0.1965 (OUTLIER) cc_final: -0.3413 (t) REVERT: A 924 GLN cc_start: 0.0554 (OUTLIER) cc_final: -0.1117 (mm-40) REVERT: A 1009 GLN cc_start: -0.0201 (OUTLIER) cc_final: -0.0406 (tm-30) REVERT: A 1017 ARG cc_start: 0.2457 (ttp80) cc_final: -0.0326 (ptp-170) REVERT: A 1070 GLU cc_start: 0.1678 (OUTLIER) cc_final: -0.2076 (mt-10) REVERT: B 175 MET cc_start: 0.2612 (tpp) cc_final: 0.1236 (ptt) REVERT: B 367 TYR cc_start: -0.1440 (m-80) cc_final: -0.2994 (m-80) REVERT: C 506 TYR cc_start: 0.2441 (m-80) cc_final: 0.1497 (m-10) REVERT: C 672 TYR cc_start: 0.3522 (t80) cc_final: 0.2557 (t80) REVERT: C 898 MET cc_start: 0.1278 (mmt) cc_final: -0.1130 (mtp) REVERT: H 82 MET cc_start: 0.3635 (mmp) cc_final: 0.0522 (pmm) REVERT: I 82 MET cc_start: 0.3053 (mmt) cc_final: 0.2325 (ppp) REVERT: I 105 MET cc_start: 0.1116 (OUTLIER) cc_final: 0.0034 (ttp) outliers start: 73 outliers final: 45 residues processed: 202 average time/residue: 0.3957 time to fit residues: 132.5484 Evaluate side-chains 174 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 924 GLN Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 852 LYS Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 210 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 185 optimal weight: 0.6980 chunk 328 optimal weight: 30.0000 chunk 237 optimal weight: 0.1980 chunk 218 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 369 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN A1034 GLN A1104 GLN B1046 HIS C 216 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN J 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.379610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.371391 restraints weight = 95742.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5665 r_free = 0.5665 target = 0.372202 restraints weight = 58092.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5668 r_free = 0.5668 target = 0.372804 restraints weight = 36737.491| |-----------------------------------------------------------------------------| r_work (final): 0.5561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0765 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30447 Z= 0.101 Angle : 0.525 13.172 41450 Z= 0.274 Chirality : 0.042 0.193 4645 Planarity : 0.004 0.075 5373 Dihedral : 4.368 58.001 4114 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 1.76 % Allowed : 14.09 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.51 (0.13), residues: 3775 helix: 0.70 (0.20), residues: 624 sheet: -0.22 (0.18), residues: 796 loop : -1.87 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 434 HIS 0.018 0.001 HIS B1046 PHE 0.031 0.001 PHE B 541 TYR 0.020 0.001 TYR C1065 ARG 0.003 0.000 ARG B1037 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 932) hydrogen bonds : angle 5.47279 ( 2493) SS BOND : bond 0.00343 ( 44) SS BOND : angle 1.25830 ( 88) covalent geometry : bond 0.00209 (30403) covalent geometry : angle 0.52256 (41362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 3.411 Fit side-chains REVERT: A 49 HIS cc_start: -0.0797 (t-90) cc_final: -0.1752 (t-90) REVERT: A 58 PHE cc_start: 0.3056 (m-10) cc_final: 0.2450 (m-80) REVERT: A 151 MET cc_start: -0.0381 (mpp) cc_final: -0.0669 (mpp) REVERT: A 338 GLU cc_start: -0.0806 (OUTLIER) cc_final: -0.1263 (mm-30) REVERT: A 793 LYS cc_start: 0.3494 (mttp) cc_final: 0.1289 (pptt) REVERT: A 866 GLU cc_start: 0.1714 (OUTLIER) cc_final: -0.0299 (pm20) REVERT: A 872 THR cc_start: -0.1737 (OUTLIER) cc_final: -0.3244 (t) REVERT: A 900 MET cc_start: -0.0144 (mtp) cc_final: -0.2253 (ptt) REVERT: A 924 GLN cc_start: 0.0849 (OUTLIER) cc_final: -0.1861 (mm-40) REVERT: A 1017 ARG cc_start: 0.2027 (ttp80) cc_final: 0.0297 (ptm160) REVERT: B 175 MET cc_start: 0.2463 (tpp) cc_final: 0.1132 (ptt) REVERT: B 189 GLU cc_start: 0.0267 (OUTLIER) cc_final: 0.0051 (pm20) REVERT: B 367 TYR cc_start: -0.0798 (m-80) cc_final: -0.2484 (m-80) REVERT: B 852 LYS cc_start: -0.0112 (mmtm) cc_final: -0.0671 (pttp) REVERT: B 867 MET cc_start: -0.1248 (ptp) cc_final: -0.1489 (ptt) REVERT: B 896 PHE cc_start: 0.2860 (OUTLIER) cc_final: 0.2571 (m-80) REVERT: C 151 MET cc_start: -0.0440 (mtt) cc_final: -0.1455 (mtm) REVERT: C 506 TYR cc_start: 0.2370 (m-80) cc_final: 0.1481 (m-10) REVERT: C 672 TYR cc_start: 0.3416 (t80) cc_final: 0.2542 (t80) REVERT: C 898 MET cc_start: 0.0868 (mmt) cc_final: -0.1435 (mtp) REVERT: H 82 MET cc_start: 0.3573 (mmp) cc_final: 0.0505 (pmm) REVERT: I 82 MET cc_start: 0.2962 (mmt) cc_final: 0.2253 (ppp) REVERT: I 105 MET cc_start: 0.1067 (OUTLIER) cc_final: -0.0091 (ttp) outliers start: 58 outliers final: 35 residues processed: 174 average time/residue: 0.3941 time to fit residues: 116.5851 Evaluate side-chains 160 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 924 GLN Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 260 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 50.0000 chunk 300 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 339 optimal weight: 50.0000 chunk 35 optimal weight: 40.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 799 ASN A 802 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1086 HIS B 530 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 ASN C 777 GLN ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5608 r_free = 0.5608 target = 0.374543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.365993 restraints weight = 95230.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.366864 restraints weight = 68991.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5633 r_free = 0.5633 target = 0.367466 restraints weight = 41030.101| |-----------------------------------------------------------------------------| r_work (final): 0.5532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1379 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 30447 Z= 0.278 Angle : 0.930 26.620 41450 Z= 0.487 Chirality : 0.055 0.607 4645 Planarity : 0.007 0.120 5373 Dihedral : 6.222 52.881 4114 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.74 % Favored : 91.02 % Rotamer: Outliers : 3.73 % Allowed : 14.48 % Favored : 81.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.30 (0.12), residues: 3775 helix: -0.96 (0.18), residues: 637 sheet: -0.37 (0.19), residues: 752 loop : -2.21 (0.11), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 884 HIS 0.071 0.003 HIS B1046 PHE 0.060 0.003 PHE C1119 TYR 0.035 0.003 TYR C 264 ARG 0.010 0.001 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.06245 ( 932) hydrogen bonds : angle 7.11423 ( 2493) SS BOND : bond 0.00956 ( 44) SS BOND : angle 1.81659 ( 88) covalent geometry : bond 0.00608 (30403) covalent geometry : angle 0.92727 (41362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 139 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.0117 (t-170) cc_final: -0.1308 (t-170) REVERT: A 151 MET cc_start: -0.1194 (mpp) cc_final: -0.1438 (mpp) REVERT: A 582 ILE cc_start: 0.2042 (OUTLIER) cc_final: 0.1630 (mt) REVERT: A 725 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1473 (tp) REVERT: A 771 GLU cc_start: 0.1900 (OUTLIER) cc_final: 0.0577 (mt-10) REVERT: A 793 LYS cc_start: 0.4416 (mttp) cc_final: 0.1891 (pptt) REVERT: A 866 GLU cc_start: 0.1973 (OUTLIER) cc_final: -0.0025 (pt0) REVERT: A 872 THR cc_start: 0.0922 (OUTLIER) cc_final: 0.0487 (m) REVERT: A 913 VAL cc_start: 0.4331 (p) cc_final: 0.3519 (t) REVERT: A 929 ILE cc_start: 0.2235 (OUTLIER) cc_final: 0.1768 (tp) REVERT: A 982 LEU cc_start: 0.2314 (OUTLIER) cc_final: 0.2050 (tt) REVERT: B 175 MET cc_start: 0.3472 (tpp) cc_final: 0.1498 (ptt) REVERT: B 454 PHE cc_start: 0.5080 (t80) cc_final: 0.4803 (t80) REVERT: C 661 ASP cc_start: -0.0794 (OUTLIER) cc_final: -0.2154 (t0) REVERT: C 672 TYR cc_start: 0.3472 (t80) cc_final: 0.2930 (t80) REVERT: C 707 ASN cc_start: 0.0513 (OUTLIER) cc_final: -0.0717 (m-40) REVERT: C 732 THR cc_start: 0.3165 (OUTLIER) cc_final: 0.1877 (m) REVERT: C 898 MET cc_start: 0.1894 (mmt) cc_final: -0.0482 (mtp) REVERT: C 904 PHE cc_start: 0.0906 (OUTLIER) cc_final: -0.0515 (m-80) REVERT: C 1047 LEU cc_start: -0.2692 (OUTLIER) cc_final: -0.3126 (tp) REVERT: C 1087 PHE cc_start: 0.2832 (OUTLIER) cc_final: -0.0054 (m-10) REVERT: G 92 MET cc_start: -0.0230 (tmm) cc_final: -0.0515 (tmm) REVERT: I 82 MET cc_start: 0.3345 (mmt) cc_final: 0.2292 (ppp) REVERT: I 105 MET cc_start: 0.1431 (OUTLIER) cc_final: 0.0355 (ttp) REVERT: K 96 SER cc_start: 0.2653 (m) cc_final: 0.2426 (t) outliers start: 123 outliers final: 70 residues processed: 245 average time/residue: 0.3818 time to fit residues: 156.9205 Evaluate side-chains 202 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 118 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 977 ASP Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1084 LYS Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 64 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 79 ASN A 237 GLN A 562 GLN A 673 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN B 775 ASN B 785 GLN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS C 407 GLN C 604 ASN C 605 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5607 r_free = 0.5607 target = 0.375227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.366129 restraints weight = 94820.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.367231 restraints weight = 65647.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5633 r_free = 0.5633 target = 0.367699 restraints weight = 42487.666| |-----------------------------------------------------------------------------| r_work (final): 0.5486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1323 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30447 Z= 0.184 Angle : 0.711 15.776 41450 Z= 0.373 Chirality : 0.047 0.300 4645 Planarity : 0.006 0.079 5373 Dihedral : 5.559 52.827 4114 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.11 (0.13), residues: 3775 helix: -0.50 (0.19), residues: 614 sheet: -0.32 (0.19), residues: 760 loop : -2.14 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1100 HIS 0.007 0.001 HIS B1086 PHE 0.031 0.002 PHE A 800 TYR 0.034 0.002 TYR C1065 ARG 0.010 0.001 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 932) hydrogen bonds : angle 6.57932 ( 2493) SS BOND : bond 0.00579 ( 44) SS BOND : angle 1.54645 ( 88) covalent geometry : bond 0.00399 (30403) covalent geometry : angle 0.70840 (41362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 128 time to evaluate : 2.982 Fit side-chains REVERT: A 49 HIS cc_start: 0.0322 (t70) cc_final: -0.0938 (t70) REVERT: A 341 ASN cc_start: 0.0424 (OUTLIER) cc_final: -0.1172 (p0) REVERT: A 541 PHE cc_start: 0.2455 (OUTLIER) cc_final: 0.1635 (m-80) REVERT: A 582 ILE cc_start: 0.1946 (OUTLIER) cc_final: 0.1531 (mt) REVERT: A 771 GLU cc_start: 0.2257 (OUTLIER) cc_final: -0.1827 (mm-30) REVERT: A 793 LYS cc_start: 0.4060 (mttp) cc_final: 0.1639 (pptt) REVERT: A 913 VAL cc_start: 0.3840 (p) cc_final: 0.3531 (p) REVERT: A 929 ILE cc_start: 0.1621 (OUTLIER) cc_final: 0.1301 (tp) REVERT: A 982 LEU cc_start: 0.2259 (OUTLIER) cc_final: 0.2048 (tt) REVERT: B 138 PHE cc_start: -0.2870 (OUTLIER) cc_final: -0.3749 (m-80) REVERT: B 175 MET cc_start: 0.3399 (tpp) cc_final: 0.1373 (ptt) REVERT: B 867 MET cc_start: -0.1081 (ptp) cc_final: -0.1309 (ptp) REVERT: B 896 PHE cc_start: 0.3522 (OUTLIER) cc_final: 0.3011 (m-80) REVERT: C 32 PHE cc_start: 0.0129 (OUTLIER) cc_final: -0.1417 (t80) REVERT: C 506 TYR cc_start: 0.2121 (m-80) cc_final: 0.1049 (m-10) REVERT: C 661 ASP cc_start: -0.1305 (OUTLIER) cc_final: -0.1953 (t0) REVERT: C 672 TYR cc_start: 0.3822 (t80) cc_final: 0.3149 (t80) REVERT: C 732 THR cc_start: 0.3045 (OUTLIER) cc_final: 0.1666 (m) REVERT: C 898 MET cc_start: 0.1659 (mmt) cc_final: -0.0584 (mtp) REVERT: C 1047 LEU cc_start: -0.2053 (OUTLIER) cc_final: -0.2420 (tp) REVERT: I 82 MET cc_start: 0.3568 (mmt) cc_final: 0.2323 (ppp) REVERT: I 105 MET cc_start: 0.1329 (OUTLIER) cc_final: 0.0171 (ttp) outliers start: 104 outliers final: 73 residues processed: 221 average time/residue: 0.3536 time to fit residues: 134.7786 Evaluate side-chains 208 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 122 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1025 THR Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 216 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 344 optimal weight: 40.0000 chunk 132 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 316 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 254 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 403 ASN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5602 r_free = 0.5602 target = 0.374107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.365356 restraints weight = 95431.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.366336 restraints weight = 60745.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.366441 restraints weight = 37309.485| |-----------------------------------------------------------------------------| r_work (final): 0.5522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1462 moved from start: 0.7473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 30447 Z= 0.197 Angle : 0.751 18.754 41450 Z= 0.395 Chirality : 0.049 0.454 4645 Planarity : 0.006 0.082 5373 Dihedral : 5.714 51.760 4114 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.19 % Favored : 90.70 % Rotamer: Outliers : 3.10 % Allowed : 16.39 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.22 (0.13), residues: 3775 helix: -0.41 (0.20), residues: 607 sheet: -0.31 (0.19), residues: 738 loop : -2.28 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1100 HIS 0.010 0.001 HIS B1046 PHE 0.033 0.002 PHE A 316 TYR 0.032 0.002 TYR C1065 ARG 0.012 0.001 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 932) hydrogen bonds : angle 6.83909 ( 2493) SS BOND : bond 0.00668 ( 44) SS BOND : angle 1.44123 ( 88) covalent geometry : bond 0.00426 (30403) covalent geometry : angle 0.74877 (41362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 124 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.0432 (t70) cc_final: -0.0748 (t70) REVERT: A 268 LEU cc_start: 0.1877 (mm) cc_final: 0.1654 (mm) REVERT: A 541 PHE cc_start: 0.2896 (OUTLIER) cc_final: 0.1988 (m-80) REVERT: A 582 ILE cc_start: 0.2298 (OUTLIER) cc_final: 0.1978 (mp) REVERT: A 771 GLU cc_start: 0.1651 (OUTLIER) cc_final: -0.2258 (mm-30) REVERT: A 900 MET cc_start: -0.0344 (mtp) cc_final: -0.0559 (mtm) REVERT: A 929 ILE cc_start: 0.1859 (OUTLIER) cc_final: 0.1475 (tp) REVERT: A 982 LEU cc_start: 0.2429 (OUTLIER) cc_final: 0.1939 (tt) REVERT: B 138 PHE cc_start: -0.2809 (OUTLIER) cc_final: -0.4262 (m-80) REVERT: B 175 MET cc_start: 0.3763 (tpp) cc_final: 0.1601 (ptt) REVERT: B 1015 GLU cc_start: -0.2188 (OUTLIER) cc_final: -0.2702 (tp30) REVERT: C 48 LEU cc_start: -0.3343 (OUTLIER) cc_final: -0.4295 (mt) REVERT: C 99 ILE cc_start: -0.0521 (OUTLIER) cc_final: -0.0861 (tt) REVERT: C 506 TYR cc_start: 0.2435 (m-80) cc_final: 0.1385 (m-10) REVERT: C 661 ASP cc_start: -0.1116 (OUTLIER) cc_final: -0.2120 (t0) REVERT: C 672 TYR cc_start: 0.3903 (t80) cc_final: 0.3232 (t80) REVERT: C 693 TYR cc_start: -0.0452 (OUTLIER) cc_final: -0.2040 (p90) REVERT: C 732 THR cc_start: 0.3261 (OUTLIER) cc_final: 0.1367 (m) REVERT: C 898 MET cc_start: 0.1723 (mmt) cc_final: 0.0798 (mmt) REVERT: C 1047 LEU cc_start: -0.1661 (OUTLIER) cc_final: -0.2072 (tp) REVERT: C 1087 PHE cc_start: 0.2788 (OUTLIER) cc_final: -0.0696 (m-10) REVERT: I 82 MET cc_start: 0.3763 (mmt) cc_final: 0.2120 (ppp) REVERT: I 105 MET cc_start: 0.1161 (OUTLIER) cc_final: 0.0102 (ttp) outliers start: 102 outliers final: 71 residues processed: 214 average time/residue: 0.3448 time to fit residues: 127.6602 Evaluate side-chains 203 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 117 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain B residue 1025 THR Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 693 TYR Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1084 LYS Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 287 optimal weight: 30.0000 chunk 374 optimal weight: 50.0000 chunk 334 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN B 243 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN C 605 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.373129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.364280 restraints weight = 94965.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.365058 restraints weight = 65214.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5624 r_free = 0.5624 target = 0.365270 restraints weight = 48263.920| |-----------------------------------------------------------------------------| r_work (final): 0.5517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1541 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30447 Z= 0.201 Angle : 0.749 16.071 41450 Z= 0.394 Chirality : 0.049 0.364 4645 Planarity : 0.006 0.078 5373 Dihedral : 5.886 51.393 4114 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.08 % Rotamer: Outliers : 3.10 % Allowed : 16.61 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.33 (0.13), residues: 3775 helix: -0.54 (0.19), residues: 612 sheet: -0.38 (0.19), residues: 760 loop : -2.37 (0.11), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1100 HIS 0.007 0.001 HIS B1086 PHE 0.042 0.002 PHE C 557 TYR 0.042 0.002 TYR A 794 ARG 0.009 0.001 ARG C 565 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 932) hydrogen bonds : angle 6.91212 ( 2493) SS BOND : bond 0.01083 ( 44) SS BOND : angle 1.50633 ( 88) covalent geometry : bond 0.00438 (30403) covalent geometry : angle 0.74698 (41362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 126 time to evaluate : 3.174 Fit side-chains REVERT: A 49 HIS cc_start: 0.0552 (t70) cc_final: -0.0623 (t70) REVERT: A 268 LEU cc_start: 0.2146 (mm) cc_final: 0.1927 (mm) REVERT: A 341 ASN cc_start: 0.0449 (OUTLIER) cc_final: -0.0746 (p0) REVERT: A 541 PHE cc_start: 0.2656 (OUTLIER) cc_final: 0.1673 (m-80) REVERT: A 582 ILE cc_start: 0.2433 (OUTLIER) cc_final: 0.2086 (mp) REVERT: A 606 VAL cc_start: -0.2057 (OUTLIER) cc_final: -0.3782 (p) REVERT: A 866 GLU cc_start: 0.1927 (OUTLIER) cc_final: -0.2115 (tt0) REVERT: A 929 ILE cc_start: 0.2350 (OUTLIER) cc_final: 0.2020 (tp) REVERT: A 982 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.2103 (tt) REVERT: A 1029 GLU cc_start: 0.5209 (mt-10) cc_final: 0.4936 (mt-10) REVERT: B 138 PHE cc_start: -0.2695 (OUTLIER) cc_final: -0.4453 (m-80) REVERT: B 175 MET cc_start: 0.4235 (tpp) cc_final: 0.1844 (ptt) REVERT: B 896 PHE cc_start: 0.3375 (OUTLIER) cc_final: 0.3007 (m-80) REVERT: B 937 SER cc_start: 0.4102 (p) cc_final: 0.3878 (t) REVERT: C 48 LEU cc_start: -0.3356 (OUTLIER) cc_final: -0.4236 (mt) REVERT: C 212 ARG cc_start: 0.1328 (OUTLIER) cc_final: 0.0422 (mtm110) REVERT: C 506 TYR cc_start: 0.2694 (m-80) cc_final: 0.1619 (m-10) REVERT: C 661 ASP cc_start: -0.1321 (OUTLIER) cc_final: -0.2470 (t0) REVERT: C 672 TYR cc_start: 0.4154 (t80) cc_final: 0.3482 (t80) REVERT: C 693 TYR cc_start: -0.0032 (OUTLIER) cc_final: -0.1379 (p90) REVERT: C 707 ASN cc_start: 0.0174 (OUTLIER) cc_final: -0.1336 (m-40) REVERT: C 738 MET cc_start: 0.2493 (tpp) cc_final: 0.0121 (ttt) REVERT: C 863 LEU cc_start: 0.0375 (tp) cc_final: -0.0108 (tp) REVERT: C 898 MET cc_start: 0.1489 (mmt) cc_final: 0.0606 (mmt) REVERT: C 1047 LEU cc_start: -0.1485 (OUTLIER) cc_final: -0.1689 (tp) REVERT: L 101 GLN cc_start: 0.0668 (OUTLIER) cc_final: -0.0698 (mm-40) REVERT: I 82 MET cc_start: 0.4056 (mmt) cc_final: 0.2196 (ppp) REVERT: I 105 MET cc_start: 0.1102 (OUTLIER) cc_final: -0.0006 (ttp) outliers start: 102 outliers final: 76 residues processed: 219 average time/residue: 0.3660 time to fit residues: 136.9271 Evaluate side-chains 215 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 122 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ARG Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 693 TYR Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1084 LYS Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 256 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 365 optimal weight: 40.0000 chunk 187 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 14 optimal weight: 0.2980 chunk 319 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** A1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.371363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5611 r_free = 0.5611 target = 0.362462 restraints weight = 95300.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5608 r_free = 0.5608 target = 0.363662 restraints weight = 67432.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5609 r_free = 0.5609 target = 0.363899 restraints weight = 44746.678| |-----------------------------------------------------------------------------| r_work (final): 0.5509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1656 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 30447 Z= 0.238 Angle : 0.830 19.277 41450 Z= 0.438 Chirality : 0.052 0.592 4645 Planarity : 0.007 0.095 5373 Dihedral : 6.249 52.211 4114 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.60 % Favored : 89.25 % Rotamer: Outliers : 3.07 % Allowed : 16.76 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.56 (0.12), residues: 3775 helix: -0.74 (0.19), residues: 609 sheet: -0.46 (0.19), residues: 717 loop : -2.50 (0.11), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1100 HIS 0.012 0.002 HIS B1046 PHE 0.076 0.003 PHE L 99 TYR 0.051 0.002 TYR A 311 ARG 0.010 0.001 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.05568 ( 932) hydrogen bonds : angle 7.34527 ( 2493) SS BOND : bond 0.00797 ( 44) SS BOND : angle 1.18306 ( 88) covalent geometry : bond 0.00516 (30403) covalent geometry : angle 0.82932 (41362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7550 Ramachandran restraints generated. 3775 Oldfield, 0 Emsley, 3775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 128 time to evaluate : 3.287 Fit side-chains revert: symmetry clash REVERT: A 311 TYR cc_start: 0.1114 (m-80) cc_final: 0.0502 (m-80) REVERT: A 541 PHE cc_start: 0.2625 (OUTLIER) cc_final: 0.1570 (m-80) REVERT: A 582 ILE cc_start: 0.2640 (OUTLIER) cc_final: 0.2391 (mp) REVERT: A 606 VAL cc_start: -0.1978 (OUTLIER) cc_final: -0.3718 (p) REVERT: A 725 LEU cc_start: 0.1687 (OUTLIER) cc_final: 0.1409 (tp) REVERT: A 866 GLU cc_start: 0.0802 (OUTLIER) cc_final: -0.0850 (pt0) REVERT: A 900 MET cc_start: -0.0258 (mtp) cc_final: -0.0509 (mtm) REVERT: A 929 ILE cc_start: 0.2882 (OUTLIER) cc_final: 0.2678 (mm) REVERT: A 1029 GLU cc_start: 0.5393 (mt-10) cc_final: 0.4994 (mt-10) REVERT: B 175 MET cc_start: 0.4313 (tpp) cc_final: 0.1874 (ptt) REVERT: B 750 LEU cc_start: -0.0508 (OUTLIER) cc_final: -0.0860 (mt) REVERT: B 925 PHE cc_start: 0.2548 (OUTLIER) cc_final: -0.0390 (t80) REVERT: B 952 HIS cc_start: -0.1907 (m170) cc_final: -0.3707 (t-90) REVERT: B 1015 GLU cc_start: -0.1845 (OUTLIER) cc_final: -0.2947 (tp30) REVERT: C 48 LEU cc_start: -0.3348 (OUTLIER) cc_final: -0.4409 (mt) REVERT: C 212 ARG cc_start: 0.1157 (OUTLIER) cc_final: 0.0384 (mtm180) REVERT: C 661 ASP cc_start: -0.1279 (OUTLIER) cc_final: -0.2677 (t0) REVERT: C 672 TYR cc_start: 0.4045 (t80) cc_final: 0.3474 (t80) REVERT: C 693 TYR cc_start: 0.0016 (OUTLIER) cc_final: -0.1221 (p90) REVERT: C 707 ASN cc_start: 0.1221 (OUTLIER) cc_final: -0.0968 (m-40) REVERT: C 738 MET cc_start: 0.2405 (tpp) cc_final: 0.2059 (mmp) REVERT: C 857 THR cc_start: 0.4213 (m) cc_final: 0.3974 (m) REVERT: C 898 MET cc_start: 0.1795 (mmt) cc_final: 0.0893 (mmt) REVERT: C 1047 LEU cc_start: -0.1744 (OUTLIER) cc_final: -0.2768 (mt) REVERT: G 82 MET cc_start: 0.5755 (mpp) cc_final: 0.4436 (mtm) REVERT: I 82 MET cc_start: 0.4198 (mmt) cc_final: 0.3373 (mmt) REVERT: I 105 MET cc_start: 0.1244 (OUTLIER) cc_final: 0.0157 (ttp) outliers start: 101 outliers final: 73 residues processed: 222 average time/residue: 0.3612 time to fit residues: 137.9999 Evaluate side-chains 210 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 121 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ARG Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 693 TYR Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1084 LYS Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 6 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 chunk 137 optimal weight: 2.9990 chunk 188 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 ASN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.372136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5619 r_free = 0.5619 target = 0.363333 restraints weight = 95247.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5619 r_free = 0.5619 target = 0.364349 restraints weight = 66538.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5620 r_free = 0.5620 target = 0.364566 restraints weight = 43005.190| |-----------------------------------------------------------------------------| r_work (final): 0.5514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1604 moved from start: 0.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 30447 Z= 0.180 Angle : 0.712 15.109 41450 Z= 0.375 Chirality : 0.048 0.371 4645 Planarity : 0.006 0.079 5373 Dihedral : 5.899 52.589 4114 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.21 % Favored : 91.68 % Rotamer: Outliers : 2.88 % Allowed : 16.94 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.40 (0.13), residues: 3775 helix: -0.45 (0.20), residues: 617 sheet: -0.43 (0.19), residues: 740 loop : -2.45 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1100 HIS 0.010 0.001 HIS B1046 PHE 0.040 0.002 PHE A 316 TYR 0.040 0.002 TYR A 794 ARG 0.009 0.001 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 932) hydrogen bonds : angle 6.97997 ( 2493) SS BOND : bond 0.00637 ( 44) SS BOND : angle 1.13519 ( 88) covalent geometry : bond 0.00394 (30403) covalent geometry : angle 0.71070 (41362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7933.08 seconds wall clock time: 140 minutes 49.22 seconds (8449.22 seconds total)