Starting phenix.real_space_refine on Fri Jun 27 12:18:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsd_38616/06_2025/8xsd_38616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsd_38616/06_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_38616/06_2025/8xsd_38616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsd_38616/06_2025/8xsd_38616.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsd_38616/06_2025/8xsd_38616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsd_38616/06_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-5710/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: 17.73, per 1000 atoms: 0.60 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: 7.92 Conformation dependent library (CDL) restraints added in 4.1 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: 4.59 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: 13.58 Time building geometry restraints manager: 9.36 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 73.480 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.150 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.100 ------------------------------------------------------------------------------- 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 : 3.005 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: 0.4260 time to fit residues: 158.0570 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 : 2.892 ------------------------------------------------------------------------------- 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 = 60)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.355773 restraints weight = 92695.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.5543 r_free = 0.5543 target = 0.357942 restraints weight = 54243.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5558 r_free = 0.5558 target = 0.359315 restraints weight = 33622.528| |-----------------------------------------------------------------------------| r_work (final): 0.5550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0689 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 59.469 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 1.45756 ( 88) covalent geometry : bond 0.00427 (30403) covalent geometry : angle 0.73534 (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 : 3.044 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0068 (t-90) cc_final: -0.1279 (t-90) REVERT: A 58 PHE cc_start: 0.2690 (m-10) cc_final: 0.2284 (m-80) REVERT: A 151 MET cc_start: -0.0904 (mpp) cc_final: -0.1233 (mpp) REVERT: A 533 LYS cc_start: 0.0583 (mmmm) cc_final: 0.0219 (pttp) REVERT: A 799 ASN cc_start: 0.4126 (t0) cc_final: 0.3743 (t0) REVERT: A 1017 ARG cc_start: 0.1603 (ttp80) cc_final: 0.1355 (ptt180) REVERT: B 175 MET cc_start: 0.0490 (tpp) cc_final: -0.0161 (ptt) REVERT: B 695 MET cc_start: 0.1832 (ptm) cc_final: 0.1424 (ppp) REVERT: B 738 MET cc_start: -0.2681 (ttm) cc_final: -0.4790 (mmm) REVERT: C 672 TYR cc_start: 0.3302 (t80) cc_final: 0.1698 (t80) REVERT: C 1027 MET cc_start: 0.4413 (ttm) cc_final: 0.3967 (ttm) REVERT: H 34 MET cc_start: 0.0084 (mmm) cc_final: -0.0172 (mmm) REVERT: H 82 MET cc_start: 0.2747 (mmp) cc_final: 0.0412 (pmm) REVERT: G 82 MET cc_start: 0.3080 (mpp) cc_final: 0.2478 (mpp) REVERT: I 57 THR cc_start: 0.4792 (OUTLIER) cc_final: 0.4567 (p) REVERT: I 82 MET cc_start: 0.2910 (mmt) cc_final: 0.2524 (ppp) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.3959 time to fit residues: 118.1391 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 : 3.279 ------------------------------------------------------------------------------- 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: 0.9980 chunk 315 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 208 optimal weight: 0.0170 chunk 127 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 345 optimal weight: 0.1980 chunk 341 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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** A1034 GLN B 52 GLN B 933 GLN B 953 ASN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.364092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5527 r_free = 0.5527 target = 0.356237 restraints weight = 92928.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.358436 restraints weight = 54336.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5562 r_free = 0.5562 target = 0.359781 restraints weight = 33900.519| |-----------------------------------------------------------------------------| r_work (final): 0.5559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0561 moved from start: 0.2646 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= 0.106 Angle : 0.534 9.330 41450 Z= 0.282 Chirality : 0.043 0.204 4645 Planarity : 0.004 0.077 5373 Dihedral : 4.557 59.118 4114 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 0.85 % Allowed : 10.14 % Favored : 89.01 % 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: -1.71 (0.13), residues: 3775 helix: 0.55 (0.21), residues: 609 sheet: -0.55 (0.18), residues: 830 loop : -1.92 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 884 HIS 0.008 0.001 HIS B1046 PHE 0.011 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 0.04339 ( 932) hydrogen bonds : angle 5.83116 ( 2493) SS BOND : bond 0.00307 ( 44) SS BOND : angle 1.02483 ( 88) covalent geometry : bond 0.00216 (30403) covalent geometry : angle 0.53252 (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 164 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 3.143 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0825 (t-90) cc_final: -0.1914 (t-90) REVERT: A 58 PHE cc_start: 0.2446 (m-10) cc_final: 0.2080 (m-80) REVERT: A 151 MET cc_start: -0.0825 (mpp) cc_final: -0.1122 (mpp) REVERT: A 533 LYS cc_start: 0.0774 (mmmm) cc_final: 0.0229 (pttt) REVERT: A 695 MET cc_start: 0.2066 (mtp) cc_final: 0.1718 (mtt) REVERT: A 793 LYS cc_start: 0.3071 (mttp) cc_final: 0.1633 (pptt) REVERT: A 872 THR cc_start: -0.2596 (m) cc_final: -0.4751 (t) REVERT: A 1017 ARG cc_start: 0.1234 (ttp80) cc_final: 0.0207 (ptt180) REVERT: B 175 MET cc_start: 0.0767 (tpp) cc_final: -0.0071 (ptt) REVERT: B 695 MET cc_start: 0.2149 (ptm) cc_final: 0.1881 (ppp) REVERT: B 738 MET cc_start: -0.2590 (ttm) cc_final: -0.4892 (mmm) REVERT: B 900 MET cc_start: 0.1797 (tpt) cc_final: 0.1565 (tpt) REVERT: C 672 TYR cc_start: 0.3260 (t80) cc_final: 0.1878 (t80) REVERT: C 1027 MET cc_start: 0.4553 (ttm) cc_final: 0.4137 (ttm) REVERT: C 1084 LYS cc_start: 0.4711 (tppt) cc_final: 0.4023 (tppt) REVERT: H 82 MET cc_start: 0.3030 (mmp) cc_final: 0.0432 (pmm) REVERT: G 82 MET cc_start: 0.3162 (mpp) cc_final: 0.2590 (mpp) REVERT: I 105 MET cc_start: 0.0969 (OUTLIER) cc_final: -0.0135 (ttp) outliers start: 28 outliers final: 12 residues processed: 158 average time/residue: 0.4088 time to fit residues: 109.0365 Evaluate side-chains 139 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 819 LEU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 310 ILE 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 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: 10.0000 chunk 180 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 343 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 358 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 A1104 GLN B 52 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5575 r_free = 0.5575 target = 0.362784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5513 r_free = 0.5513 target = 0.354725 restraints weight = 92352.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.356945 restraints weight = 54151.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.358312 restraints weight = 33660.140| |-----------------------------------------------------------------------------| r_work (final): 0.5546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0686 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30447 Z= 0.110 Angle : 0.535 17.091 41450 Z= 0.279 Chirality : 0.043 0.254 4645 Planarity : 0.004 0.076 5373 Dihedral : 4.385 59.829 4114 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 1.00 % Allowed : 12.20 % Favored : 86.79 % 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: -1.56 (0.13), residues: 3775 helix: 0.78 (0.21), residues: 617 sheet: -0.40 (0.18), residues: 834 loop : -1.89 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1100 HIS 0.008 0.001 HIS C1099 PHE 0.023 0.001 PHE C1101 TYR 0.017 0.001 TYR C1065 ARG 0.004 0.000 ARG A1017 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 932) hydrogen bonds : angle 5.52331 ( 2493) SS BOND : bond 0.00388 ( 44) SS BOND : angle 1.13555 ( 88) covalent geometry : bond 0.00229 (30403) covalent geometry : angle 0.53345 (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 163 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0700 (t-90) cc_final: -0.1835 (t-90) REVERT: A 58 PHE cc_start: 0.2714 (m-10) cc_final: 0.2311 (m-80) REVERT: A 151 MET cc_start: -0.0972 (mpp) cc_final: -0.1265 (mpp) REVERT: A 533 LYS cc_start: 0.0586 (mmmm) cc_final: 0.0089 (pttt) REVERT: A 695 MET cc_start: 0.2100 (mtp) cc_final: 0.1602 (mtt) REVERT: A 793 LYS cc_start: 0.3327 (mttp) cc_final: 0.1663 (pptt) REVERT: A 866 GLU cc_start: 0.2246 (OUTLIER) cc_final: -0.1161 (mt-10) REVERT: A 924 GLN cc_start: 0.0737 (OUTLIER) cc_final: -0.1416 (mm-40) REVERT: A 1017 ARG cc_start: 0.1295 (ttp80) cc_final: -0.0156 (ptt180) REVERT: B 175 MET cc_start: 0.0918 (tpp) cc_final: 0.0035 (ptt) REVERT: B 695 MET cc_start: 0.2246 (ptm) cc_final: 0.1885 (ppp) REVERT: B 738 MET cc_start: -0.2314 (ttm) cc_final: -0.4554 (mmm) REVERT: B 1112 ILE cc_start: 0.1382 (mm) cc_final: 0.0679 (pt) REVERT: C 151 MET cc_start: -0.1270 (mtt) cc_final: -0.1814 (mtm) REVERT: C 672 TYR cc_start: 0.3377 (t80) cc_final: 0.2078 (t80) REVERT: C 898 MET cc_start: 0.1398 (mmt) cc_final: -0.1535 (mtp) REVERT: C 1027 MET cc_start: 0.4456 (ttm) cc_final: 0.4040 (ttm) REVERT: C 1084 LYS cc_start: 0.4707 (tppt) cc_final: 0.4421 (tppp) REVERT: H 82 MET cc_start: 0.3253 (mmp) cc_final: 0.0434 (pmm) REVERT: G 82 MET cc_start: 0.2934 (mpp) cc_final: 0.2425 (mpp) REVERT: I 105 MET cc_start: 0.1073 (OUTLIER) cc_final: -0.0033 (ttp) outliers start: 33 outliers final: 18 residues processed: 156 average time/residue: 0.4924 time to fit residues: 130.0366 Evaluate side-chains 144 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 730 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 924 GLN 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 428 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1126 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: 2.9990 chunk 39 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 328 optimal weight: 8.9990 chunk 237 optimal weight: 0.4980 chunk 218 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 273 optimal weight: 0.8980 chunk 279 optimal weight: 0.0000 chunk 121 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 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 = 0.5641 r_free = 0.5641 target = 0.380904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5662 r_free = 0.5662 target = 0.372426 restraints weight = 95550.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5670 r_free = 0.5670 target = 0.373330 restraints weight = 55835.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.373898 restraints weight = 34201.225| |-----------------------------------------------------------------------------| r_work (final): 0.5565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0603 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30447 Z= 0.097 Angle : 0.503 12.891 41450 Z= 0.263 Chirality : 0.042 0.167 4645 Planarity : 0.004 0.074 5373 Dihedral : 4.187 59.156 4114 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 1.21 % Allowed : 13.45 % Favored : 85.34 % 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: -1.40 (0.13), residues: 3775 helix: 1.00 (0.21), residues: 623 sheet: -0.25 (0.18), residues: 823 loop : -1.83 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 884 HIS 0.006 0.001 HIS B1046 PHE 0.031 0.001 PHE B 541 TYR 0.018 0.001 TYR C1065 ARG 0.009 0.000 ARG A 903 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 932) hydrogen bonds : angle 5.33669 ( 2493) SS BOND : bond 0.00353 ( 44) SS BOND : angle 0.91268 ( 88) covalent geometry : bond 0.00203 (30403) covalent geometry : angle 0.50190 (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 167 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0481 (t-90) cc_final: -0.1657 (t-90) REVERT: A 58 PHE cc_start: 0.2826 (m-10) cc_final: 0.2430 (m-80) REVERT: A 151 MET cc_start: -0.0809 (mpp) cc_final: -0.1085 (mpp) REVERT: A 533 LYS cc_start: 0.0832 (mmmm) cc_final: 0.0224 (pttt) REVERT: A 695 MET cc_start: 0.1926 (mtp) cc_final: 0.1360 (mtt) REVERT: A 793 LYS cc_start: 0.3079 (mttp) cc_final: 0.1252 (pptt) REVERT: A 866 GLU cc_start: 0.1806 (OUTLIER) cc_final: -0.0191 (mt-10) REVERT: A 872 THR cc_start: -0.2862 (OUTLIER) cc_final: -0.4378 (t) REVERT: A 924 GLN cc_start: -0.0489 (OUTLIER) cc_final: -0.2164 (mm-40) REVERT: A 1017 ARG cc_start: 0.1728 (ttp80) cc_final: 0.0415 (ptp-170) REVERT: B 175 MET cc_start: 0.2236 (tpp) cc_final: 0.1035 (ptt) REVERT: B 695 MET cc_start: 0.2043 (ptm) cc_final: 0.1789 (ppp) REVERT: B 738 MET cc_start: -0.2047 (ttm) cc_final: -0.4647 (mmm) REVERT: B 1112 ILE cc_start: 0.1054 (mm) cc_final: 0.0584 (pt) REVERT: C 151 MET cc_start: -0.0328 (mtt) cc_final: -0.1188 (mtm) REVERT: C 189 GLU cc_start: -0.1015 (OUTLIER) cc_final: -0.1271 (mp0) REVERT: C 672 TYR cc_start: 0.3158 (t80) cc_final: 0.2046 (t80) REVERT: C 1027 MET cc_start: 0.4592 (ttm) cc_final: 0.4074 (ttm) REVERT: C 1084 LYS cc_start: 0.4276 (tppt) cc_final: 0.3996 (tppp) REVERT: H 82 MET cc_start: 0.3339 (mmp) cc_final: 0.0412 (pmm) REVERT: I 105 MET cc_start: 0.0842 (OUTLIER) cc_final: -0.0265 (ttp) outliers start: 40 outliers final: 25 residues processed: 160 average time/residue: 0.6094 time to fit residues: 170.8849 Evaluate side-chains 150 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 7.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 819 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 924 GLN Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain B residue 128 VAL 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 856 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 907 ILE 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 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: 0.0170 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 50.0000 chunk 300 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 371 optimal weight: 30.0000 chunk 352 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 339 optimal weight: 50.0000 chunk 35 optimal weight: 3.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 854 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 216 GLN C 237 GLN ** 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** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.377324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5653 r_free = 0.5653 target = 0.369132 restraints weight = 95990.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5654 r_free = 0.5654 target = 0.369972 restraints weight = 57497.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5653 r_free = 0.5653 target = 0.370207 restraints weight = 36481.898| |-----------------------------------------------------------------------------| r_work (final): 0.5544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1073 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30447 Z= 0.218 Angle : 0.766 19.905 41450 Z= 0.403 Chirality : 0.050 0.402 4645 Planarity : 0.006 0.074 5373 Dihedral : 5.345 55.072 4114 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 2.82 % Allowed : 13.69 % Favored : 83.49 % Cbeta Deviations : 0.03 % 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: -1.85 (0.13), residues: 3775 helix: -0.08 (0.19), residues: 617 sheet: -0.22 (0.19), residues: 766 loop : -2.00 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 884 HIS 0.010 0.002 HIS B 49 PHE 0.051 0.002 PHE C1101 TYR 0.033 0.002 TYR B 739 ARG 0.010 0.001 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 932) hydrogen bonds : angle 6.34937 ( 2493) SS BOND : bond 0.00636 ( 44) SS BOND : angle 1.78011 ( 88) covalent geometry : bond 0.00455 (30403) covalent geometry : angle 0.76208 (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 228 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 135 time to evaluate : 3.455 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0139 (t-90) cc_final: -0.1381 (t-90) REVERT: A 151 MET cc_start: -0.1075 (mpp) cc_final: -0.1435 (mpp) REVERT: A 338 GLU cc_start: -0.0704 (OUTLIER) cc_final: -0.1334 (mm-30) REVERT: A 582 ILE cc_start: 0.1723 (OUTLIER) cc_final: 0.1350 (mt) REVERT: A 771 GLU cc_start: 0.0973 (OUTLIER) cc_final: -0.2981 (mm-30) REVERT: A 793 LYS cc_start: 0.4533 (mttp) cc_final: 0.1985 (pptt) REVERT: A 866 GLU cc_start: 0.1578 (OUTLIER) cc_final: -0.3205 (tt0) REVERT: A 872 THR cc_start: -0.0817 (OUTLIER) cc_final: -0.1588 (p) REVERT: A 929 ILE cc_start: 0.0044 (OUTLIER) cc_final: -0.0380 (tp) REVERT: A 1070 GLU cc_start: 0.1790 (OUTLIER) cc_final: -0.0822 (pm20) REVERT: B 175 MET cc_start: 0.2776 (tpp) cc_final: 0.1270 (ptt) REVERT: B 189 GLU cc_start: 0.0432 (OUTLIER) cc_final: 0.0089 (pm20) REVERT: C 64 TRP cc_start: -0.0089 (p90) cc_final: -0.2580 (p-90) REVERT: C 672 TYR cc_start: 0.3494 (t80) cc_final: 0.2617 (t80) REVERT: C 707 ASN cc_start: 0.0432 (OUTLIER) cc_final: -0.0358 (m-40) REVERT: C 898 MET cc_start: 0.1144 (mmt) cc_final: -0.1349 (mtp) REVERT: C 1087 PHE cc_start: 0.2642 (OUTLIER) cc_final: -0.0988 (m-10) REVERT: C 1090 GLU cc_start: 0.5566 (tp30) cc_final: 0.5154 (pp20) REVERT: H 82 MET cc_start: 0.3807 (mmp) cc_final: 0.0596 (pmm) REVERT: G 82 MET cc_start: 0.4414 (mpp) cc_final: 0.3629 (mtm) REVERT: I 82 MET cc_start: 0.2992 (mmt) cc_final: 0.2304 (ppp) REVERT: I 105 MET cc_start: 0.1176 (OUTLIER) cc_final: 0.0107 (ttp) REVERT: K 96 SER cc_start: 0.2758 (m) cc_final: 0.2503 (t) outliers start: 93 outliers final: 57 residues processed: 213 average time/residue: 0.4716 time to fit residues: 175.2488 Evaluate side-chains 189 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 5.087 ------------------------------------------------------------------------------- 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 338 GLU 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 582 ILE 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 789 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 820 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 875 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 946 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 189 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 428 THR Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 59 PHE 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 729 MET Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 852 LYS Chi-restraints excluded: chain C residue 857 THR 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 1037 ARG Chi-restraints excluded: chain C residue 1065 TYR 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 1100 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 64 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 105 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 357 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1009 GLN A1046 HIS ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5630 r_free = 0.5630 target = 0.378026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5653 r_free = 0.5653 target = 0.369815 restraints weight = 95535.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5656 r_free = 0.5656 target = 0.370631 restraints weight = 57199.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5660 r_free = 0.5660 target = 0.371076 restraints weight = 37505.385| |-----------------------------------------------------------------------------| r_work (final): 0.5512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0978 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30447 Z= 0.116 Angle : 0.567 12.044 41450 Z= 0.296 Chirality : 0.043 0.202 4645 Planarity : 0.005 0.072 5373 Dihedral : 4.666 55.175 4114 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.91 % Allowed : 15.24 % Favored : 82.85 % 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: -1.63 (0.13), residues: 3775 helix: 0.43 (0.20), residues: 618 sheet: -0.18 (0.18), residues: 810 loop : -1.95 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 434 HIS 0.007 0.001 HIS A1056 PHE 0.018 0.001 PHE A 327 TYR 0.024 0.001 TYR C1065 ARG 0.006 0.000 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 932) hydrogen bonds : angle 5.69853 ( 2493) SS BOND : bond 0.00628 ( 44) SS BOND : angle 1.48485 ( 88) covalent geometry : bond 0.00247 (30403) covalent geometry : angle 0.56383 (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 192 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 129 time to evaluate : 3.030 Fit side-chains REVERT: A 49 HIS cc_start: -0.0274 (t-90) cc_final: -0.1493 (t-90) REVERT: A 151 MET cc_start: -0.0477 (mpp) cc_final: -0.0791 (mpp) REVERT: A 338 GLU cc_start: -0.0404 (OUTLIER) cc_final: -0.1340 (mm-30) REVERT: A 582 ILE cc_start: 0.1409 (OUTLIER) cc_final: 0.1048 (mt) REVERT: A 771 GLU cc_start: 0.1380 (OUTLIER) cc_final: -0.2781 (mm-30) REVERT: A 793 LYS cc_start: 0.4250 (mttp) cc_final: 0.1959 (pptt) REVERT: A 872 THR cc_start: -0.1014 (OUTLIER) cc_final: -0.1701 (p) REVERT: A 929 ILE cc_start: 0.0391 (OUTLIER) cc_final: -0.0031 (mm) REVERT: A 982 LEU cc_start: 0.2068 (OUTLIER) cc_final: 0.1794 (tt) REVERT: B 175 MET cc_start: 0.2962 (tpp) cc_final: 0.1445 (ptt) REVERT: B 189 GLU cc_start: 0.0489 (OUTLIER) cc_final: 0.0150 (pm20) REVERT: B 867 MET cc_start: -0.1040 (ptp) cc_final: -0.1396 (ptt) REVERT: C 32 PHE cc_start: -0.0166 (m-80) cc_final: -0.0581 (t80) REVERT: C 506 TYR cc_start: 0.2072 (m-80) cc_final: 0.1040 (m-10) REVERT: C 661 ASP cc_start: -0.0821 (OUTLIER) cc_final: -0.1410 (t0) REVERT: C 672 TYR cc_start: 0.3501 (t80) cc_final: 0.2833 (t80) REVERT: C 898 MET cc_start: 0.1217 (mmt) cc_final: -0.1190 (mtp) REVERT: C 1027 MET cc_start: 0.4932 (ttm) cc_final: 0.4380 (ttt) REVERT: G 82 MET cc_start: 0.4569 (mpp) cc_final: 0.3349 (mtm) REVERT: G 92 MET cc_start: -0.0651 (tmm) cc_final: -0.0882 (tmm) REVERT: I 82 MET cc_start: 0.3110 (mmt) cc_final: 0.2455 (ppp) REVERT: I 105 MET cc_start: 0.1197 (OUTLIER) cc_final: 0.0035 (ttp) outliers start: 63 outliers final: 40 residues processed: 185 average time/residue: 0.3856 time to fit residues: 122.7671 Evaluate side-chains 170 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 356 ILE 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 593 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 789 THR 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 929 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 189 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 428 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 VAL 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 C residue 59 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 147 ASN 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 661 ASP 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 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 1094 VAL 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 G residue 80 LEU 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: 10.0000 chunk 29 optimal weight: 50.0000 chunk 344 optimal weight: 20.0000 chunk 132 optimal weight: 0.0370 chunk 33 optimal weight: 40.0000 chunk 316 optimal weight: 30.0000 chunk 44 optimal weight: 50.0000 chunk 254 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN A 688 GLN A 802 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS B 530 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 605 GLN C 642 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** H 6 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 = 0.5603 r_free = 0.5603 target = 0.373863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5617 r_free = 0.5617 target = 0.365232 restraints weight = 95210.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5622 r_free = 0.5622 target = 0.366297 restraints weight = 66294.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.366616 restraints weight = 40863.962| |-----------------------------------------------------------------------------| r_work (final): 0.5479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1421 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 30447 Z= 0.267 Angle : 0.884 22.450 41450 Z= 0.463 Chirality : 0.053 0.590 4645 Planarity : 0.007 0.122 5373 Dihedral : 6.074 51.057 4114 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.79 % Favored : 90.94 % Rotamer: Outliers : 2.82 % Allowed : 15.00 % Favored : 82.18 % 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: -2.20 (0.13), residues: 3775 helix: -0.81 (0.19), residues: 630 sheet: -0.24 (0.19), residues: 739 loop : -2.17 (0.11), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1100 HIS 0.012 0.002 HIS C1046 PHE 0.051 0.003 PHE C1119 TYR 0.041 0.002 TYR B 739 ARG 0.017 0.001 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.05961 ( 932) hydrogen bonds : angle 7.00604 ( 2493) SS BOND : bond 0.00879 ( 44) SS BOND : angle 1.77175 ( 88) covalent geometry : bond 0.00587 (30403) covalent geometry : angle 0.88109 (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 235 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 3.147 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0160 (t-170) cc_final: -0.1348 (t-170) REVERT: A 151 MET cc_start: -0.0550 (mpp) cc_final: -0.0794 (mpp) REVERT: A 338 GLU cc_start: -0.0046 (OUTLIER) cc_final: -0.0606 (mm-30) REVERT: A 582 ILE cc_start: 0.2199 (OUTLIER) cc_final: 0.1773 (mt) REVERT: A 725 LEU cc_start: 0.2113 (OUTLIER) cc_final: 0.1761 (tp) REVERT: A 771 GLU cc_start: 0.1671 (OUTLIER) cc_final: -0.2467 (mm-30) REVERT: A 929 ILE cc_start: 0.1137 (OUTLIER) cc_final: 0.0409 (tp) REVERT: A 982 LEU cc_start: 0.2327 (OUTLIER) cc_final: 0.2051 (tt) REVERT: A 1070 GLU cc_start: 0.2874 (OUTLIER) cc_final: 0.2512 (pm20) REVERT: B 175 MET cc_start: 0.3587 (tpp) cc_final: 0.1487 (ptt) REVERT: B 937 SER cc_start: 0.4124 (p) cc_final: 0.3795 (t) REVERT: C 59 PHE cc_start: 0.1623 (OUTLIER) cc_final: 0.0336 (t80) REVERT: C 506 TYR cc_start: 0.2477 (m-80) cc_final: 0.1192 (m-10) REVERT: C 661 ASP cc_start: -0.0760 (OUTLIER) cc_final: -0.1995 (t0) REVERT: C 672 TYR cc_start: 0.3692 (t80) cc_final: 0.3148 (t80) REVERT: C 732 THR cc_start: 0.3014 (OUTLIER) cc_final: 0.1625 (m) REVERT: C 898 MET cc_start: 0.1967 (mmt) cc_final: -0.0283 (mtp) REVERT: H 82 MET cc_start: 0.3552 (OUTLIER) cc_final: 0.2903 (mmp) REVERT: G 82 MET cc_start: 0.4576 (mpp) cc_final: 0.3444 (mtm) REVERT: I 82 MET cc_start: 0.3559 (mmt) cc_final: 0.2304 (ppp) REVERT: I 105 MET cc_start: 0.1275 (OUTLIER) cc_final: 0.0129 (ttp) outliers start: 93 outliers final: 63 residues processed: 223 average time/residue: 0.3740 time to fit residues: 142.1892 Evaluate side-chains 195 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 120 time to evaluate : 2.936 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 322 GLU 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 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 608 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 771 GLU 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 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 1030 CYS Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 510 VAL 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 1039 ASP Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 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 567 ILE Chi-restraints excluded: chain C residue 605 GLN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 852 LYS Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE 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 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL 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 82 MET Chi-restraints excluded: chain L residue 59 ILE 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: 0.9980 chunk 51 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 374 optimal weight: 30.0000 chunk 334 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN B 947 GLN B1086 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** C1034 GLN ** 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 = 0.5613 r_free = 0.5613 target = 0.375907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5641 r_free = 0.5641 target = 0.367259 restraints weight = 95249.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5644 r_free = 0.5644 target = 0.368122 restraints weight = 60676.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5645 r_free = 0.5645 target = 0.368757 restraints weight = 35605.145| |-----------------------------------------------------------------------------| r_work (final): 0.5495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1236 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30447 Z= 0.136 Angle : 0.638 14.977 41450 Z= 0.332 Chirality : 0.045 0.254 4645 Planarity : 0.005 0.071 5373 Dihedral : 5.274 52.153 4114 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.70 % Favored : 93.19 % Rotamer: Outliers : 1.91 % Allowed : 16.24 % Favored : 81.85 % 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: -2.01 (0.13), residues: 3775 helix: -0.18 (0.20), residues: 624 sheet: -0.38 (0.18), residues: 794 loop : -2.12 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.013 0.001 HIS B1046 PHE 0.035 0.002 PHE A 590 TYR 0.035 0.001 TYR C1065 ARG 0.012 0.001 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 932) hydrogen bonds : angle 6.28869 ( 2493) SS BOND : bond 0.00464 ( 44) SS BOND : angle 1.49166 ( 88) covalent geometry : bond 0.00292 (30403) covalent geometry : angle 0.63487 (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 188 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 3.277 Fit side-chains REVERT: A 49 HIS cc_start: 0.0184 (t-170) cc_final: -0.1135 (t-90) REVERT: A 322 GLU cc_start: -0.1130 (OUTLIER) cc_final: -0.1719 (mp0) REVERT: A 338 GLU cc_start: -0.0026 (OUTLIER) cc_final: -0.0654 (mm-30) REVERT: A 541 PHE cc_start: 0.2651 (OUTLIER) cc_final: 0.0573 (m-80) REVERT: A 582 ILE cc_start: 0.1894 (OUTLIER) cc_final: 0.1453 (mt) REVERT: A 771 GLU cc_start: 0.2171 (OUTLIER) cc_final: -0.1550 (mm-30) REVERT: A 793 LYS cc_start: 0.3897 (mttp) cc_final: 0.1582 (pptt) REVERT: A 929 ILE cc_start: 0.0276 (OUTLIER) cc_final: -0.0195 (tp) REVERT: A 982 LEU cc_start: 0.2285 (OUTLIER) cc_final: 0.2052 (tt) REVERT: B 175 MET cc_start: 0.3715 (tpp) cc_final: 0.1539 (ptt) REVERT: C 59 PHE cc_start: 0.1629 (OUTLIER) cc_final: 0.0500 (t80) REVERT: C 506 TYR cc_start: 0.2162 (m-80) cc_final: 0.1102 (m-10) REVERT: C 661 ASP cc_start: -0.1131 (OUTLIER) cc_final: -0.1600 (t0) REVERT: C 672 TYR cc_start: 0.3568 (t80) cc_final: 0.3075 (t80) REVERT: C 738 MET cc_start: 0.2051 (tpp) cc_final: -0.0293 (ttt) REVERT: C 898 MET cc_start: 0.1599 (mmt) cc_final: -0.0583 (mtp) REVERT: C 1047 LEU cc_start: -0.2072 (OUTLIER) cc_final: -0.2462 (tp) REVERT: C 1087 PHE cc_start: 0.2342 (OUTLIER) cc_final: -0.0983 (m-10) REVERT: G 82 MET cc_start: 0.4761 (mpp) cc_final: 0.3447 (mtm) REVERT: I 82 MET cc_start: 0.3487 (mmt) cc_final: 0.2263 (ppp) REVERT: I 105 MET cc_start: 0.1201 (OUTLIER) cc_final: 0.0008 (ttp) outliers start: 63 outliers final: 45 residues processed: 182 average time/residue: 0.4202 time to fit residues: 131.8702 Evaluate side-chains 175 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 3.256 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 322 GLU 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 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 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 387 ASP 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 510 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain C residue 59 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 661 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 852 LYS Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1034 GLN 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 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL 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 82 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 256 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 772 GLN A 802 GLN A 899 GLN A1034 GLN C 407 GLN C 605 GLN C 673 GLN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN C1034 GLN C1046 HIS ** H 6 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 = 0.5620 r_free = 0.5620 target = 0.376701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5646 r_free = 0.5646 target = 0.368192 restraints weight = 96129.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5650 r_free = 0.5650 target = 0.369119 restraints weight = 59373.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5651 r_free = 0.5651 target = 0.369654 restraints weight = 34122.254| |-----------------------------------------------------------------------------| r_work (final): 0.5502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1146 moved from start: 0.6611 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= 0.111 Angle : 0.567 13.489 41450 Z= 0.295 Chirality : 0.043 0.199 4645 Planarity : 0.005 0.119 5373 Dihedral : 4.757 52.421 4114 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 1.67 % Allowed : 16.48 % Favored : 81.85 % 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: -1.74 (0.13), residues: 3775 helix: 0.34 (0.20), residues: 628 sheet: -0.19 (0.19), residues: 764 loop : -2.03 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 36 HIS 0.018 0.001 HIS C1046 PHE 0.025 0.001 PHE B 454 TYR 0.028 0.001 TYR C1065 ARG 0.009 0.000 ARG C 496 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 932) hydrogen bonds : angle 5.83203 ( 2493) SS BOND : bond 0.00337 ( 44) SS BOND : angle 1.34191 ( 88) covalent geometry : bond 0.00238 (30403) covalent geometry : angle 0.56457 (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 173 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 5.028 Fit side-chains REVERT: A 49 HIS cc_start: 0.0077 (t-170) cc_final: -0.1328 (t-90) REVERT: A 338 GLU cc_start: -0.0044 (OUTLIER) cc_final: -0.0722 (mm-30) REVERT: A 541 PHE cc_start: 0.2548 (OUTLIER) cc_final: 0.0619 (m-80) REVERT: A 582 ILE cc_start: 0.1776 (OUTLIER) cc_final: 0.1359 (mt) REVERT: A 793 LYS cc_start: 0.3926 (mttp) cc_final: 0.1628 (pptt) REVERT: A 866 GLU cc_start: 0.1913 (OUTLIER) cc_final: -0.1812 (tt0) REVERT: A 982 LEU cc_start: 0.2270 (OUTLIER) cc_final: 0.2029 (tt) REVERT: B 175 MET cc_start: 0.3796 (tpp) cc_final: 0.1628 (ptt) REVERT: B 738 MET cc_start: -0.1720 (mtp) cc_final: -0.3396 (mmt) REVERT: B 867 MET cc_start: -0.1090 (ptp) cc_final: -0.1331 (ptt) REVERT: C 59 PHE cc_start: 0.1767 (OUTLIER) cc_final: 0.0566 (t80) REVERT: C 506 TYR cc_start: 0.2475 (m-80) cc_final: 0.1488 (m-10) REVERT: C 672 TYR cc_start: 0.3586 (t80) cc_final: 0.2941 (t80) REVERT: C 738 MET cc_start: 0.1705 (tpp) cc_final: -0.0558 (ttt) REVERT: C 898 MET cc_start: 0.1315 (mmt) cc_final: -0.0900 (mtp) REVERT: C 904 PHE cc_start: -0.0694 (OUTLIER) cc_final: -0.1369 (m-80) REVERT: H 82 MET cc_start: 0.3430 (OUTLIER) cc_final: 0.2861 (mmp) REVERT: G 82 MET cc_start: 0.4722 (mpp) cc_final: 0.3404 (mtm) REVERT: I 82 MET cc_start: 0.3472 (mmt) cc_final: 0.2378 (ppp) REVERT: I 105 MET cc_start: 0.1059 (OUTLIER) cc_final: -0.0105 (ttp) outliers start: 55 outliers final: 38 residues processed: 169 average time/residue: 0.4732 time to fit residues: 139.1472 Evaluate side-chains 158 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 4.721 ------------------------------------------------------------------------------- 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 206 THR 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 541 PHE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 982 LEU 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 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 510 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain C residue 59 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 729 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 852 LYS 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 950 VAL 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 1100 TRP Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 6 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 chunk 137 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 245 optimal weight: 0.4980 chunk 226 optimal weight: 6.9990 chunk 162 optimal weight: 0.0270 chunk 227 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 GLN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5620 r_free = 0.5620 target = 0.376645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5648 r_free = 0.5648 target = 0.368125 restraints weight = 95735.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5650 r_free = 0.5650 target = 0.369031 restraints weight = 58390.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5650 r_free = 0.5650 target = 0.369223 restraints weight = 36922.334| |-----------------------------------------------------------------------------| r_work (final): 0.5500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1163 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 30447 Z= 0.155 Angle : 0.706 59.200 41450 Z= 0.390 Chirality : 0.044 0.259 4645 Planarity : 0.005 0.104 5373 Dihedral : 4.746 52.347 4114 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 1.76 % Allowed : 16.36 % Favored : 81.88 % Cbeta Deviations : 0.03 % 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: -1.73 (0.13), residues: 3775 helix: 0.36 (0.20), residues: 628 sheet: -0.19 (0.19), residues: 764 loop : -2.02 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 36 HIS 0.013 0.001 HIS B 49 PHE 0.028 0.001 PHE C1060 TYR 0.028 0.001 TYR C1065 ARG 0.010 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 932) hydrogen bonds : angle 5.83333 ( 2493) SS BOND : bond 0.02637 ( 44) SS BOND : angle 3.13118 ( 88) covalent geometry : bond 0.00317 (30403) covalent geometry : angle 0.69167 (41362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9479.14 seconds wall clock time: 170 minutes 33.89 seconds (10233.89 seconds total)