Starting phenix.real_space_refine on Tue Aug 26 00:02:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsd_38616/08_2025/8xsd_38616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsd_38616/08_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_38616/08_2025/8xsd_38616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsd_38616/08_2025/8xsd_38616.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsd_38616/08_2025/8xsd_38616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsd_38616/08_2025/8xsd_38616.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.83, per 1000 atoms: 0.23 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.50 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: 7.66 Time building geometry restraints manager: 3.37 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.250 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- 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 : 7.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 344 TYR 0.025 0.001 TYR J 37 PHE 0.038 0.002 PHE C 369 TRP 0.019 0.002 TRP A 351 HIS 0.013 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00374 (30403) covalent geometry : angle 0.80657 (41362) SS BOND : bond 0.00405 ( 44) SS BOND : angle 1.34292 ( 88) hydrogen bonds : bond 0.26267 ( 932) hydrogen bonds : angle 9.18976 ( 2493) *********************** 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 : 1.132 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: -0.1034 (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: 0.2147 (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: 0.1553 (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: 0.2310 (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: -0.1233 (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: 0.2521 (mpp) REVERT: I 82 MET cc_start: 0.2539 (mmt) cc_final: 0.1671 (ppp) outliers start: 9 outliers final: 4 residues processed: 232 average time/residue: 0.2049 time to fit residues: 76.2600 Evaluate side-chains 138 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 20.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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 412 GLN B 688 GLN B 947 GLN B 953 ASN ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 407 GLN C1099 HIS C1117 ASN G 83 ASN K 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5646 r_free = 0.5646 target = 0.382051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5669 r_free = 0.5669 target = 0.374124 restraints weight = 96511.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5674 r_free = 0.5674 target = 0.374880 restraints weight = 57411.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5683 r_free = 0.5683 target = 0.375455 restraints weight = 36941.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.375839 restraints weight = 23634.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.376020 restraints weight = 15511.906| |-----------------------------------------------------------------------------| r_work (final): 0.5583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0431 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30447 Z= 0.173 Angle : 0.665 8.845 41450 Z= 0.352 Chirality : 0.047 0.418 4645 Planarity : 0.006 0.078 5373 Dihedral : 5.060 58.767 4122 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 0.76 % Allowed : 7.01 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.13), residues: 3775 helix: -0.14 (0.19), residues: 615 sheet: -0.66 (0.17), residues: 825 loop : -2.05 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 455 TYR 0.020 0.002 TYR A 902 PHE 0.031 0.002 PHE C1101 TRP 0.026 0.002 TRP A 884 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00365 (30403) covalent geometry : angle 0.66244 (41362) SS BOND : bond 0.00552 ( 44) SS BOND : angle 1.36029 ( 88) hydrogen bonds : bond 0.05265 ( 932) hydrogen bonds : angle 6.38484 ( 2493) *********************** 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 166 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0351 (t-90) cc_final: -0.1501 (t-90) REVERT: A 533 LYS cc_start: 0.1201 (mmmm) cc_final: 0.0908 (pttt) REVERT: A 649 ILE cc_start: -0.0612 (pt) cc_final: -0.1130 (tt) REVERT: A 799 ASN cc_start: 0.4130 (t0) cc_final: 0.3664 (t0) REVERT: B 175 MET cc_start: 0.2125 (tpp) cc_final: 0.1090 (ptt) REVERT: B 695 MET cc_start: 0.1773 (ptm) cc_final: 0.1404 (ppp) REVERT: B 738 MET cc_start: -0.2956 (ttm) cc_final: -0.4952 (mmm) REVERT: C 672 TYR cc_start: 0.3172 (t80) cc_final: 0.1576 (t80) REVERT: C 1027 MET cc_start: 0.4370 (ttm) cc_final: 0.3905 (ttm) REVERT: C 1084 LYS cc_start: 0.4990 (tppt) cc_final: 0.4335 (tppt) REVERT: H 82 MET cc_start: 0.2205 (mmp) cc_final: 0.0178 (pmm) REVERT: G 82 MET cc_start: 0.5239 (mpp) cc_final: 0.4789 (mpp) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.1631 time to fit residues: 44.2987 Evaluate side-chains 141 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 946 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL 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 717 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 258 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 311 optimal weight: 0.0870 chunk 122 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 335 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 854 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN A 924 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 GLN B1034 GLN B1046 HIS C 205 HIS C 237 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN C 953 ASN ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5628 r_free = 0.5628 target = 0.378560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5650 r_free = 0.5650 target = 0.369929 restraints weight = 96348.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5655 r_free = 0.5655 target = 0.370776 restraints weight = 55906.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5662 r_free = 0.5662 target = 0.371303 restraints weight = 34886.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5665 r_free = 0.5665 target = 0.371630 restraints weight = 23451.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5668 r_free = 0.5668 target = 0.371888 restraints weight = 16630.839| |-----------------------------------------------------------------------------| r_work (final): 0.5554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0952 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30447 Z= 0.220 Angle : 0.762 15.322 41450 Z= 0.407 Chirality : 0.050 0.357 4645 Planarity : 0.006 0.090 5373 Dihedral : 5.545 57.094 4114 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.77 % Rotamer: Outliers : 1.94 % Allowed : 11.54 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.13), residues: 3775 helix: -0.41 (0.19), residues: 616 sheet: -0.61 (0.18), residues: 790 loop : -2.05 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1017 TYR 0.025 0.002 TYR C1136 PHE 0.068 0.002 PHE C1101 TRP 0.024 0.002 TRP A 884 HIS 0.009 0.002 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00459 (30403) covalent geometry : angle 0.75968 (41362) SS BOND : bond 0.00992 ( 44) SS BOND : angle 1.46718 ( 88) hydrogen bonds : bond 0.05923 ( 932) hydrogen bonds : angle 6.59102 ( 2493) *********************** 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 221 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 157 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.1011 (t-170) cc_final: -0.1781 (t-90) REVERT: A 58 PHE cc_start: 0.3299 (m-10) cc_final: 0.2647 (m-80) REVERT: A 194 ASN cc_start: 0.2404 (OUTLIER) cc_final: -0.0179 (t0) REVERT: A 318 VAL cc_start: -0.1504 (OUTLIER) cc_final: -0.3125 (p) REVERT: A 582 ILE cc_start: 0.1701 (OUTLIER) cc_final: 0.1360 (mt) REVERT: A 793 LYS cc_start: 0.3863 (mttp) cc_final: 0.1482 (pptt) REVERT: A 866 GLU cc_start: 0.1784 (OUTLIER) cc_final: -0.0540 (pt0) REVERT: A 924 GLN cc_start: 0.1236 (OUTLIER) cc_final: -0.1054 (mm-40) REVERT: A 1009 GLN cc_start: 0.0204 (OUTLIER) cc_final: -0.0011 (tm-30) REVERT: A 1027 MET cc_start: 0.6029 (tpp) cc_final: 0.5798 (tpp) REVERT: A 1070 GLU cc_start: 0.1527 (OUTLIER) cc_final: 0.1156 (mp0) REVERT: B 175 MET cc_start: 0.2382 (tpp) cc_final: 0.1118 (ptt) REVERT: B 367 TYR cc_start: -0.1184 (m-80) cc_final: -0.2693 (m-80) REVERT: B 1140 GLN cc_start: 0.2214 (mm-40) cc_final: 0.1240 (mm-40) REVERT: C 64 TRP cc_start: -0.0713 (p90) cc_final: -0.3840 (p-90) REVERT: C 506 TYR cc_start: 0.2150 (m-80) cc_final: 0.1290 (m-10) REVERT: C 672 TYR cc_start: 0.3734 (t80) cc_final: 0.2688 (t80) REVERT: C 898 MET cc_start: 0.1430 (mmt) cc_final: 0.1008 (mpp) REVERT: C 1027 MET cc_start: 0.5007 (ttm) cc_final: 0.4388 (ttm) REVERT: H 82 MET cc_start: 0.3473 (mmp) cc_final: 0.0445 (pmm) REVERT: G 82 MET cc_start: 0.5187 (mpp) cc_final: 0.4901 (mpp) REVERT: I 82 MET cc_start: 0.3311 (mmt) cc_final: 0.2524 (ppp) REVERT: I 105 MET cc_start: 0.1224 (OUTLIER) cc_final: 0.0200 (ttp) outliers start: 64 outliers final: 34 residues processed: 213 average time/residue: 0.1736 time to fit residues: 61.5360 Evaluate side-chains 175 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN 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 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 866 GLU 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 924 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1070 GLU 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 452 ARG Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain C residue 94 GLU 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 733 SER Chi-restraints excluded: chain C residue 852 LYS Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1099 HIS 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 I residue 105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 248 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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 799 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN B 947 GLN ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 GLN C1133 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5567 r_free = 0.5567 target = 0.361075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.352770 restraints weight = 91848.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5522 r_free = 0.5522 target = 0.354942 restraints weight = 53345.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.5535 r_free = 0.5535 target = 0.356376 restraints weight = 33101.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.5543 r_free = 0.5543 target = 0.357258 restraints weight = 21641.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.357805 restraints weight = 14974.723| |-----------------------------------------------------------------------------| r_work (final): 0.5546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0948 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30447 Z= 0.113 Angle : 0.563 15.349 41450 Z= 0.295 Chirality : 0.043 0.257 4645 Planarity : 0.005 0.074 5373 Dihedral : 4.750 57.126 4114 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 1.58 % Allowed : 13.36 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.13), residues: 3775 helix: 0.17 (0.20), residues: 627 sheet: -0.40 (0.18), residues: 804 loop : -1.96 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1105 TYR 0.021 0.001 TYR C1065 PHE 0.017 0.001 PHE B 541 TRP 0.019 0.001 TRP C1100 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00236 (30403) covalent geometry : angle 0.56002 (41362) SS BOND : bond 0.00330 ( 44) SS BOND : angle 1.29111 ( 88) hydrogen bonds : bond 0.03966 ( 932) hydrogen bonds : angle 5.88094 ( 2493) *********************** 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 184 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.934 Fit side-chains REVERT: A 49 HIS cc_start: -0.0873 (t-170) cc_final: -0.1735 (t-90) REVERT: A 793 LYS cc_start: 0.3665 (mttp) cc_final: 0.1605 (pptt) REVERT: A 900 MET cc_start: -0.4052 (ptt) cc_final: -0.4281 (ttp) REVERT: B 175 MET cc_start: 0.1482 (tpp) cc_final: 0.0377 (ptt) REVERT: B 367 TYR cc_start: -0.0777 (m-80) cc_final: -0.2376 (m-80) REVERT: B 852 LYS cc_start: 0.0029 (mmtm) cc_final: -0.0643 (pttp) REVERT: B 1140 GLN cc_start: 0.2249 (mm-40) cc_final: 0.1296 (mm-40) REVERT: C 506 TYR cc_start: 0.2263 (m-80) cc_final: 0.1388 (m-10) REVERT: C 672 TYR cc_start: 0.3491 (t80) cc_final: 0.2577 (t80) REVERT: C 898 MET cc_start: 0.2097 (mmt) cc_final: -0.1108 (mtp) REVERT: C 1027 MET cc_start: 0.4638 (ttm) cc_final: 0.4117 (ttm) REVERT: H 82 MET cc_start: 0.3581 (mmp) cc_final: 0.0478 (pmm) REVERT: G 82 MET cc_start: 0.3042 (mpp) cc_final: 0.2598 (mpp) REVERT: I 82 MET cc_start: 0.3078 (mmt) cc_final: 0.2177 (ppp) REVERT: I 105 MET cc_start: 0.0970 (OUTLIER) cc_final: -0.0109 (ttp) outliers start: 52 outliers final: 29 residues processed: 177 average time/residue: 0.1670 time to fit residues: 49.7374 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 : 0.979 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 1039 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 1037 ARG Chi-restraints excluded: chain C residue 1096 ASN Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain H residue 51 ILE 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 104 optimal weight: 40.0000 chunk 262 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 chunk 341 optimal weight: 30.0000 chunk 290 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 216 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 HIS A1009 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN B 530 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN ** B1086 HIS ** 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 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN C 923 ASN C1096 ASN ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.372865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5607 r_free = 0.5607 target = 0.364069 restraints weight = 95029.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.365008 restraints weight = 70113.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.365398 restraints weight = 45839.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.365482 restraints weight = 32934.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5618 r_free = 0.5618 target = 0.365638 restraints weight = 29896.556| |-----------------------------------------------------------------------------| r_work (final): 0.5519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1502 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 30447 Z= 0.356 Angle : 1.033 25.327 41450 Z= 0.544 Chirality : 0.057 0.648 4645 Planarity : 0.008 0.112 5373 Dihedral : 6.750 51.744 4114 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.51 % Favored : 90.23 % Rotamer: Outliers : 4.22 % Allowed : 14.78 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.12), residues: 3775 helix: -1.28 (0.18), residues: 632 sheet: -0.49 (0.18), residues: 752 loop : -2.36 (0.11), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1017 TYR 0.039 0.003 TYR C 264 PHE 0.064 0.003 PHE C1119 TRP 0.026 0.003 TRP A 884 HIS 0.012 0.002 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00780 (30403) covalent geometry : angle 1.02928 (41362) SS BOND : bond 0.02570 ( 44) SS BOND : angle 2.11208 ( 88) hydrogen bonds : bond 0.07042 ( 932) hydrogen bonds : angle 7.61931 ( 2493) *********************** 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 269 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 130 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0038 (t-170) cc_final: -0.1019 (t-170) REVERT: A 322 GLU cc_start: 0.0924 (OUTLIER) cc_final: -0.0728 (mm-30) REVERT: A 341 ASN cc_start: 0.0733 (OUTLIER) cc_final: -0.0721 (p0) REVERT: A 541 PHE cc_start: 0.2612 (OUTLIER) cc_final: 0.0707 (m-80) REVERT: A 582 ILE cc_start: 0.2356 (OUTLIER) cc_final: 0.1881 (mt) REVERT: A 725 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.1364 (tp) REVERT: A 793 LYS cc_start: 0.3962 (mttp) cc_final: 0.1593 (pptt) REVERT: A 866 GLU cc_start: 0.2091 (OUTLIER) cc_final: -0.2591 (tt0) REVERT: A 900 MET cc_start: -0.3452 (ptt) cc_final: -0.3938 (ttp) REVERT: A 929 ILE cc_start: 0.1752 (OUTLIER) cc_final: 0.1105 (mm) REVERT: A 982 LEU cc_start: 0.2470 (OUTLIER) cc_final: 0.2187 (tt) REVERT: A 1070 GLU cc_start: 0.2897 (OUTLIER) cc_final: 0.1803 (pm20) REVERT: B 138 PHE cc_start: -0.2872 (OUTLIER) cc_final: -0.3410 (m-80) REVERT: B 175 MET cc_start: 0.3343 (tpp) cc_final: 0.1336 (ptt) REVERT: B 778 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.0128 (tt0) REVERT: B 925 PHE cc_start: 0.3770 (OUTLIER) cc_final: 0.0207 (t80) REVERT: C 175 MET cc_start: 0.1436 (ptm) cc_final: 0.0909 (ptt) REVERT: C 442 LYS cc_start: 0.6445 (mtpt) cc_final: 0.6195 (ttpt) REVERT: C 661 ASP cc_start: -0.0226 (OUTLIER) cc_final: -0.1736 (t0) REVERT: C 672 TYR cc_start: 0.3731 (t80) cc_final: 0.3058 (t80) REVERT: C 693 TYR cc_start: -0.1105 (OUTLIER) cc_final: -0.3347 (p90) REVERT: C 707 ASN cc_start: 0.0454 (OUTLIER) cc_final: -0.0912 (m-40) REVERT: C 732 THR cc_start: 0.2914 (OUTLIER) cc_final: 0.1786 (m) REVERT: C 898 MET cc_start: 0.2177 (mmt) cc_final: -0.0315 (mtp) REVERT: C 1047 LEU cc_start: -0.2588 (OUTLIER) cc_final: -0.3056 (tp) REVERT: G 82 MET cc_start: 0.5116 (mpp) cc_final: 0.3738 (mtt) REVERT: I 105 MET cc_start: 0.1599 (OUTLIER) cc_final: 0.0522 (ttp) outliers start: 139 outliers final: 78 residues processed: 249 average time/residue: 0.1704 time to fit residues: 71.6022 Evaluate side-chains 210 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 114 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU 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 341 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1031 VAL 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 138 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 605 GLN Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 693 TYR Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 716 PHE Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 977 ASP Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 34 MET 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 133 optimal weight: 0.1980 chunk 249 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 194 ASN A 673 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 ASN B 785 GLN B 893 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 HIS B1086 HIS C 407 GLN C 604 ASN C 605 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1056 HIS ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5607 r_free = 0.5607 target = 0.374355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.365900 restraints weight = 94825.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5630 r_free = 0.5630 target = 0.366956 restraints weight = 64468.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5635 r_free = 0.5635 target = 0.367442 restraints weight = 37736.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5635 r_free = 0.5635 target = 0.367446 restraints weight = 25426.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.367631 restraints weight = 24863.265| |-----------------------------------------------------------------------------| r_work (final): 0.5484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1321 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30447 Z= 0.158 Angle : 0.677 15.398 41450 Z= 0.354 Chirality : 0.046 0.274 4645 Planarity : 0.005 0.085 5373 Dihedral : 5.624 53.065 4114 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.03 % Rotamer: Outliers : 3.25 % Allowed : 16.33 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.13), residues: 3775 helix: -0.48 (0.19), residues: 619 sheet: -0.42 (0.19), residues: 771 loop : -2.23 (0.11), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1105 TYR 0.029 0.001 TYR C1065 PHE 0.032 0.002 PHE A1146 TRP 0.011 0.001 TRP C1100 HIS 0.006 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00339 (30403) covalent geometry : angle 0.67386 (41362) SS BOND : bond 0.00481 ( 44) SS BOND : angle 1.51470 ( 88) hydrogen bonds : bond 0.04651 ( 932) hydrogen bonds : angle 6.61629 ( 2493) *********************** 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 233 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 126 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: -0.0446 (t70) cc_final: -0.1081 (t70) REVERT: A 322 GLU cc_start: -0.0788 (OUTLIER) cc_final: -0.1310 (mp0) REVERT: A 541 PHE cc_start: 0.2502 (OUTLIER) cc_final: 0.0139 (m-80) REVERT: A 793 LYS cc_start: 0.3939 (mttp) cc_final: 0.1567 (pptt) REVERT: A 929 ILE cc_start: 0.1318 (OUTLIER) cc_final: 0.0898 (tp) REVERT: A 982 LEU cc_start: 0.2332 (OUTLIER) cc_final: 0.2119 (tt) REVERT: A 1021 ASN cc_start: 0.0704 (OUTLIER) cc_final: -0.0041 (t0) REVERT: B 175 MET cc_start: 0.3426 (tpp) cc_final: 0.1375 (ptt) REVERT: B 893 GLN cc_start: 0.4114 (tm-30) cc_final: 0.0868 (mt0) REVERT: B 1015 GLU cc_start: -0.2010 (OUTLIER) cc_final: -0.2658 (tp30) REVERT: C 212 ARG cc_start: 0.1343 (OUTLIER) cc_final: 0.0597 (mtm180) REVERT: C 506 TYR cc_start: 0.2205 (m-80) cc_final: 0.1182 (m-10) REVERT: C 661 ASP cc_start: -0.1647 (OUTLIER) cc_final: -0.2316 (t0) REVERT: C 672 TYR cc_start: 0.3653 (t80) cc_final: 0.3157 (t80) REVERT: C 732 THR cc_start: 0.3077 (OUTLIER) cc_final: 0.2023 (m) REVERT: C 898 MET cc_start: 0.1583 (mmt) cc_final: -0.0707 (mtp) REVERT: C 1047 LEU cc_start: -0.2155 (OUTLIER) cc_final: -0.2588 (tp) REVERT: G 92 MET cc_start: -0.0486 (tmm) cc_final: -0.0703 (tmm) REVERT: I 82 MET cc_start: 0.3569 (mmt) cc_final: 0.2257 (ppp) REVERT: I 105 MET cc_start: 0.1240 (OUTLIER) cc_final: 0.0162 (ttp) outliers start: 107 outliers final: 75 residues processed: 215 average time/residue: 0.1723 time to fit residues: 62.8283 Evaluate side-chains 203 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 117 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 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 360 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 914 LEU 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 1021 ASN Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain B residue 1025 THR Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 605 GLN Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1022 LEU 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 1073 PHE 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 1096 ASN Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 139 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 136 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.8682 ------------------------------------------------------------------------------- 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 237 GLN A 639 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1046 HIS B 953 ASN B1046 HIS C 605 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.375393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5637 r_free = 0.5637 target = 0.366765 restraints weight = 95051.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5639 r_free = 0.5639 target = 0.367568 restraints weight = 61079.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5639 r_free = 0.5639 target = 0.367975 restraints weight = 37817.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5640 r_free = 0.5640 target = 0.368158 restraints weight = 31337.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5640 r_free = 0.5640 target = 0.368168 restraints weight = 26034.622| |-----------------------------------------------------------------------------| r_work (final): 0.5491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1281 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30447 Z= 0.133 Angle : 0.622 12.424 41450 Z= 0.325 Chirality : 0.045 0.260 4645 Planarity : 0.005 0.076 5373 Dihedral : 5.261 52.451 4114 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.68 % Favored : 92.24 % Rotamer: Outliers : 3.13 % Allowed : 17.03 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.13), residues: 3775 helix: -0.08 (0.20), residues: 618 sheet: -0.33 (0.19), residues: 757 loop : -2.14 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1105 TYR 0.026 0.001 TYR C1065 PHE 0.022 0.001 PHE B 539 TRP 0.012 0.001 TRP L 36 HIS 0.011 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00284 (30403) covalent geometry : angle 0.61971 (41362) SS BOND : bond 0.00557 ( 44) SS BOND : angle 1.32622 ( 88) hydrogen bonds : bond 0.04202 ( 932) hydrogen bonds : angle 6.34856 ( 2493) *********************** 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 219 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 116 time to evaluate : 1.050 Fit side-chains REVERT: A 49 HIS cc_start: -0.0232 (t70) cc_final: -0.0998 (t70) REVERT: A 322 GLU cc_start: -0.0897 (OUTLIER) cc_final: -0.1287 (mp0) REVERT: A 341 ASN cc_start: 0.0849 (OUTLIER) cc_final: -0.0799 (p0) REVERT: A 582 ILE cc_start: 0.1897 (OUTLIER) cc_final: 0.1532 (mt) REVERT: A 793 LYS cc_start: 0.3967 (mttp) cc_final: 0.1588 (pptt) REVERT: A 875 LEU cc_start: 0.7486 (mt) cc_final: 0.7056 (mt) REVERT: A 982 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.2136 (tt) REVERT: A 1021 ASN cc_start: 0.0335 (OUTLIER) cc_final: -0.0696 (t0) REVERT: B 175 MET cc_start: 0.3426 (tpp) cc_final: 0.1351 (ptt) REVERT: B 778 GLU cc_start: 0.2230 (OUTLIER) cc_final: -0.0002 (tt0) REVERT: B 896 PHE cc_start: 0.3264 (OUTLIER) cc_final: 0.3007 (m-80) REVERT: B 1015 GLU cc_start: -0.2284 (OUTLIER) cc_final: -0.2809 (tp30) REVERT: C 108 LEU cc_start: -0.0247 (OUTLIER) cc_final: -0.0567 (pp) REVERT: C 212 ARG cc_start: 0.1442 (OUTLIER) cc_final: 0.0349 (ptp90) REVERT: C 506 TYR cc_start: 0.1999 (m-80) cc_final: 0.1366 (m-10) REVERT: C 661 ASP cc_start: -0.1702 (OUTLIER) cc_final: -0.2370 (t0) REVERT: C 672 TYR cc_start: 0.3865 (t80) cc_final: 0.3113 (t80) REVERT: C 732 THR cc_start: 0.2845 (OUTLIER) cc_final: 0.1716 (m) REVERT: C 898 MET cc_start: 0.1675 (mmt) cc_final: -0.0485 (mtp) REVERT: C 1047 LEU cc_start: -0.2227 (OUTLIER) cc_final: -0.2665 (tp) REVERT: I 82 MET cc_start: 0.3599 (mmt) cc_final: 0.2239 (ppp) REVERT: I 105 MET cc_start: 0.1170 (OUTLIER) cc_final: 0.0119 (ttp) outliers start: 103 outliers final: 74 residues processed: 207 average time/residue: 0.1796 time to fit residues: 63.0157 Evaluate side-chains 202 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 114 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 237 GLN 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 360 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 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 661 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 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 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain B residue 1025 THR Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain B residue 1046 HIS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1027 MET 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 1073 PHE 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 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 184 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 112 optimal weight: 0.0000 chunk 362 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 318 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 311 optimal weight: 0.5980 chunk 203 optimal weight: 0.0670 chunk 376 optimal weight: 5.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN A1021 ASN B 775 ASN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 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 = 0.5619 r_free = 0.5619 target = 0.376536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5646 r_free = 0.5646 target = 0.367963 restraints weight = 95394.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5649 r_free = 0.5649 target = 0.368843 restraints weight = 58551.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5649 r_free = 0.5649 target = 0.369220 restraints weight = 37804.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5651 r_free = 0.5651 target = 0.369440 restraints weight = 28760.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5652 r_free = 0.5652 target = 0.369571 restraints weight = 23790.504| |-----------------------------------------------------------------------------| r_work (final): 0.5502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1163 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30447 Z= 0.103 Angle : 0.559 11.245 41450 Z= 0.291 Chirality : 0.043 0.205 4645 Planarity : 0.005 0.074 5373 Dihedral : 4.792 52.475 4114 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.43 % Allowed : 17.97 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.13), residues: 3775 helix: 0.31 (0.20), residues: 629 sheet: -0.23 (0.19), residues: 770 loop : -2.07 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 496 TYR 0.024 0.001 TYR C 499 PHE 0.028 0.001 PHE A 236 TRP 0.014 0.001 TRP L 36 HIS 0.037 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00220 (30403) covalent geometry : angle 0.55651 (41362) SS BOND : bond 0.00358 ( 44) SS BOND : angle 1.29751 ( 88) hydrogen bonds : bond 0.03562 ( 932) hydrogen bonds : angle 5.90080 ( 2493) *********************** 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 200 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 120 time to evaluate : 1.060 Fit side-chains REVERT: A 49 HIS cc_start: -0.0517 (t70) cc_final: -0.1161 (t70) REVERT: A 341 ASN cc_start: 0.0680 (OUTLIER) cc_final: -0.0850 (p0) REVERT: A 582 ILE cc_start: 0.1554 (OUTLIER) cc_final: 0.1219 (mt) REVERT: A 793 LYS cc_start: 0.4134 (mttp) cc_final: 0.1760 (tmmt) REVERT: A 982 LEU cc_start: 0.2287 (OUTLIER) cc_final: 0.2047 (tt) REVERT: A 1021 ASN cc_start: -0.0314 (OUTLIER) cc_final: -0.0865 (t0) REVERT: B 175 MET cc_start: 0.3430 (tpp) cc_final: 0.1366 (ptt) REVERT: B 739 TYR cc_start: 0.0521 (t80) cc_final: -0.1309 (t80) REVERT: B 778 GLU cc_start: 0.1100 (OUTLIER) cc_final: 0.0025 (tt0) REVERT: B 896 PHE cc_start: 0.3263 (OUTLIER) cc_final: 0.2965 (m-80) REVERT: C 506 TYR cc_start: 0.2205 (m-80) cc_final: 0.1570 (m-10) REVERT: C 672 TYR cc_start: 0.3504 (t80) cc_final: 0.2890 (t80) REVERT: C 732 THR cc_start: 0.2658 (OUTLIER) cc_final: 0.1497 (m) REVERT: C 898 MET cc_start: 0.1546 (mmt) cc_final: -0.0608 (mtp) REVERT: C 904 PHE cc_start: -0.0760 (OUTLIER) cc_final: -0.1451 (m-80) REVERT: H 82 MET cc_start: 0.3490 (OUTLIER) cc_final: 0.2864 (mmp) REVERT: I 82 MET cc_start: 0.3490 (mmt) cc_final: 0.2207 (ppp) REVERT: I 105 MET cc_start: 0.1067 (OUTLIER) cc_final: 0.0011 (ttp) outliers start: 80 outliers final: 56 residues processed: 190 average time/residue: 0.1744 time to fit residues: 56.5898 Evaluate side-chains 179 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 530 ASN 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 729 MET Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 950 VAL Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1099 HIS 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 H residue 105 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 LEU 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 17 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 342 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 HIS ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.371782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.362444 restraints weight = 94313.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.363114 restraints weight = 69174.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5603 r_free = 0.5603 target = 0.363710 restraints weight = 49083.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5603 r_free = 0.5603 target = 0.363688 restraints weight = 39974.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5604 r_free = 0.5604 target = 0.363812 restraints weight = 35180.430| |-----------------------------------------------------------------------------| r_work (final): 0.5503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1663 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 30447 Z= 0.302 Angle : 0.947 21.465 41450 Z= 0.501 Chirality : 0.056 0.759 4645 Planarity : 0.007 0.119 5373 Dihedral : 6.505 49.563 4114 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.09 % Favored : 89.64 % Rotamer: Outliers : 3.79 % Allowed : 17.18 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.12), residues: 3775 helix: -1.11 (0.18), residues: 622 sheet: -0.31 (0.19), residues: 725 loop : -2.37 (0.11), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1037 TYR 0.038 0.002 TYR A 794 PHE 0.052 0.003 PHE A1146 TRP 0.024 0.002 TRP B1100 HIS 0.015 0.002 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00647 (30403) covalent geometry : angle 0.94434 (41362) SS BOND : bond 0.01111 ( 44) SS BOND : angle 1.68293 ( 88) hydrogen bonds : bond 0.06389 ( 932) hydrogen bonds : angle 7.49340 ( 2493) *********************** 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 237 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 112 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.0293 (t70) cc_final: -0.0723 (t70) REVERT: A 541 PHE cc_start: 0.2382 (OUTLIER) cc_final: 0.1282 (m-80) REVERT: A 549 VAL cc_start: 0.0374 (OUTLIER) cc_final: -0.0471 (t) REVERT: A 582 ILE cc_start: 0.2485 (OUTLIER) cc_final: 0.2185 (mp) REVERT: A 725 LEU cc_start: 0.2335 (OUTLIER) cc_final: 0.2006 (tp) REVERT: A 866 GLU cc_start: 0.0911 (OUTLIER) cc_final: -0.2548 (tp30) REVERT: B 138 PHE cc_start: -0.2471 (OUTLIER) cc_final: -0.4191 (m-80) REVERT: B 175 MET cc_start: 0.3873 (tpp) cc_final: 0.1614 (ptt) REVERT: B 778 GLU cc_start: 0.3656 (OUTLIER) cc_final: -0.0682 (mt-10) REVERT: B 896 PHE cc_start: 0.3229 (OUTLIER) cc_final: 0.2821 (m-80) REVERT: B 1015 GLU cc_start: -0.1713 (OUTLIER) cc_final: -0.2494 (tp30) REVERT: C 212 ARG cc_start: 0.1720 (OUTLIER) cc_final: 0.0847 (mtm180) REVERT: C 506 TYR cc_start: 0.2473 (m-80) cc_final: 0.1082 (m-10) REVERT: C 672 TYR cc_start: 0.4247 (t80) cc_final: 0.3455 (t80) REVERT: C 707 ASN cc_start: 0.0305 (OUTLIER) cc_final: -0.0537 (m110) REVERT: C 732 THR cc_start: 0.3377 (OUTLIER) cc_final: 0.1902 (m) REVERT: C 738 MET cc_start: 0.2748 (tpp) cc_final: 0.2375 (mmp) REVERT: C 898 MET cc_start: 0.1824 (mmt) cc_final: -0.0256 (mtp) REVERT: C 1047 LEU cc_start: -0.1266 (OUTLIER) cc_final: -0.1626 (tp) REVERT: C 1087 PHE cc_start: 0.2913 (OUTLIER) cc_final: -0.0512 (m-10) REVERT: G 82 MET cc_start: 0.5093 (mpp) cc_final: 0.3843 (mtm) REVERT: I 105 MET cc_start: 0.1242 (OUTLIER) cc_final: 0.0207 (ttp) outliers start: 125 outliers final: 85 residues processed: 225 average time/residue: 0.1607 time to fit residues: 62.3989 Evaluate side-chains 210 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 110 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 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 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 707 ASN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1073 PHE Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1113 ILE Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1141 PRO Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain K residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 232 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 44 optimal weight: 50.0000 chunk 218 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN B 947 GLN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5601 r_free = 0.5601 target = 0.373799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5625 r_free = 0.5625 target = 0.365285 restraints weight = 94794.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.366090 restraints weight = 62202.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.366234 restraints weight = 41260.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.366393 restraints weight = 41231.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.366636 restraints weight = 33356.381| |-----------------------------------------------------------------------------| r_work (final): 0.5526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1438 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30447 Z= 0.144 Angle : 0.661 13.549 41450 Z= 0.345 Chirality : 0.046 0.283 4645 Planarity : 0.005 0.075 5373 Dihedral : 5.610 51.169 4114 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 2.58 % Allowed : 18.15 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.13), residues: 3775 helix: -0.25 (0.20), residues: 619 sheet: -0.39 (0.19), residues: 773 loop : -2.28 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1105 TYR 0.030 0.001 TYR C1065 PHE 0.029 0.002 PHE A 316 TRP 0.023 0.001 TRP A 884 HIS 0.006 0.001 HIS C1099 Details of bonding type rmsd covalent geometry : bond 0.00311 (30403) covalent geometry : angle 0.65831 (41362) SS BOND : bond 0.00544 ( 44) SS BOND : angle 1.47712 ( 88) hydrogen bonds : bond 0.04469 ( 932) hydrogen bonds : angle 6.61550 ( 2493) ********************** 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 205 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 120 time to evaluate : 1.124 Fit side-chains REVERT: A 49 HIS cc_start: 0.0152 (t70) cc_final: -0.0667 (t70) REVERT: A 311 TYR cc_start: 0.0757 (m-80) cc_final: 0.0405 (m-80) REVERT: A 341 ASN cc_start: 0.0896 (OUTLIER) cc_final: -0.0303 (p0) REVERT: A 541 PHE cc_start: 0.2434 (OUTLIER) cc_final: 0.1290 (m-80) REVERT: A 582 ILE cc_start: 0.2304 (OUTLIER) cc_final: 0.1998 (mp) REVERT: A 606 VAL cc_start: -0.2232 (OUTLIER) cc_final: -0.3874 (p) REVERT: A 789 THR cc_start: -0.0450 (OUTLIER) cc_final: -0.2328 (t) REVERT: A 1021 ASN cc_start: 0.0992 (OUTLIER) cc_final: -0.1175 (m-40) REVERT: B 138 PHE cc_start: -0.2858 (OUTLIER) cc_final: -0.4458 (m-80) REVERT: B 175 MET cc_start: 0.3890 (tpp) cc_final: 0.1637 (ptt) REVERT: B 738 MET cc_start: -0.2041 (ttm) cc_final: -0.2252 (tmm) REVERT: B 778 GLU cc_start: 0.2691 (OUTLIER) cc_final: 0.0128 (tt0) REVERT: B 896 PHE cc_start: 0.3095 (OUTLIER) cc_final: 0.2812 (m-80) REVERT: C 212 ARG cc_start: 0.1138 (OUTLIER) cc_final: 0.0464 (mtm180) REVERT: C 506 TYR cc_start: 0.2661 (m-80) cc_final: 0.1396 (m-10) REVERT: C 672 TYR cc_start: 0.4018 (t80) cc_final: 0.3408 (t80) REVERT: C 693 TYR cc_start: -0.0134 (OUTLIER) cc_final: -0.1424 (p90) REVERT: C 738 MET cc_start: 0.2533 (tpp) cc_final: 0.0011 (ttt) REVERT: C 898 MET cc_start: 0.1820 (mmt) cc_final: -0.0117 (mtp) REVERT: C 1087 PHE cc_start: 0.2351 (OUTLIER) cc_final: -0.0394 (m-10) REVERT: G 82 MET cc_start: 0.5037 (mpp) cc_final: 0.3798 (mtm) REVERT: I 82 MET cc_start: 0.3987 (mmt) cc_final: 0.2112 (ppp) REVERT: I 105 MET cc_start: 0.1131 (OUTLIER) cc_final: 0.0071 (ttp) outliers start: 85 outliers final: 67 residues processed: 197 average time/residue: 0.1770 time to fit residues: 59.3852 Evaluate side-chains 194 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 114 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 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 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 886 PHE Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 896 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 925 PHE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 693 TYR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1070 GLU Chi-restraints excluded: chain C residue 1071 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1087 PHE Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain C residue 1111 GLN Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 336 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 172 optimal weight: 0.0020 chunk 253 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 258 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 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 = 0.5601 r_free = 0.5601 target = 0.373843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5626 r_free = 0.5626 target = 0.365211 restraints weight = 94818.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.366241 restraints weight = 62825.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.366581 restraints weight = 37365.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.366690 restraints weight = 34740.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5629 r_free = 0.5629 target = 0.366762 restraints weight = 26907.957| |-----------------------------------------------------------------------------| r_work (final): 0.5526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1441 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.231 30447 Z= 0.163 Angle : 0.767 59.195 41450 Z= 0.426 Chirality : 0.046 0.397 4645 Planarity : 0.005 0.075 5373 Dihedral : 5.590 51.113 4114 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.45 % Rotamer: Outliers : 2.58 % Allowed : 18.15 % Favored : 79.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.13), residues: 3775 helix: -0.23 (0.20), residues: 619 sheet: -0.40 (0.19), residues: 773 loop : -2.28 (0.11), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1105 TYR 0.029 0.001 TYR C1065 PHE 0.029 0.001 PHE A 316 TRP 0.019 0.001 TRP A 884 HIS 0.006 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00359 (30403) covalent geometry : angle 0.76530 (41362) SS BOND : bond 0.00507 ( 44) SS BOND : angle 1.41322 ( 88) hydrogen bonds : bond 0.04472 ( 932) hydrogen bonds : angle 6.60892 ( 2493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4304.92 seconds wall clock time: 75 minutes 46.42 seconds (4546.42 seconds total)