Starting phenix.real_space_refine on Thu Jan 15 19:36:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ycy_33742/01_2026/7ycy_33742.map" } resolution = 3.74 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 18653 2.51 5 N 4836 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29175 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "I" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 7.44, per 1000 atoms: 0.26 Number of scatterers: 29175 At special positions: 0 Unit cell: (142.576, 177.688, 200.032, 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 135 16.00 O 5551 8.00 N 4836 7.00 C 18653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 59 sheets defined 18.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.568A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.925A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.524A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.541A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 901 through 907 removed outlier: 3.562A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.519A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.887A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.680A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.516A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.731A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.807A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.915A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.356A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.792A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.059A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.782A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.530A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.870A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.525A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.595A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.516A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.837A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.515A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.803A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.838A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.684A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.657A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.597A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.656A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.581A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.885A pdb=" N SER A 94 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.579A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.673A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.714A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.554A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.585A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.569A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.402A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.554A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.669A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.831A pdb=" N PHE B 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.770A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.130A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.506A pdb=" N GLU B 189 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 203 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.540A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.644A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.582A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.512A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.859A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.715A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.574A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.772A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.585A pdb=" N TYR C 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 201 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.611A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 310 through 319 removed outlier: 3.548A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.626A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.914A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.800A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.800A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.436A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.488A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.525A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.680A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 41 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 93 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 114 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AF4, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.584A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.651A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.773A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN F 41 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 94 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 114 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.531A pdb=" N GLY G 12 " --> pdb=" O THR G 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.481A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.601A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.708A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 93 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.189A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 17 through 19 861 hydrogen bonds defined for protein. 2352 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: 6.82 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9307 1.34 - 1.46: 5449 1.46 - 1.58: 14933 1.58 - 1.70: 0 1.70 - 1.81: 171 Bond restraints: 29860 Sorted by residual: bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.523 1.476 0.046 1.37e-02 5.33e+03 1.15e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.38e-02 5.25e+03 4.75e+00 bond pdb=" CA GLY C 885 " pdb=" C GLY C 885 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.41e+00 bond pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.42e-02 4.96e+03 2.36e+00 bond pdb=" CA GLY I 30 " pdb=" C GLY I 30 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.28e+00 ... (remaining 29855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 40168 1.99 - 3.99: 480 3.99 - 5.98: 23 5.98 - 7.98: 4 7.98 - 9.97: 3 Bond angle restraints: 40678 Sorted by residual: angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.33 120.14 -8.81 1.43e+00 4.89e-01 3.80e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 108.91 117.37 -8.46 1.53e+00 4.27e-01 3.05e+01 angle pdb=" N ILE C 332 " pdb=" CA ILE C 332 " pdb=" C ILE C 332 " ideal model delta sigma weight residual 110.36 115.84 -5.48 1.05e+00 9.07e-01 2.73e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 121.48 131.45 -9.97 2.04e+00 2.40e-01 2.39e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.40 4.31 9.50e-01 1.11e+00 2.06e+01 ... (remaining 40673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 17056 17.31 - 34.62: 631 34.62 - 51.93: 96 51.93 - 69.23: 18 69.23 - 86.54: 3 Dihedral angle restraints: 17804 sinusoidal: 6834 harmonic: 10970 Sorted by residual: dihedral pdb=" CA ASP G 52 " pdb=" C ASP G 52 " pdb=" N VAL G 53 " pdb=" CA VAL G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP I 52 " pdb=" C ASP I 52 " pdb=" N VAL I 53 " pdb=" CA VAL I 53 " ideal model delta harmonic sigma weight residual 180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA PRO C 330 " pdb=" C PRO C 330 " pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 17801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4116 0.062 - 0.125: 534 0.125 - 0.187: 6 0.187 - 0.249: 0 0.249 - 0.312: 1 Chirality restraints: 4657 Sorted by residual: chirality pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" C PRO C 330 " pdb=" CB PRO C 330 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA THR C 333 " pdb=" N THR C 333 " pdb=" C THR C 333 " pdb=" CB THR C 333 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4654 not shown) Planarity restraints: 5239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO C 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.028 5.00e-02 4.00e+02 ... (remaining 5236 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5297 2.77 - 3.31: 27522 3.31 - 3.84: 48137 3.84 - 4.37: 54826 4.37 - 4.90: 95876 Nonbonded interactions: 231658 Sorted by model distance: nonbonded pdb=" O ILE F 106 " pdb=" OH TYR G 38 " model vdw 2.242 3.040 nonbonded pdb=" OG SER I 65 " pdb=" OG1 THR I 76 " model vdw 2.243 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.246 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 21 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OG1 THR B 998 " model vdw 2.251 3.040 ... (remaining 231653 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' selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.160 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.002 0.047 29905 Z= 0.120 Angle : 0.526 9.974 40768 Z= 0.322 Chirality : 0.040 0.312 4657 Planarity : 0.004 0.052 5239 Dihedral : 8.830 86.542 10613 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.56 % Allowed : 5.98 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.11), residues: 3713 helix: -1.38 (0.18), residues: 628 sheet: -2.81 (0.16), residues: 780 loop : -3.60 (0.10), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.005 0.000 TYR A1138 PHE 0.008 0.001 PHE C 329 TRP 0.005 0.001 TRP B 886 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00194 (29860) covalent geometry : angle 0.52598 (40678) SS BOND : bond 0.00112 ( 45) SS BOND : angle 0.38748 ( 90) hydrogen bonds : bond 0.25766 ( 849) hydrogen bonds : angle 9.23732 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 901 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8239 (t) cc_final: 0.7989 (t) REVERT: A 47 VAL cc_start: 0.8978 (m) cc_final: 0.8706 (p) REVERT: A 67 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6512 (t) REVERT: A 87 ASN cc_start: 0.7359 (p0) cc_final: 0.6514 (p0) REVERT: A 188 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6149 (mmt-90) REVERT: A 190 PHE cc_start: 0.7157 (m-80) cc_final: 0.6453 (m-80) REVERT: A 192 PHE cc_start: 0.6940 (m-10) cc_final: 0.6577 (m-10) REVERT: A 276 LEU cc_start: 0.8199 (tp) cc_final: 0.7883 (tt) REVERT: A 281 GLU cc_start: 0.7101 (pp20) cc_final: 0.6854 (pp20) REVERT: A 297 SER cc_start: 0.8419 (m) cc_final: 0.8110 (p) REVERT: A 403 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7503 (ttm-80) REVERT: A 534 VAL cc_start: 0.8672 (t) cc_final: 0.8332 (m) REVERT: A 541 PHE cc_start: 0.7716 (p90) cc_final: 0.7450 (p90) REVERT: A 578 ASP cc_start: 0.6140 (t70) cc_final: 0.5522 (t70) REVERT: A 589 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7510 (Cg_endo) REVERT: A 599 THR cc_start: 0.8313 (m) cc_final: 0.8056 (t) REVERT: A 644 GLN cc_start: 0.7572 (tp40) cc_final: 0.6195 (tp40) REVERT: A 656 VAL cc_start: 0.8421 (p) cc_final: 0.8199 (m) REVERT: A 659 SER cc_start: 0.8232 (m) cc_final: 0.7966 (p) REVERT: A 674 TYR cc_start: 0.8044 (t80) cc_final: 0.7447 (t80) REVERT: A 698 SER cc_start: 0.8727 (t) cc_final: 0.8196 (p) REVERT: A 705 VAL cc_start: 0.8353 (t) cc_final: 0.8090 (m) REVERT: A 714 ILE cc_start: 0.8420 (mm) cc_final: 0.8177 (mt) REVERT: A 745 ASP cc_start: 0.6037 (m-30) cc_final: 0.5833 (m-30) REVERT: A 754 LEU cc_start: 0.8384 (mt) cc_final: 0.8133 (mt) REVERT: A 763 LEU cc_start: 0.8242 (mt) cc_final: 0.7983 (mt) REVERT: A 773 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5466 (tm-30) REVERT: A 778 THR cc_start: 0.8288 (p) cc_final: 0.7782 (t) REVERT: A 803 SER cc_start: 0.8420 (m) cc_final: 0.8104 (p) REVERT: A 816 SER cc_start: 0.7762 (p) cc_final: 0.7412 (m) REVERT: A 854 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8041 (tmtt) REVERT: A 868 GLU cc_start: 0.7369 (tp30) cc_final: 0.7048 (tp30) REVERT: A 869 MET cc_start: 0.8161 (mtt) cc_final: 0.7952 (mtm) REVERT: A 878 LEU cc_start: 0.8316 (mt) cc_final: 0.7808 (mp) REVERT: A 921 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8092 (mmmm) REVERT: A 922 LEU cc_start: 0.8327 (tp) cc_final: 0.8066 (tp) REVERT: A 925 ASN cc_start: 0.8499 (m-40) cc_final: 0.8072 (m-40) REVERT: A 933 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7586 (mtmm) REVERT: A 934 ILE cc_start: 0.8242 (mm) cc_final: 0.7962 (mm) REVERT: A 945 LEU cc_start: 0.8691 (mm) cc_final: 0.8369 (mp) REVERT: A 949 GLN cc_start: 0.8166 (mm110) cc_final: 0.7275 (mm-40) REVERT: A 953 ASN cc_start: 0.8293 (m-40) cc_final: 0.7773 (m110) REVERT: A 960 ASN cc_start: 0.7764 (m110) cc_final: 0.7522 (m-40) REVERT: A 979 ASP cc_start: 0.7167 (m-30) cc_final: 0.6879 (m-30) REVERT: A 994 ASP cc_start: 0.7304 (m-30) cc_final: 0.6909 (m-30) REVERT: A 1019 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7306 (ttp80) REVERT: A 1028 LYS cc_start: 0.8193 (mttt) cc_final: 0.7945 (mttt) REVERT: A 1050 MET cc_start: 0.7045 (ttm) cc_final: 0.6652 (mtp) REVERT: A 1084 ASP cc_start: 0.8411 (m-30) cc_final: 0.8111 (m-30) REVERT: A 1117 THR cc_start: 0.8159 (p) cc_final: 0.7944 (t) REVERT: A 1129 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 1141 LEU cc_start: 0.8343 (tp) cc_final: 0.7993 (tt) REVERT: B 41 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7872 (mtpt) REVERT: B 50 SER cc_start: 0.9056 (t) cc_final: 0.8791 (p) REVERT: B 105 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 106 PHE cc_start: 0.7067 (m-80) cc_final: 0.6591 (m-80) REVERT: B 135 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6684 (p90) REVERT: B 224 GLU cc_start: 0.8040 (pm20) cc_final: 0.7799 (pm20) REVERT: B 265 TYR cc_start: 0.7308 (p90) cc_final: 0.7085 (p90) REVERT: B 267 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 278 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8401 (ttmm) REVERT: B 286 THR cc_start: 0.7867 (p) cc_final: 0.7020 (p) REVERT: B 300 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7764 (mtmt) REVERT: B 307 THR cc_start: 0.7221 (m) cc_final: 0.6888 (p) REVERT: B 332 ILE cc_start: 0.7971 (mm) cc_final: 0.7564 (tp) REVERT: B 340 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 353 TRP cc_start: 0.8258 (p-90) cc_final: 0.8003 (p-90) REVERT: B 354 ASN cc_start: 0.8100 (m110) cc_final: 0.7717 (m110) REVERT: B 380 TYR cc_start: 0.6485 (m-80) cc_final: 0.6152 (m-80) REVERT: B 390 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 408 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7218 (ttp80) REVERT: B 433 VAL cc_start: 0.8389 (p) cc_final: 0.8108 (m) REVERT: B 513 LEU cc_start: 0.7767 (mp) cc_final: 0.7248 (mm) REVERT: B 514 SER cc_start: 0.7825 (m) cc_final: 0.7510 (t) REVERT: B 516 GLU cc_start: 0.6312 (mm-30) cc_final: 0.6037 (mm-30) REVERT: B 535 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7991 (mtpp) REVERT: B 542 ASN cc_start: 0.7836 (t0) cc_final: 0.7610 (t0) REVERT: B 546 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7918 (tm) REVERT: B 644 GLN cc_start: 0.8054 (tp40) cc_final: 0.7347 (tp40) REVERT: B 645 THR cc_start: 0.7955 (p) cc_final: 0.6896 (m) REVERT: B 651 ILE cc_start: 0.8389 (mt) cc_final: 0.8172 (mt) REVERT: B 659 SER cc_start: 0.8658 (m) cc_final: 0.8150 (p) REVERT: B 703 ASN cc_start: 0.8211 (t0) cc_final: 0.7918 (t0) REVERT: B 705 VAL cc_start: 0.8562 (t) cc_final: 0.8338 (p) REVERT: B 707 TYR cc_start: 0.7790 (t80) cc_final: 0.7574 (t80) REVERT: B 732 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8202 (p) REVERT: B 737 ASP cc_start: 0.7484 (t0) cc_final: 0.7159 (t0) REVERT: B 774 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7350 (mm-40) REVERT: B 776 LYS cc_start: 0.8106 (tmmt) cc_final: 0.7736 (ttmt) REVERT: B 850 ILE cc_start: 0.8258 (mm) cc_final: 0.7871 (tp) REVERT: B 851 CYS cc_start: 0.7867 (t) cc_final: 0.7466 (m) REVERT: B 854 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7955 (tttp) REVERT: B 866 THR cc_start: 0.8152 (p) cc_final: 0.7943 (t) REVERT: B 921 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8491 (mmmt) REVERT: B 933 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7851 (ttmm) REVERT: B 950 ASP cc_start: 0.7113 (t70) cc_final: 0.6275 (t70) REVERT: B 968 SER cc_start: 0.8289 (m) cc_final: 0.8088 (m) REVERT: B 990 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 994 ASP cc_start: 0.7404 (m-30) cc_final: 0.6844 (m-30) REVERT: B 997 ILE cc_start: 0.8433 (tt) cc_final: 0.8084 (pt) REVERT: B 1002 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7349 (tm-30) REVERT: B 1003 SER cc_start: 0.8636 (m) cc_final: 0.7959 (t) REVERT: B 1010 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: B 1019 ARG cc_start: 0.6619 (ttm110) cc_final: 0.6321 (ttp80) REVERT: B 1061 VAL cc_start: 0.8679 (t) cc_final: 0.8288 (p) REVERT: B 1097 SER cc_start: 0.8689 (t) cc_final: 0.7842 (p) REVERT: C 41 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7173 (mtpp) REVERT: C 54 LEU cc_start: 0.8071 (mt) cc_final: 0.7779 (mt) REVERT: C 65 PHE cc_start: 0.6655 (m-80) cc_final: 0.6340 (m-80) REVERT: C 90 VAL cc_start: 0.8586 (m) cc_final: 0.8355 (p) REVERT: C 106 PHE cc_start: 0.6787 (m-80) cc_final: 0.6474 (m-80) REVERT: C 189 GLU cc_start: 0.7072 (pm20) cc_final: 0.6204 (pm20) REVERT: C 192 PHE cc_start: 0.7976 (m-80) cc_final: 0.7593 (m-80) REVERT: C 199 PHE cc_start: 0.7661 (t80) cc_final: 0.7445 (t80) REVERT: C 224 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6741 (mm-30) REVERT: C 267 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7167 (p) REVERT: C 271 GLN cc_start: 0.7472 (mt0) cc_final: 0.7106 (mt0) REVERT: C 275 PHE cc_start: 0.7757 (m-80) cc_final: 0.7436 (m-10) REVERT: C 289 VAL cc_start: 0.8597 (t) cc_final: 0.8373 (m) REVERT: C 297 SER cc_start: 0.7910 (m) cc_final: 0.7364 (p) REVERT: C 436 TRP cc_start: 0.7755 (p90) cc_final: 0.7267 (p-90) REVERT: C 501 TYR cc_start: 0.7145 (m-10) cc_final: 0.6696 (m-10) REVERT: C 531 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8083 (p) REVERT: C 542 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7467 (t0) REVERT: C 563 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6880 (mm-40) REVERT: C 569 ILE cc_start: 0.8400 (pp) cc_final: 0.8163 (mp) REVERT: C 588 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7781 (p) REVERT: C 619 GLU cc_start: 0.6589 (mp0) cc_final: 0.6075 (mp0) REVERT: C 644 GLN cc_start: 0.7967 (tp40) cc_final: 0.7254 (tp40) REVERT: C 675 GLN cc_start: 0.6533 (mm-40) cc_final: 0.6279 (mm-40) REVERT: C 697 MET cc_start: 0.7797 (ptm) cc_final: 0.7582 (ptm) REVERT: C 718 PHE cc_start: 0.6887 (p90) cc_final: 0.6650 (p90) REVERT: C 725 GLU cc_start: 0.7261 (tt0) cc_final: 0.6905 (tt0) REVERT: C 759 PHE cc_start: 0.7362 (t80) cc_final: 0.6400 (t80) REVERT: C 762 GLN cc_start: 0.7696 (tt0) cc_final: 0.7301 (tt0) REVERT: C 763 LEU cc_start: 0.8173 (mt) cc_final: 0.7499 (mp) REVERT: C 764 LYS cc_start: 0.8336 (tttm) cc_final: 0.7872 (ttpp) REVERT: C 765 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7457 (mtm110) REVERT: C 773 GLU cc_start: 0.7155 (tt0) cc_final: 0.6826 (tt0) REVERT: C 816 SER cc_start: 0.8264 (p) cc_final: 0.7890 (m) REVERT: C 821 LEU cc_start: 0.8594 (tp) cc_final: 0.7956 (tp) REVERT: C 854 LYS cc_start: 0.8258 (tmmt) cc_final: 0.7691 (tptp) REVERT: C 855 PHE cc_start: 0.7727 (m-10) cc_final: 0.7295 (m-80) REVERT: C 905 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.6700 (mmt180) REVERT: C 950 ASP cc_start: 0.7303 (t70) cc_final: 0.6814 (t70) REVERT: C 1002 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7174 (tp-100) REVERT: C 1014 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7240 (ttm110) REVERT: C 1017 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 1019 ARG cc_start: 0.7388 (ttm110) cc_final: 0.6613 (ttm110) REVERT: C 1031 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 1039 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6728 (mtp180) REVERT: C 1081 ILE cc_start: 0.8609 (pt) cc_final: 0.8262 (mm) REVERT: C 1111 GLU cc_start: 0.7470 (tt0) cc_final: 0.7151 (tt0) REVERT: C 1125 ASN cc_start: 0.7103 (p0) cc_final: 0.6407 (p0) REVERT: C 1127 ASP cc_start: 0.6959 (p0) cc_final: 0.6188 (p0) REVERT: E 50 ILE cc_start: 0.1574 (OUTLIER) cc_final: 0.1211 (pt) REVERT: E 75 LEU cc_start: 0.0142 (OUTLIER) cc_final: -0.0247 (tt) REVERT: F 84 MET cc_start: 0.2315 (ptp) cc_final: 0.2103 (ptm) REVERT: H 20 LEU cc_start: 0.8257 (tt) cc_final: 0.7964 (tt) REVERT: H 54 TYR cc_start: 0.6959 (m-80) cc_final: 0.6525 (m-80) REVERT: H 78 ASN cc_start: 0.5360 (m110) cc_final: 0.4831 (t0) REVERT: H 83 THR cc_start: 0.6792 (p) cc_final: 0.6517 (p) REVERT: H 114 THR cc_start: 0.3704 (p) cc_final: 0.1779 (m) outliers start: 148 outliers final: 43 residues processed: 1020 average time/residue: 0.1948 time to fit residues: 313.1895 Evaluate side-chains 782 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 721 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 205 HIS A 271 GLN A 334 ASN A 370 ASN A 409 GLN A 460 ASN A 542 ASN A 580 GLN A 644 GLN A 690 GLN A 784 GLN A 901 GLN A 907 ASN A 913 GLN A 965 GLN A1005 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1101 HIS A1106 GLN A1119 ASN B 52 GLN B 121 ASN B 173 GLN B 186 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 784 GLN B 853 GLN B 901 GLN B 954 HIS B1002 GLN B1010 GLN B1011 GLN B1125 ASN C 173 GLN C 181 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 370 ASN C 409 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 540 ASN C 613 GLN C 710 ASN C 901 GLN C 913 GLN C1002 GLN C1005 GLN C1011 GLN C1048 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN E 39 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 41 GLN G 39 GLN G 40 GLN G 71 ASN G 81 GLN H 41 GLN I 40 GLN I 81 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128937 restraints weight = 56813.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133070 restraints weight = 24918.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135567 restraints weight = 13892.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137118 restraints weight = 9269.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138053 restraints weight = 7113.987| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29905 Z= 0.188 Angle : 0.636 12.409 40768 Z= 0.327 Chirality : 0.046 0.294 4657 Planarity : 0.005 0.073 5239 Dihedral : 5.791 61.860 4156 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.84 % Allowed : 12.24 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.12), residues: 3713 helix: -0.02 (0.20), residues: 656 sheet: -2.21 (0.17), residues: 770 loop : -3.19 (0.11), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.024 0.001 TYR A 495 PHE 0.028 0.002 PHE C 55 TRP 0.025 0.001 TRP A 104 HIS 0.011 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00402 (29860) covalent geometry : angle 0.62790 (40678) SS BOND : bond 0.00447 ( 45) SS BOND : angle 2.22696 ( 90) hydrogen bonds : bond 0.04717 ( 849) hydrogen bonds : angle 6.20885 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 759 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7326 (p0) cc_final: 0.7098 (p0) REVERT: A 111 ASP cc_start: 0.5241 (OUTLIER) cc_final: 0.4940 (p0) REVERT: A 190 PHE cc_start: 0.7212 (m-80) cc_final: 0.6738 (m-80) REVERT: A 233 ILE cc_start: 0.8479 (tt) cc_final: 0.8065 (pt) REVERT: A 281 GLU cc_start: 0.7366 (pp20) cc_final: 0.7078 (pp20) REVERT: A 297 SER cc_start: 0.8401 (m) cc_final: 0.8117 (p) REVERT: A 326 ILE cc_start: 0.7953 (mp) cc_final: 0.7683 (mt) REVERT: A 403 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7605 (ptp-110) REVERT: A 478 LYS cc_start: -0.0618 (OUTLIER) cc_final: -0.1921 (ptmt) REVERT: A 505 HIS cc_start: 0.7176 (t-90) cc_final: 0.6897 (t-90) REVERT: A 535 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8131 (mttp) REVERT: A 542 ASN cc_start: 0.8173 (t0) cc_final: 0.7943 (t0) REVERT: A 592 PHE cc_start: 0.7849 (p90) cc_final: 0.7363 (p90) REVERT: A 599 THR cc_start: 0.8434 (m) cc_final: 0.8215 (t) REVERT: A 615 VAL cc_start: 0.8413 (t) cc_final: 0.8197 (m) REVERT: A 674 TYR cc_start: 0.8232 (t80) cc_final: 0.7950 (t80) REVERT: A 692 ILE cc_start: 0.8781 (mt) cc_final: 0.8579 (pt) REVERT: A 697 MET cc_start: 0.7226 (ttp) cc_final: 0.6679 (mtp) REVERT: A 698 SER cc_start: 0.8626 (t) cc_final: 0.8208 (p) REVERT: A 737 ASP cc_start: 0.7555 (t70) cc_final: 0.7334 (t0) REVERT: A 745 ASP cc_start: 0.6535 (m-30) cc_final: 0.5979 (t0) REVERT: A 751 ASN cc_start: 0.7945 (m-40) cc_final: 0.7714 (m-40) REVERT: A 754 LEU cc_start: 0.8312 (mt) cc_final: 0.8087 (mt) REVERT: A 759 PHE cc_start: 0.6827 (m-80) cc_final: 0.6411 (m-80) REVERT: A 762 GLN cc_start: 0.7490 (pt0) cc_final: 0.7245 (pt0) REVERT: A 763 LEU cc_start: 0.8429 (mt) cc_final: 0.8149 (mt) REVERT: A 773 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5781 (tm-30) REVERT: A 803 SER cc_start: 0.8697 (m) cc_final: 0.8259 (p) REVERT: A 816 SER cc_start: 0.7846 (p) cc_final: 0.7382 (t) REVERT: A 825 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8107 (mmtm) REVERT: A 854 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8054 (tttt) REVERT: A 855 PHE cc_start: 0.8268 (m-80) cc_final: 0.7962 (m-80) REVERT: A 868 GLU cc_start: 0.7377 (tp30) cc_final: 0.7044 (tp30) REVERT: A 869 MET cc_start: 0.8216 (mtt) cc_final: 0.7965 (mtm) REVERT: A 878 LEU cc_start: 0.8250 (mt) cc_final: 0.7895 (mp) REVERT: A 921 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8178 (mmmm) REVERT: A 925 ASN cc_start: 0.8545 (m-40) cc_final: 0.8042 (m-40) REVERT: A 933 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7835 (mtmm) REVERT: A 945 LEU cc_start: 0.8696 (mm) cc_final: 0.8350 (mp) REVERT: A 953 ASN cc_start: 0.8334 (m-40) cc_final: 0.8015 (m110) REVERT: A 960 ASN cc_start: 0.8005 (m110) cc_final: 0.7697 (m-40) REVERT: A 978 ASN cc_start: 0.7867 (m-40) cc_final: 0.7472 (m-40) REVERT: A 1019 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7319 (ttp80) REVERT: A 1029 MET cc_start: 0.8347 (tpp) cc_final: 0.7565 (ttm) REVERT: A 1038 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8240 (mttt) REVERT: A 1050 MET cc_start: 0.7146 (ttm) cc_final: 0.6511 (mtp) REVERT: A 1117 THR cc_start: 0.8464 (p) cc_final: 0.8210 (t) REVERT: A 1129 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 1141 LEU cc_start: 0.8262 (tp) cc_final: 0.7915 (tt) REVERT: B 104 TRP cc_start: 0.7068 (m-90) cc_final: 0.6683 (m-90) REVERT: B 105 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7524 (mm) REVERT: B 106 PHE cc_start: 0.7352 (m-80) cc_final: 0.6897 (m-80) REVERT: B 130 VAL cc_start: 0.5950 (OUTLIER) cc_final: 0.5549 (p) REVERT: B 187 LEU cc_start: 0.7902 (tp) cc_final: 0.7624 (tt) REVERT: B 190 PHE cc_start: 0.8014 (m-10) cc_final: 0.7800 (m-80) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7598 (pm20) REVERT: B 267 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 278 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8396 (ttmt) REVERT: B 286 THR cc_start: 0.7717 (p) cc_final: 0.7374 (p) REVERT: B 307 THR cc_start: 0.7261 (m) cc_final: 0.6861 (p) REVERT: B 317 ASN cc_start: 0.8323 (p0) cc_final: 0.8052 (p0) REVERT: B 329 PHE cc_start: 0.7900 (m-10) cc_final: 0.7564 (m-80) REVERT: B 353 TRP cc_start: 0.8306 (p-90) cc_final: 0.7991 (p-90) REVERT: B 354 ASN cc_start: 0.7992 (m110) cc_final: 0.7628 (m110) REVERT: B 380 TYR cc_start: 0.6772 (m-80) cc_final: 0.6360 (m-80) REVERT: B 402 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 408 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7535 (ptm-80) REVERT: B 429 PHE cc_start: 0.8341 (t80) cc_final: 0.7910 (t80) REVERT: B 515 PHE cc_start: 0.7398 (m-80) cc_final: 0.7114 (m-80) REVERT: B 546 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7892 (tm) REVERT: B 547 LYS cc_start: 0.8473 (tptp) cc_final: 0.8243 (tttm) REVERT: B 589 PRO cc_start: 0.7897 (Cg_exo) cc_final: 0.7685 (Cg_endo) REVERT: B 651 ILE cc_start: 0.8283 (mt) cc_final: 0.8010 (mp) REVERT: B 659 SER cc_start: 0.8787 (m) cc_final: 0.8213 (p) REVERT: B 703 ASN cc_start: 0.8336 (t0) cc_final: 0.8108 (t0) REVERT: B 705 VAL cc_start: 0.8622 (t) cc_final: 0.8379 (p) REVERT: B 725 GLU cc_start: 0.7464 (tt0) cc_final: 0.6544 (tt0) REVERT: B 737 ASP cc_start: 0.7651 (t0) cc_final: 0.7290 (t70) REVERT: B 776 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7799 (ttpp) REVERT: B 797 PHE cc_start: 0.7662 (m-10) cc_final: 0.7343 (m-80) REVERT: B 850 ILE cc_start: 0.8262 (mm) cc_final: 0.7939 (tp) REVERT: B 851 CYS cc_start: 0.8067 (t) cc_final: 0.7602 (m) REVERT: B 854 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8157 (tttp) REVERT: B 921 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8480 (mmmm) REVERT: B 933 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7819 (mtmm) REVERT: B 950 ASP cc_start: 0.7393 (t70) cc_final: 0.6753 (t70) REVERT: B 961 THR cc_start: 0.8808 (m) cc_final: 0.8577 (m) REVERT: B 969 LYS cc_start: 0.7858 (pttm) cc_final: 0.7566 (pttm) REVERT: B 994 ASP cc_start: 0.7560 (m-30) cc_final: 0.7024 (m-30) REVERT: B 997 ILE cc_start: 0.8332 (tt) cc_final: 0.8025 (pt) REVERT: B 1002 GLN cc_start: 0.7960 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 1003 SER cc_start: 0.8676 (m) cc_final: 0.8037 (t) REVERT: B 1005 GLN cc_start: 0.8298 (tp40) cc_final: 0.8072 (tp40) REVERT: B 1010 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: B 1028 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8091 (mttt) REVERT: B 1041 ASP cc_start: 0.7202 (t70) cc_final: 0.6655 (t0) REVERT: B 1050 MET cc_start: 0.7282 (mtp) cc_final: 0.6951 (mtp) REVERT: B 1061 VAL cc_start: 0.8788 (t) cc_final: 0.8411 (p) REVERT: B 1072 GLU cc_start: 0.7923 (pm20) cc_final: 0.7602 (pm20) REVERT: B 1081 ILE cc_start: 0.8362 (pt) cc_final: 0.8121 (mt) REVERT: B 1086 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8123 (ptpp) REVERT: B 1097 SER cc_start: 0.8486 (t) cc_final: 0.7886 (p) REVERT: C 41 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7179 (mtpp) REVERT: C 105 ILE cc_start: 0.8321 (mp) cc_final: 0.7664 (pt) REVERT: C 188 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.7024 (mtp85) REVERT: C 192 PHE cc_start: 0.8368 (m-80) cc_final: 0.8043 (m-80) REVERT: C 199 PHE cc_start: 0.7785 (t80) cc_final: 0.7349 (t80) REVERT: C 201 ILE cc_start: 0.8807 (mt) cc_final: 0.8508 (mp) REVERT: C 224 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6794 (mm-30) REVERT: C 271 GLN cc_start: 0.7331 (mt0) cc_final: 0.7074 (mt0) REVERT: C 297 SER cc_start: 0.7902 (m) cc_final: 0.6995 (p) REVERT: C 326 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6696 (pt) REVERT: C 531 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8304 (p) REVERT: C 542 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7359 (t0) REVERT: C 563 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7016 (mm-40) REVERT: C 576 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6933 (m) REVERT: C 588 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 619 GLU cc_start: 0.6945 (mp0) cc_final: 0.6352 (mp0) REVERT: C 644 GLN cc_start: 0.7702 (tp40) cc_final: 0.6944 (tp40) REVERT: C 705 VAL cc_start: 0.8274 (t) cc_final: 0.8015 (m) REVERT: C 725 GLU cc_start: 0.7258 (tt0) cc_final: 0.7029 (tt0) REVERT: C 764 LYS cc_start: 0.8243 (tttm) cc_final: 0.7817 (ttpp) REVERT: C 765 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7689 (ttp-110) REVERT: C 768 THR cc_start: 0.8625 (m) cc_final: 0.8425 (p) REVERT: C 776 LYS cc_start: 0.8456 (tptp) cc_final: 0.8161 (tptp) REVERT: C 801 ASN cc_start: 0.5586 (t0) cc_final: 0.5197 (t0) REVERT: C 811 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8142 (ttmm) REVERT: C 825 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8154 (ttmm) REVERT: C 854 LYS cc_start: 0.8396 (tmmt) cc_final: 0.8036 (tptp) REVERT: C 867 ASP cc_start: 0.7711 (m-30) cc_final: 0.7498 (m-30) REVERT: C 902 MET cc_start: 0.8022 (mtp) cc_final: 0.7688 (mmm) REVERT: C 922 LEU cc_start: 0.8978 (tp) cc_final: 0.8745 (tt) REVERT: C 945 LEU cc_start: 0.8480 (mm) cc_final: 0.8220 (mt) REVERT: C 998 THR cc_start: 0.8320 (t) cc_final: 0.8102 (p) REVERT: C 1014 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7639 (ttm-80) REVERT: C 1029 MET cc_start: 0.8285 (ttm) cc_final: 0.8077 (tpp) REVERT: C 1081 ILE cc_start: 0.8562 (pt) cc_final: 0.8357 (mt) REVERT: C 1125 ASN cc_start: 0.7450 (p0) cc_final: 0.7193 (p0) REVERT: D 84 MET cc_start: 0.3520 (mpp) cc_final: 0.3290 (mpp) REVERT: F 55 TRP cc_start: 0.6294 (p-90) cc_final: 0.6035 (p-90) REVERT: H 54 TYR cc_start: 0.7125 (m-80) cc_final: 0.6880 (m-80) REVERT: H 60 ARG cc_start: 0.5446 (mmm160) cc_final: 0.4890 (mmt90) REVERT: H 78 ASN cc_start: 0.5588 (m110) cc_final: 0.5111 (t0) outliers start: 157 outliers final: 75 residues processed: 865 average time/residue: 0.1914 time to fit residues: 263.3050 Evaluate side-chains 803 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 709 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 299 optimal weight: 0.8980 chunk 327 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 334 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 275 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 chunk 254 optimal weight: 0.0970 chunk 167 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A1010 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 762 GLN C 955 ASN C 957 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS E 40 GLN G 33 ASN I 39 GLN I 44 GLN I 71 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.173606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129746 restraints weight = 56441.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133855 restraints weight = 24800.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136343 restraints weight = 13821.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137885 restraints weight = 9212.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138773 restraints weight = 7082.062| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29905 Z= 0.122 Angle : 0.592 13.286 40768 Z= 0.298 Chirality : 0.044 0.352 4657 Planarity : 0.004 0.068 5239 Dihedral : 5.381 60.651 4132 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.63 % Allowed : 15.29 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.95 (0.13), residues: 3713 helix: 0.54 (0.21), residues: 653 sheet: -1.84 (0.17), residues: 783 loop : -2.94 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.031 0.001 TYR A 495 PHE 0.036 0.001 PHE C 106 TRP 0.027 0.001 TRP D 110 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (29860) covalent geometry : angle 0.58494 (40678) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.99083 ( 90) hydrogen bonds : bond 0.04093 ( 849) hydrogen bonds : angle 5.70444 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 727 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7961 (mtpt) REVERT: A 53 ASP cc_start: 0.7664 (p0) cc_final: 0.7462 (p0) REVERT: A 87 ASN cc_start: 0.7240 (p0) cc_final: 0.7023 (p0) REVERT: A 111 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4962 (p0) REVERT: A 190 PHE cc_start: 0.7361 (m-80) cc_final: 0.7053 (m-80) REVERT: A 233 ILE cc_start: 0.8412 (tt) cc_final: 0.8181 (mp) REVERT: A 281 GLU cc_start: 0.7368 (pp20) cc_final: 0.7000 (pp20) REVERT: A 297 SER cc_start: 0.8371 (m) cc_final: 0.8068 (p) REVERT: A 326 ILE cc_start: 0.7897 (mp) cc_final: 0.7622 (mt) REVERT: A 478 LYS cc_start: -0.0633 (OUTLIER) cc_final: -0.1389 (ptmt) REVERT: A 535 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8137 (mttm) REVERT: A 542 ASN cc_start: 0.8210 (t0) cc_final: 0.7852 (m-40) REVERT: A 592 PHE cc_start: 0.7842 (p90) cc_final: 0.7174 (p90) REVERT: A 599 THR cc_start: 0.8367 (m) cc_final: 0.8165 (t) REVERT: A 618 THR cc_start: 0.8370 (p) cc_final: 0.8113 (p) REVERT: A 674 TYR cc_start: 0.8197 (t80) cc_final: 0.7848 (t80) REVERT: A 697 MET cc_start: 0.7304 (ttp) cc_final: 0.6987 (mtp) REVERT: A 698 SER cc_start: 0.8596 (t) cc_final: 0.8019 (p) REVERT: A 745 ASP cc_start: 0.6527 (m-30) cc_final: 0.6289 (t0) REVERT: A 751 ASN cc_start: 0.7971 (m-40) cc_final: 0.7707 (m-40) REVERT: A 754 LEU cc_start: 0.8453 (mt) cc_final: 0.8193 (mt) REVERT: A 759 PHE cc_start: 0.6829 (m-80) cc_final: 0.6487 (m-80) REVERT: A 763 LEU cc_start: 0.8393 (mt) cc_final: 0.8170 (mt) REVERT: A 773 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6081 (tm-30) REVERT: A 803 SER cc_start: 0.8731 (m) cc_final: 0.8193 (p) REVERT: A 816 SER cc_start: 0.7815 (p) cc_final: 0.7573 (t) REVERT: A 825 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8188 (mmtm) REVERT: A 854 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8031 (tttt) REVERT: A 868 GLU cc_start: 0.7376 (tp30) cc_final: 0.7064 (tp30) REVERT: A 869 MET cc_start: 0.8199 (mtt) cc_final: 0.7965 (mtm) REVERT: A 878 LEU cc_start: 0.8260 (mt) cc_final: 0.7901 (mp) REVERT: A 921 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8133 (mmmm) REVERT: A 925 ASN cc_start: 0.8477 (m-40) cc_final: 0.7921 (m-40) REVERT: A 933 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7641 (mtmm) REVERT: A 945 LEU cc_start: 0.8660 (mm) cc_final: 0.8397 (mp) REVERT: A 949 GLN cc_start: 0.8292 (mm110) cc_final: 0.7454 (mm-40) REVERT: A 953 ASN cc_start: 0.8292 (m-40) cc_final: 0.7909 (m110) REVERT: A 960 ASN cc_start: 0.8039 (m110) cc_final: 0.7720 (m-40) REVERT: A 979 ASP cc_start: 0.7610 (t0) cc_final: 0.7368 (t0) REVERT: A 983 ARG cc_start: 0.8385 (mtm180) cc_final: 0.7953 (mtp85) REVERT: A 994 ASP cc_start: 0.7096 (m-30) cc_final: 0.6844 (m-30) REVERT: A 1028 LYS cc_start: 0.8490 (mttt) cc_final: 0.8128 (mttt) REVERT: A 1029 MET cc_start: 0.8272 (tpp) cc_final: 0.7596 (ttm) REVERT: A 1038 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8256 (mttt) REVERT: A 1050 MET cc_start: 0.7081 (ttm) cc_final: 0.6583 (mtp) REVERT: A 1117 THR cc_start: 0.8451 (p) cc_final: 0.8176 (t) REVERT: A 1129 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 1141 LEU cc_start: 0.8235 (tp) cc_final: 0.7920 (tt) REVERT: B 60 SER cc_start: 0.8548 (t) cc_final: 0.8298 (t) REVERT: B 104 TRP cc_start: 0.7117 (m-90) cc_final: 0.6666 (m-90) REVERT: B 106 PHE cc_start: 0.7339 (m-80) cc_final: 0.6929 (m-80) REVERT: B 200 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7617 (mmmm) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7610 (pm20) REVERT: B 267 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8144 (p) REVERT: B 278 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8392 (ttmt) REVERT: B 286 THR cc_start: 0.7616 (p) cc_final: 0.7315 (p) REVERT: B 307 THR cc_start: 0.7257 (m) cc_final: 0.7013 (p) REVERT: B 329 PHE cc_start: 0.7722 (m-10) cc_final: 0.7504 (m-80) REVERT: B 343 ASN cc_start: 0.6528 (t0) cc_final: 0.5984 (t0) REVERT: B 353 TRP cc_start: 0.8356 (p-90) cc_final: 0.8008 (p-90) REVERT: B 354 ASN cc_start: 0.7859 (m110) cc_final: 0.7319 (m110) REVERT: B 380 TYR cc_start: 0.6747 (m-80) cc_final: 0.6291 (m-80) REVERT: B 394 ASN cc_start: 0.7434 (t0) cc_final: 0.6904 (p0) REVERT: B 429 PHE cc_start: 0.8303 (t80) cc_final: 0.7904 (t80) REVERT: B 515 PHE cc_start: 0.7429 (m-80) cc_final: 0.7202 (m-80) REVERT: B 517 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7324 (tt) REVERT: B 547 LYS cc_start: 0.8422 (tptp) cc_final: 0.8169 (tttm) REVERT: B 564 GLN cc_start: 0.8128 (pm20) cc_final: 0.7555 (pm20) REVERT: B 651 ILE cc_start: 0.8328 (mt) cc_final: 0.8002 (mm) REVERT: B 659 SER cc_start: 0.8716 (m) cc_final: 0.8181 (p) REVERT: B 705 VAL cc_start: 0.8656 (t) cc_final: 0.8420 (p) REVERT: B 737 ASP cc_start: 0.7507 (t0) cc_final: 0.7191 (t70) REVERT: B 773 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: B 776 LYS cc_start: 0.8244 (tmmt) cc_final: 0.7830 (ttpp) REVERT: B 823 PHE cc_start: 0.7121 (m-10) cc_final: 0.6877 (m-10) REVERT: B 850 ILE cc_start: 0.8322 (mm) cc_final: 0.7995 (tp) REVERT: B 851 CYS cc_start: 0.8147 (t) cc_final: 0.7610 (m) REVERT: B 854 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7990 (tttp) REVERT: B 911 VAL cc_start: 0.8427 (t) cc_final: 0.8157 (m) REVERT: B 913 GLN cc_start: 0.7878 (pt0) cc_final: 0.7631 (pt0) REVERT: B 921 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8462 (mmmm) REVERT: B 933 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7902 (mtmm) REVERT: B 950 ASP cc_start: 0.7495 (t70) cc_final: 0.6858 (t70) REVERT: B 969 LYS cc_start: 0.7888 (pttm) cc_final: 0.7590 (pttm) REVERT: B 997 ILE cc_start: 0.8341 (tt) cc_final: 0.7933 (pt) REVERT: B 1002 GLN cc_start: 0.7869 (tp40) cc_final: 0.7357 (tm-30) REVERT: B 1003 SER cc_start: 0.8768 (m) cc_final: 0.8021 (t) REVERT: B 1010 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: B 1061 VAL cc_start: 0.8760 (t) cc_final: 0.8343 (p) REVERT: B 1086 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (ptpp) REVERT: B 1097 SER cc_start: 0.8488 (t) cc_final: 0.7894 (p) REVERT: C 41 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7310 (mttt) REVERT: C 53 ASP cc_start: 0.7437 (t0) cc_final: 0.7055 (m-30) REVERT: C 199 PHE cc_start: 0.7806 (t80) cc_final: 0.7345 (t80) REVERT: C 201 ILE cc_start: 0.8852 (mt) cc_final: 0.8622 (mp) REVERT: C 224 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6764 (mm-30) REVERT: C 297 SER cc_start: 0.7918 (m) cc_final: 0.7181 (p) REVERT: C 301 CYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5518 (m) REVERT: C 308 VAL cc_start: 0.8558 (t) cc_final: 0.8253 (p) REVERT: C 324 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 326 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6347 (pt) REVERT: C 332 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6277 (pp) REVERT: C 436 TRP cc_start: 0.7425 (p-90) cc_final: 0.6862 (p-90) REVERT: C 542 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7252 (t0) REVERT: C 563 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6972 (mm-40) REVERT: C 588 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7754 (p) REVERT: C 619 GLU cc_start: 0.6961 (mp0) cc_final: 0.6389 (mp0) REVERT: C 644 GLN cc_start: 0.7629 (tp40) cc_final: 0.6973 (tp40) REVERT: C 705 VAL cc_start: 0.8284 (t) cc_final: 0.8013 (m) REVERT: C 725 GLU cc_start: 0.7259 (tt0) cc_final: 0.7039 (tt0) REVERT: C 740 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7296 (tpp) REVERT: C 759 PHE cc_start: 0.6953 (t80) cc_final: 0.6113 (t80) REVERT: C 764 LYS cc_start: 0.8247 (tttm) cc_final: 0.7911 (ttpp) REVERT: C 776 LYS cc_start: 0.8448 (tptp) cc_final: 0.8064 (tptp) REVERT: C 801 ASN cc_start: 0.5566 (t0) cc_final: 0.5353 (t0) REVERT: C 825 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8152 (ttmm) REVERT: C 854 LYS cc_start: 0.8285 (tmmt) cc_final: 0.7848 (tptp) REVERT: C 904 TYR cc_start: 0.7854 (m-10) cc_final: 0.7648 (m-10) REVERT: C 918 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 921 LYS cc_start: 0.8466 (tptp) cc_final: 0.8202 (tptp) REVERT: C 922 LEU cc_start: 0.8926 (tp) cc_final: 0.8700 (tt) REVERT: C 945 LEU cc_start: 0.8499 (mm) cc_final: 0.8238 (mt) REVERT: C 957 GLN cc_start: 0.8078 (tt0) cc_final: 0.7853 (tt0) REVERT: C 964 LYS cc_start: 0.8604 (tppt) cc_final: 0.8205 (ttmm) REVERT: C 990 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7226 (mm-30) REVERT: C 1005 GLN cc_start: 0.8137 (tp40) cc_final: 0.6994 (tp-100) REVERT: C 1014 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7417 (ttm110) REVERT: C 1072 GLU cc_start: 0.8261 (pm20) cc_final: 0.7924 (pm20) REVERT: C 1081 ILE cc_start: 0.8566 (pt) cc_final: 0.8355 (mt) REVERT: C 1101 HIS cc_start: 0.8584 (m-70) cc_final: 0.8166 (m90) REVERT: E 39 GLN cc_start: 0.4024 (mm110) cc_final: 0.3013 (mm110) REVERT: H 60 ARG cc_start: 0.5476 (mmm160) cc_final: 0.4984 (mmt90) outliers start: 150 outliers final: 86 residues processed: 831 average time/residue: 0.1914 time to fit residues: 252.8111 Evaluate side-chains 796 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 693 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 222 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 4 optimal weight: 0.0770 chunk 9 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 122 ASN C 913 GLN C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.172645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128485 restraints weight = 56214.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.132559 restraints weight = 24896.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135031 restraints weight = 13949.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136563 restraints weight = 9321.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137450 restraints weight = 7156.057| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29905 Z= 0.119 Angle : 0.581 13.006 40768 Z= 0.293 Chirality : 0.044 0.265 4657 Planarity : 0.004 0.049 5239 Dihedral : 5.237 61.382 4122 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.63 % Allowed : 16.44 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.66 (0.13), residues: 3713 helix: 0.81 (0.21), residues: 655 sheet: -1.64 (0.17), residues: 795 loop : -2.76 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 99 TYR 0.027 0.001 TYR A 495 PHE 0.032 0.001 PHE C 106 TRP 0.028 0.001 TRP D 110 HIS 0.013 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (29860) covalent geometry : angle 0.57703 (40678) SS BOND : bond 0.00421 ( 45) SS BOND : angle 1.60262 ( 90) hydrogen bonds : bond 0.03831 ( 849) hydrogen bonds : angle 5.40685 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 704 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8008 (mtpt) REVERT: A 111 ASP cc_start: 0.5300 (OUTLIER) cc_final: 0.5006 (p0) REVERT: A 188 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6479 (mmt180) REVERT: A 233 ILE cc_start: 0.8340 (tt) cc_final: 0.8126 (mp) REVERT: A 276 LEU cc_start: 0.8244 (tp) cc_final: 0.7954 (tp) REVERT: A 281 GLU cc_start: 0.7355 (pp20) cc_final: 0.6991 (pp20) REVERT: A 297 SER cc_start: 0.8426 (m) cc_final: 0.8060 (p) REVERT: A 326 ILE cc_start: 0.7877 (mp) cc_final: 0.7600 (mt) REVERT: A 478 LYS cc_start: -0.0684 (OUTLIER) cc_final: -0.1222 (ptmt) REVERT: A 535 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8065 (mttp) REVERT: A 542 ASN cc_start: 0.8225 (t0) cc_final: 0.7838 (m-40) REVERT: A 592 PHE cc_start: 0.7774 (p90) cc_final: 0.7260 (p90) REVERT: A 599 THR cc_start: 0.8328 (m) cc_final: 0.8118 (t) REVERT: A 615 VAL cc_start: 0.8481 (t) cc_final: 0.8256 (m) REVERT: A 654 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7032 (mm-30) REVERT: A 674 TYR cc_start: 0.8169 (t80) cc_final: 0.7869 (t80) REVERT: A 697 MET cc_start: 0.7347 (ttp) cc_final: 0.6881 (mtp) REVERT: A 698 SER cc_start: 0.8490 (t) cc_final: 0.7929 (p) REVERT: A 745 ASP cc_start: 0.6578 (m-30) cc_final: 0.6340 (t0) REVERT: A 759 PHE cc_start: 0.6915 (m-80) cc_final: 0.6486 (m-80) REVERT: A 763 LEU cc_start: 0.8411 (mt) cc_final: 0.8157 (mt) REVERT: A 773 GLU cc_start: 0.6719 (tm-30) cc_final: 0.5765 (tm-30) REVERT: A 803 SER cc_start: 0.8718 (m) cc_final: 0.8198 (p) REVERT: A 825 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8238 (mmtm) REVERT: A 854 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7983 (tmtt) REVERT: A 868 GLU cc_start: 0.7406 (tp30) cc_final: 0.7043 (tp30) REVERT: A 869 MET cc_start: 0.8200 (mtt) cc_final: 0.7948 (mtm) REVERT: A 878 LEU cc_start: 0.8254 (mt) cc_final: 0.7903 (mp) REVERT: A 921 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8138 (mmmm) REVERT: A 925 ASN cc_start: 0.8469 (m-40) cc_final: 0.7910 (m-40) REVERT: A 933 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7619 (mtmm) REVERT: A 949 GLN cc_start: 0.8306 (mm110) cc_final: 0.7444 (mm-40) REVERT: A 953 ASN cc_start: 0.8323 (m-40) cc_final: 0.7862 (m110) REVERT: A 957 GLN cc_start: 0.8105 (tt0) cc_final: 0.7895 (tt0) REVERT: A 960 ASN cc_start: 0.8060 (m110) cc_final: 0.7751 (m-40) REVERT: A 979 ASP cc_start: 0.7653 (t0) cc_final: 0.7237 (t0) REVERT: A 994 ASP cc_start: 0.7157 (m-30) cc_final: 0.6669 (m-30) REVERT: A 1002 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 1028 LYS cc_start: 0.8498 (mttt) cc_final: 0.8141 (mttt) REVERT: A 1029 MET cc_start: 0.8239 (tpp) cc_final: 0.7659 (ttm) REVERT: A 1038 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8253 (mttt) REVERT: A 1050 MET cc_start: 0.7049 (ttm) cc_final: 0.6399 (mtp) REVERT: A 1117 THR cc_start: 0.8452 (p) cc_final: 0.8163 (t) REVERT: A 1125 ASN cc_start: 0.7925 (p0) cc_final: 0.7713 (p0) REVERT: A 1129 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8386 (m) REVERT: A 1141 LEU cc_start: 0.8260 (tp) cc_final: 0.7952 (tt) REVERT: B 60 SER cc_start: 0.8555 (t) cc_final: 0.8292 (t) REVERT: B 104 TRP cc_start: 0.7294 (m-90) cc_final: 0.6928 (m-90) REVERT: B 105 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (mm) REVERT: B 106 PHE cc_start: 0.7429 (m-80) cc_final: 0.6984 (m-80) REVERT: B 170 TYR cc_start: 0.8057 (t80) cc_final: 0.7767 (t80) REVERT: B 200 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7551 (mmmm) REVERT: B 224 GLU cc_start: 0.8040 (pm20) cc_final: 0.7634 (pm20) REVERT: B 267 VAL cc_start: 0.8511 (m) cc_final: 0.8295 (p) REVERT: B 278 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8318 (ttmt) REVERT: B 286 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7307 (p) REVERT: B 287 ASP cc_start: 0.7065 (p0) cc_final: 0.6834 (p0) REVERT: B 343 ASN cc_start: 0.6607 (t0) cc_final: 0.6046 (t0) REVERT: B 353 TRP cc_start: 0.8377 (p-90) cc_final: 0.8089 (p-90) REVERT: B 354 ASN cc_start: 0.7859 (m110) cc_final: 0.7327 (m110) REVERT: B 357 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7266 (mtp85) REVERT: B 380 TYR cc_start: 0.6744 (m-80) cc_final: 0.6269 (m-80) REVERT: B 394 ASN cc_start: 0.7466 (t0) cc_final: 0.6935 (p0) REVERT: B 408 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7242 (ppp-140) REVERT: B 429 PHE cc_start: 0.8337 (t80) cc_final: 0.7919 (t80) REVERT: B 512 VAL cc_start: 0.8785 (m) cc_final: 0.8417 (p) REVERT: B 515 PHE cc_start: 0.7501 (m-80) cc_final: 0.7241 (m-80) REVERT: B 517 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 547 LYS cc_start: 0.8353 (tptp) cc_final: 0.8127 (tttm) REVERT: B 564 GLN cc_start: 0.8110 (pm20) cc_final: 0.7390 (pm20) REVERT: B 616 ASN cc_start: 0.5949 (t0) cc_final: 0.5721 (t0) REVERT: B 651 ILE cc_start: 0.8334 (mt) cc_final: 0.8060 (mm) REVERT: B 659 SER cc_start: 0.8693 (m) cc_final: 0.8165 (p) REVERT: B 725 GLU cc_start: 0.7653 (tt0) cc_final: 0.7014 (tp30) REVERT: B 759 PHE cc_start: 0.7329 (t80) cc_final: 0.6752 (t80) REVERT: B 773 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: B 776 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7843 (ttpp) REVERT: B 823 PHE cc_start: 0.7109 (m-10) cc_final: 0.6778 (m-10) REVERT: B 850 ILE cc_start: 0.8312 (mm) cc_final: 0.7973 (tp) REVERT: B 851 CYS cc_start: 0.8173 (t) cc_final: 0.7577 (m) REVERT: B 854 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7964 (tttp) REVERT: B 856 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8432 (mmmm) REVERT: B 911 VAL cc_start: 0.8436 (t) cc_final: 0.8158 (m) REVERT: B 913 GLN cc_start: 0.7880 (pt0) cc_final: 0.7599 (pt0) REVERT: B 921 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8450 (mmmm) REVERT: B 933 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7888 (mtmm) REVERT: B 950 ASP cc_start: 0.7532 (t70) cc_final: 0.6889 (t70) REVERT: B 969 LYS cc_start: 0.7900 (pttm) cc_final: 0.7614 (pttm) REVERT: B 1002 GLN cc_start: 0.7829 (tp40) cc_final: 0.7383 (tm-30) REVERT: B 1003 SER cc_start: 0.8757 (m) cc_final: 0.8069 (t) REVERT: B 1005 GLN cc_start: 0.8329 (tp40) cc_final: 0.7683 (tp40) REVERT: B 1010 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: B 1028 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8264 (mttt) REVERT: B 1061 VAL cc_start: 0.8756 (t) cc_final: 0.8356 (p) REVERT: B 1086 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (ptpp) REVERT: B 1097 SER cc_start: 0.8515 (t) cc_final: 0.7888 (p) REVERT: C 41 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7210 (mtpp) REVERT: C 53 ASP cc_start: 0.7288 (t0) cc_final: 0.6973 (m-30) REVERT: C 199 PHE cc_start: 0.7827 (t80) cc_final: 0.7394 (t80) REVERT: C 201 ILE cc_start: 0.8855 (mt) cc_final: 0.8576 (mp) REVERT: C 224 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6758 (mm-30) REVERT: C 297 SER cc_start: 0.7849 (m) cc_final: 0.7037 (p) REVERT: C 301 CYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5556 (m) REVERT: C 308 VAL cc_start: 0.8552 (t) cc_final: 0.8230 (p) REVERT: C 324 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 332 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6284 (pp) REVERT: C 436 TRP cc_start: 0.7490 (p-90) cc_final: 0.6935 (p-90) REVERT: C 542 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7252 (t0) REVERT: C 563 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6944 (mm-40) REVERT: C 588 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 619 GLU cc_start: 0.6988 (mp0) cc_final: 0.6446 (mp0) REVERT: C 644 GLN cc_start: 0.7659 (tp40) cc_final: 0.6999 (tp40) REVERT: C 674 TYR cc_start: 0.7924 (t80) cc_final: 0.7655 (t80) REVERT: C 705 VAL cc_start: 0.8275 (t) cc_final: 0.7996 (m) REVERT: C 725 GLU cc_start: 0.7268 (tt0) cc_final: 0.7031 (tt0) REVERT: C 740 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7200 (tpp) REVERT: C 759 PHE cc_start: 0.6815 (t80) cc_final: 0.6565 (t80) REVERT: C 764 LYS cc_start: 0.8257 (tttm) cc_final: 0.7781 (ttpp) REVERT: C 765 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.7662 (ttm-80) REVERT: C 768 THR cc_start: 0.8579 (m) cc_final: 0.8329 (p) REVERT: C 776 LYS cc_start: 0.8428 (tptp) cc_final: 0.8030 (tptp) REVERT: C 801 ASN cc_start: 0.5545 (t0) cc_final: 0.5246 (t0) REVERT: C 825 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8122 (ttmm) REVERT: C 854 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7813 (tptp) REVERT: C 904 TYR cc_start: 0.7878 (m-10) cc_final: 0.7650 (m-10) REVERT: C 918 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6966 (tt0) REVERT: C 921 LYS cc_start: 0.8426 (tptp) cc_final: 0.8182 (tptp) REVERT: C 964 LYS cc_start: 0.8627 (tppt) cc_final: 0.8173 (ttmm) REVERT: C 990 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 1014 ARG cc_start: 0.7911 (ttm110) cc_final: 0.7439 (ttm110) REVERT: C 1072 GLU cc_start: 0.8280 (pm20) cc_final: 0.7922 (pm20) REVERT: C 1101 HIS cc_start: 0.8582 (m-70) cc_final: 0.8181 (m90) REVERT: D 4 LEU cc_start: 0.8262 (mt) cc_final: 0.7404 (tt) REVERT: E 39 GLN cc_start: 0.4359 (mm110) cc_final: 0.3994 (mm110) outliers start: 150 outliers final: 92 residues processed: 807 average time/residue: 0.1905 time to fit residues: 244.2219 Evaluate side-chains 785 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 674 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 36 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 307 optimal weight: 0.0570 chunk 266 optimal weight: 0.0020 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 417 ASN A 613 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 762 GLN A 774 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 542 ASN C 122 ASN C 913 GLN C 957 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.172866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128691 restraints weight = 56002.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132737 restraints weight = 24864.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135197 restraints weight = 13983.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136736 restraints weight = 9354.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137642 restraints weight = 7176.426| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29905 Z= 0.113 Angle : 0.578 12.801 40768 Z= 0.290 Chirality : 0.044 0.225 4657 Planarity : 0.004 0.048 5239 Dihedral : 5.176 61.151 4117 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.56 % Allowed : 17.27 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.46 (0.13), residues: 3713 helix: 0.93 (0.21), residues: 662 sheet: -1.55 (0.17), residues: 788 loop : -2.60 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 99 TYR 0.018 0.001 TYR B 707 PHE 0.028 0.001 PHE C 106 TRP 0.038 0.001 TRP D 110 HIS 0.013 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00253 (29860) covalent geometry : angle 0.57375 (40678) SS BOND : bond 0.00474 ( 45) SS BOND : angle 1.60398 ( 90) hydrogen bonds : bond 0.03685 ( 849) hydrogen bonds : angle 5.24598 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 669 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8000 (mtpt) REVERT: A 188 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6495 (mmt180) REVERT: A 190 PHE cc_start: 0.7415 (m-80) cc_final: 0.7186 (m-10) REVERT: A 233 ILE cc_start: 0.8239 (tt) cc_final: 0.7872 (pt) REVERT: A 276 LEU cc_start: 0.8292 (tp) cc_final: 0.8036 (tp) REVERT: A 281 GLU cc_start: 0.7346 (pp20) cc_final: 0.7031 (pp20) REVERT: A 290 ASP cc_start: 0.7982 (t0) cc_final: 0.7735 (t0) REVERT: A 297 SER cc_start: 0.8331 (m) cc_final: 0.8036 (p) REVERT: A 436 TRP cc_start: 0.6956 (p-90) cc_final: 0.6608 (p90) REVERT: A 542 ASN cc_start: 0.8200 (t0) cc_final: 0.7950 (t0) REVERT: A 547 LYS cc_start: 0.8336 (mttp) cc_final: 0.8042 (mppt) REVERT: A 592 PHE cc_start: 0.7723 (p90) cc_final: 0.7351 (p90) REVERT: A 599 THR cc_start: 0.8324 (m) cc_final: 0.8104 (t) REVERT: A 660 TYR cc_start: 0.7887 (m-10) cc_final: 0.7640 (m-10) REVERT: A 674 TYR cc_start: 0.8200 (t80) cc_final: 0.7802 (t80) REVERT: A 697 MET cc_start: 0.7353 (ttp) cc_final: 0.7013 (mtp) REVERT: A 698 SER cc_start: 0.8467 (t) cc_final: 0.7894 (p) REVERT: A 710 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7272 (p0) REVERT: A 737 ASP cc_start: 0.7535 (t70) cc_final: 0.7314 (t70) REVERT: A 759 PHE cc_start: 0.6898 (m-80) cc_final: 0.6469 (m-80) REVERT: A 763 LEU cc_start: 0.8421 (mt) cc_final: 0.8192 (mt) REVERT: A 773 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6023 (tm-30) REVERT: A 803 SER cc_start: 0.8720 (m) cc_final: 0.8255 (p) REVERT: A 825 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8194 (mmtt) REVERT: A 854 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7986 (tttt) REVERT: A 868 GLU cc_start: 0.7376 (tp30) cc_final: 0.7062 (tp30) REVERT: A 869 MET cc_start: 0.8200 (mtt) cc_final: 0.7959 (mtm) REVERT: A 902 MET cc_start: 0.8016 (tpp) cc_final: 0.7679 (tpp) REVERT: A 921 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8132 (mmmm) REVERT: A 925 ASN cc_start: 0.8448 (m-40) cc_final: 0.7885 (m-40) REVERT: A 933 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7649 (mtmm) REVERT: A 949 GLN cc_start: 0.8357 (mm110) cc_final: 0.7447 (mm-40) REVERT: A 953 ASN cc_start: 0.8313 (m-40) cc_final: 0.7854 (m110) REVERT: A 960 ASN cc_start: 0.8092 (m110) cc_final: 0.7826 (m-40) REVERT: A 979 ASP cc_start: 0.7499 (t0) cc_final: 0.7271 (t0) REVERT: A 1029 MET cc_start: 0.8230 (tpp) cc_final: 0.7643 (ttm) REVERT: A 1038 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8252 (mttt) REVERT: A 1050 MET cc_start: 0.6849 (ttm) cc_final: 0.6568 (ttm) REVERT: A 1117 THR cc_start: 0.8474 (p) cc_final: 0.8186 (t) REVERT: A 1141 LEU cc_start: 0.8255 (tp) cc_final: 0.7958 (tt) REVERT: B 105 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7494 (mm) REVERT: B 106 PHE cc_start: 0.7429 (m-80) cc_final: 0.7037 (m-80) REVERT: B 224 GLU cc_start: 0.8041 (pm20) cc_final: 0.7629 (pm20) REVERT: B 278 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8341 (ttmt) REVERT: B 343 ASN cc_start: 0.6581 (t0) cc_final: 0.6274 (t0) REVERT: B 353 TRP cc_start: 0.8404 (p-90) cc_final: 0.8085 (p-90) REVERT: B 354 ASN cc_start: 0.7853 (m110) cc_final: 0.7337 (m110) REVERT: B 380 TYR cc_start: 0.6754 (m-80) cc_final: 0.6393 (m-80) REVERT: B 392 PHE cc_start: 0.6979 (m-80) cc_final: 0.6702 (m-80) REVERT: B 394 ASN cc_start: 0.7453 (t0) cc_final: 0.7015 (p0) REVERT: B 408 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7521 (ptm-80) REVERT: B 515 PHE cc_start: 0.7494 (m-80) cc_final: 0.7253 (m-80) REVERT: B 528 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6378 (ptpp) REVERT: B 542 ASN cc_start: 0.7963 (t0) cc_final: 0.7756 (t0) REVERT: B 547 LYS cc_start: 0.8343 (tptp) cc_final: 0.8125 (tttm) REVERT: B 564 GLN cc_start: 0.7997 (pm20) cc_final: 0.7230 (pm20) REVERT: B 651 ILE cc_start: 0.8333 (mt) cc_final: 0.8078 (mm) REVERT: B 659 SER cc_start: 0.8638 (m) cc_final: 0.8215 (p) REVERT: B 725 GLU cc_start: 0.7648 (tt0) cc_final: 0.6989 (tp30) REVERT: B 737 ASP cc_start: 0.7463 (t0) cc_final: 0.7213 (t0) REVERT: B 759 PHE cc_start: 0.7499 (t80) cc_final: 0.6350 (t80) REVERT: B 773 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: B 776 LYS cc_start: 0.8275 (tmmt) cc_final: 0.7876 (ttpt) REVERT: B 850 ILE cc_start: 0.8317 (mm) cc_final: 0.7977 (tp) REVERT: B 851 CYS cc_start: 0.8195 (t) cc_final: 0.7561 (m) REVERT: B 854 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7936 (tttp) REVERT: B 911 VAL cc_start: 0.8433 (t) cc_final: 0.8150 (m) REVERT: B 913 GLN cc_start: 0.7842 (pt0) cc_final: 0.7431 (pm20) REVERT: B 921 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8422 (mmmm) REVERT: B 933 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7936 (ttmm) REVERT: B 950 ASP cc_start: 0.7561 (t70) cc_final: 0.6902 (t70) REVERT: B 969 LYS cc_start: 0.7913 (pttm) cc_final: 0.7673 (pttm) REVERT: B 1002 GLN cc_start: 0.7863 (tp40) cc_final: 0.7430 (tm-30) REVERT: B 1003 SER cc_start: 0.8756 (m) cc_final: 0.8036 (t) REVERT: B 1005 GLN cc_start: 0.8361 (tp40) cc_final: 0.7668 (tp40) REVERT: B 1028 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8270 (mttt) REVERT: B 1061 VAL cc_start: 0.8750 (t) cc_final: 0.8354 (p) REVERT: B 1086 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8060 (ptpp) REVERT: B 1097 SER cc_start: 0.8510 (t) cc_final: 0.7906 (p) REVERT: C 40 ASP cc_start: 0.7708 (t70) cc_final: 0.7486 (m-30) REVERT: C 41 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7068 (mtpp) REVERT: C 53 ASP cc_start: 0.7334 (t0) cc_final: 0.6951 (m-30) REVERT: C 65 PHE cc_start: 0.7021 (m-80) cc_final: 0.6682 (m-80) REVERT: C 199 PHE cc_start: 0.7837 (t80) cc_final: 0.7391 (t80) REVERT: C 201 ILE cc_start: 0.8859 (mt) cc_final: 0.8602 (mp) REVERT: C 224 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6794 (mm-30) REVERT: C 297 SER cc_start: 0.7897 (m) cc_final: 0.7045 (p) REVERT: C 301 CYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5531 (m) REVERT: C 308 VAL cc_start: 0.8528 (t) cc_final: 0.8223 (p) REVERT: C 324 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 332 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6253 (pp) REVERT: C 436 TRP cc_start: 0.7500 (p-90) cc_final: 0.6927 (p-90) REVERT: C 542 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7330 (t0) REVERT: C 563 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6997 (mm-40) REVERT: C 619 GLU cc_start: 0.6999 (mp0) cc_final: 0.6494 (mp0) REVERT: C 644 GLN cc_start: 0.7647 (tp40) cc_final: 0.6967 (tp40) REVERT: C 674 TYR cc_start: 0.7972 (t80) cc_final: 0.7665 (t80) REVERT: C 705 VAL cc_start: 0.8263 (t) cc_final: 0.7987 (m) REVERT: C 725 GLU cc_start: 0.7263 (tt0) cc_final: 0.7046 (tt0) REVERT: C 739 THR cc_start: 0.7967 (m) cc_final: 0.7244 (m) REVERT: C 764 LYS cc_start: 0.8240 (tttm) cc_final: 0.7751 (ttpp) REVERT: C 765 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7809 (ttm-80) REVERT: C 768 THR cc_start: 0.8557 (m) cc_final: 0.8332 (p) REVERT: C 776 LYS cc_start: 0.8443 (tptp) cc_final: 0.8032 (tptp) REVERT: C 801 ASN cc_start: 0.5574 (t0) cc_final: 0.5340 (t0) REVERT: C 825 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8088 (ttmm) REVERT: C 854 LYS cc_start: 0.8205 (tmmt) cc_final: 0.7767 (tptp) REVERT: C 917 TYR cc_start: 0.7828 (m-10) cc_final: 0.7623 (m-10) REVERT: C 921 LYS cc_start: 0.8394 (tptp) cc_final: 0.8114 (tptp) REVERT: C 957 GLN cc_start: 0.8035 (tt0) cc_final: 0.7737 (tp40) REVERT: C 964 LYS cc_start: 0.8624 (tppt) cc_final: 0.8226 (ttmm) REVERT: C 990 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 1014 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7512 (ttm110) REVERT: C 1050 MET cc_start: 0.7197 (mtm) cc_final: 0.6946 (mtp) REVERT: C 1101 HIS cc_start: 0.8577 (m-70) cc_final: 0.8210 (m90) REVERT: D 4 LEU cc_start: 0.8273 (mt) cc_final: 0.7730 (tt) REVERT: D 96 TYR cc_start: 0.2355 (m-80) cc_final: 0.1433 (m-80) REVERT: H 60 ARG cc_start: 0.5181 (mmt90) cc_final: 0.4883 (mmt90) outliers start: 148 outliers final: 107 residues processed: 772 average time/residue: 0.1926 time to fit residues: 235.7692 Evaluate side-chains 770 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 651 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 94 optimal weight: 1.9990 chunk 304 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 354 optimal weight: 0.0370 chunk 86 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 306 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 273 optimal weight: 0.0170 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 613 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 122 ASN C 690 GLN C 913 GLN C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.173089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128973 restraints weight = 55955.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133015 restraints weight = 24932.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135484 restraints weight = 13998.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136969 restraints weight = 9345.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137934 restraints weight = 7202.532| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29905 Z= 0.104 Angle : 0.572 12.192 40768 Z= 0.287 Chirality : 0.044 0.219 4657 Planarity : 0.004 0.093 5239 Dihedral : 5.087 60.759 4112 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.35 % Allowed : 18.07 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.35 (0.13), residues: 3713 helix: 1.02 (0.21), residues: 664 sheet: -1.49 (0.17), residues: 804 loop : -2.53 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 99 TYR 0.024 0.001 TYR C 655 PHE 0.025 0.001 PHE C 106 TRP 0.024 0.001 TRP D 110 HIS 0.010 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00237 (29860) covalent geometry : angle 0.56807 (40678) SS BOND : bond 0.00527 ( 45) SS BOND : angle 1.58348 ( 90) hydrogen bonds : bond 0.03573 ( 849) hydrogen bonds : angle 5.11350 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 677 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8024 (mtpt) REVERT: A 188 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6428 (mmt180) REVERT: A 202 TYR cc_start: 0.8052 (m-80) cc_final: 0.7833 (m-80) REVERT: A 233 ILE cc_start: 0.8222 (tt) cc_final: 0.7884 (pt) REVERT: A 276 LEU cc_start: 0.8270 (tp) cc_final: 0.8033 (tp) REVERT: A 281 GLU cc_start: 0.7336 (pp20) cc_final: 0.6954 (pp20) REVERT: A 297 SER cc_start: 0.8309 (m) cc_final: 0.7912 (p) REVERT: A 299 THR cc_start: 0.8136 (m) cc_final: 0.7640 (p) REVERT: A 436 TRP cc_start: 0.6950 (p-90) cc_final: 0.6601 (p90) REVERT: A 535 LYS cc_start: 0.8328 (mttp) cc_final: 0.8096 (mmtm) REVERT: A 542 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7988 (t0) REVERT: A 599 THR cc_start: 0.8325 (m) cc_final: 0.8099 (t) REVERT: A 654 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 660 TYR cc_start: 0.7864 (m-10) cc_final: 0.7627 (m-10) REVERT: A 674 TYR cc_start: 0.8204 (t80) cc_final: 0.7678 (t80) REVERT: A 697 MET cc_start: 0.7357 (ttp) cc_final: 0.7093 (mtp) REVERT: A 698 SER cc_start: 0.8458 (t) cc_final: 0.7890 (p) REVERT: A 737 ASP cc_start: 0.7504 (t70) cc_final: 0.6953 (t70) REVERT: A 759 PHE cc_start: 0.6886 (m-80) cc_final: 0.6236 (m-80) REVERT: A 763 LEU cc_start: 0.8371 (mt) cc_final: 0.8157 (mt) REVERT: A 773 GLU cc_start: 0.6743 (tm-30) cc_final: 0.5957 (tm-30) REVERT: A 803 SER cc_start: 0.8712 (m) cc_final: 0.8203 (p) REVERT: A 825 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8185 (mmtt) REVERT: A 854 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7952 (tttt) REVERT: A 868 GLU cc_start: 0.7369 (tp30) cc_final: 0.7054 (tp30) REVERT: A 869 MET cc_start: 0.8196 (mtt) cc_final: 0.7964 (mtm) REVERT: A 902 MET cc_start: 0.8029 (tpp) cc_final: 0.7675 (tpp) REVERT: A 921 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8122 (mmmm) REVERT: A 925 ASN cc_start: 0.8428 (m-40) cc_final: 0.7847 (m-40) REVERT: A 949 GLN cc_start: 0.8359 (mm110) cc_final: 0.7434 (mm-40) REVERT: A 953 ASN cc_start: 0.8274 (m-40) cc_final: 0.7792 (m110) REVERT: A 979 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7310 (t0) REVERT: A 980 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 994 ASP cc_start: 0.7250 (m-30) cc_final: 0.6977 (t0) REVERT: A 1029 MET cc_start: 0.8212 (tpp) cc_final: 0.7662 (ttm) REVERT: A 1050 MET cc_start: 0.6780 (ttm) cc_final: 0.6238 (mtm) REVERT: A 1117 THR cc_start: 0.8474 (p) cc_final: 0.8173 (t) REVERT: A 1141 LEU cc_start: 0.8251 (tp) cc_final: 0.7967 (tt) REVERT: B 105 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7528 (mm) REVERT: B 106 PHE cc_start: 0.7473 (m-80) cc_final: 0.7043 (m-80) REVERT: B 193 LYS cc_start: 0.7949 (mttt) cc_final: 0.7641 (mttp) REVERT: B 200 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7470 (mmmm) REVERT: B 224 GLU cc_start: 0.8052 (pm20) cc_final: 0.7633 (pm20) REVERT: B 278 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8327 (ttmm) REVERT: B 343 ASN cc_start: 0.6552 (t0) cc_final: 0.6240 (t0) REVERT: B 353 TRP cc_start: 0.8393 (p-90) cc_final: 0.8053 (p-90) REVERT: B 380 TYR cc_start: 0.6739 (m-80) cc_final: 0.6370 (m-80) REVERT: B 392 PHE cc_start: 0.7012 (m-80) cc_final: 0.6672 (m-80) REVERT: B 408 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7454 (ptm-80) REVERT: B 439 ASN cc_start: 0.8057 (t0) cc_final: 0.7784 (t0) REVERT: B 528 LYS cc_start: 0.6681 (mmmt) cc_final: 0.6283 (ptpp) REVERT: B 542 ASN cc_start: 0.7959 (t0) cc_final: 0.7753 (t0) REVERT: B 564 GLN cc_start: 0.7975 (pm20) cc_final: 0.7153 (pm20) REVERT: B 602 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 645 THR cc_start: 0.8227 (p) cc_final: 0.6999 (m) REVERT: B 651 ILE cc_start: 0.8369 (mt) cc_final: 0.8138 (pt) REVERT: B 659 SER cc_start: 0.8656 (m) cc_final: 0.8218 (p) REVERT: B 725 GLU cc_start: 0.7547 (tt0) cc_final: 0.6962 (tp30) REVERT: B 737 ASP cc_start: 0.7481 (t0) cc_final: 0.7234 (t0) REVERT: B 759 PHE cc_start: 0.7322 (t80) cc_final: 0.6420 (t80) REVERT: B 773 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6967 (tp30) REVERT: B 776 LYS cc_start: 0.8283 (tmmt) cc_final: 0.7830 (ttpp) REVERT: B 850 ILE cc_start: 0.8318 (mm) cc_final: 0.7966 (tp) REVERT: B 851 CYS cc_start: 0.8216 (t) cc_final: 0.7540 (m) REVERT: B 854 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7929 (tttp) REVERT: B 856 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8419 (mmmm) REVERT: B 911 VAL cc_start: 0.8438 (t) cc_final: 0.8134 (m) REVERT: B 913 GLN cc_start: 0.7856 (pt0) cc_final: 0.7444 (pm20) REVERT: B 921 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8435 (mmmm) REVERT: B 933 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7936 (ttmm) REVERT: B 934 ILE cc_start: 0.8391 (tp) cc_final: 0.8132 (tp) REVERT: B 950 ASP cc_start: 0.7555 (t70) cc_final: 0.6912 (t70) REVERT: B 969 LYS cc_start: 0.7928 (pttm) cc_final: 0.7680 (pttm) REVERT: B 1002 GLN cc_start: 0.7825 (tp40) cc_final: 0.7409 (tm-30) REVERT: B 1003 SER cc_start: 0.8736 (m) cc_final: 0.8059 (t) REVERT: B 1005 GLN cc_start: 0.8334 (tp40) cc_final: 0.7818 (tp40) REVERT: B 1028 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8262 (mttt) REVERT: B 1061 VAL cc_start: 0.8745 (t) cc_final: 0.8319 (p) REVERT: B 1086 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: B 1097 SER cc_start: 0.8488 (t) cc_final: 0.7846 (p) REVERT: B 1115 ILE cc_start: 0.8895 (mt) cc_final: 0.8482 (tp) REVERT: C 40 ASP cc_start: 0.7666 (t70) cc_final: 0.7425 (m-30) REVERT: C 41 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7038 (mtpp) REVERT: C 43 PHE cc_start: 0.8275 (t80) cc_final: 0.7941 (t80) REVERT: C 53 ASP cc_start: 0.7306 (t0) cc_final: 0.6932 (m-30) REVERT: C 65 PHE cc_start: 0.6966 (m-80) cc_final: 0.6688 (m-80) REVERT: C 199 PHE cc_start: 0.7824 (t80) cc_final: 0.7363 (t80) REVERT: C 201 ILE cc_start: 0.8847 (mt) cc_final: 0.8585 (mp) REVERT: C 224 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 297 SER cc_start: 0.7847 (m) cc_final: 0.6991 (p) REVERT: C 301 CYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5562 (m) REVERT: C 308 VAL cc_start: 0.8508 (t) cc_final: 0.8203 (p) REVERT: C 324 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 326 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6637 (pt) REVERT: C 332 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6251 (pp) REVERT: C 436 TRP cc_start: 0.7491 (p-90) cc_final: 0.6911 (p-90) REVERT: C 541 PHE cc_start: 0.7532 (p90) cc_final: 0.7259 (p90) REVERT: C 562 PHE cc_start: 0.8152 (p90) cc_final: 0.7771 (p90) REVERT: C 619 GLU cc_start: 0.7034 (mp0) cc_final: 0.6538 (mp0) REVERT: C 644 GLN cc_start: 0.7598 (tp40) cc_final: 0.6901 (tp40) REVERT: C 705 VAL cc_start: 0.8250 (t) cc_final: 0.8019 (m) REVERT: C 725 GLU cc_start: 0.7266 (tt0) cc_final: 0.7038 (tt0) REVERT: C 764 LYS cc_start: 0.8303 (tttm) cc_final: 0.7739 (ttpp) REVERT: C 765 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7874 (ttp-110) REVERT: C 768 THR cc_start: 0.8566 (m) cc_final: 0.8344 (p) REVERT: C 776 LYS cc_start: 0.8439 (tptp) cc_final: 0.8021 (tptp) REVERT: C 787 GLN cc_start: 0.7711 (mt0) cc_final: 0.7334 (mt0) REVERT: C 801 ASN cc_start: 0.5560 (t0) cc_final: 0.5318 (t0) REVERT: C 917 TYR cc_start: 0.7814 (m-10) cc_final: 0.7585 (m-10) REVERT: C 921 LYS cc_start: 0.8383 (tptp) cc_final: 0.8105 (tptp) REVERT: C 950 ASP cc_start: 0.7703 (t70) cc_final: 0.6977 (t0) REVERT: C 955 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7815 (t0) REVERT: C 964 LYS cc_start: 0.8636 (tppt) cc_final: 0.8219 (ttmm) REVERT: C 980 ILE cc_start: 0.8457 (mt) cc_final: 0.8175 (mt) REVERT: C 990 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7277 (mm-30) REVERT: C 1014 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7513 (ttm110) REVERT: C 1101 HIS cc_start: 0.8577 (m-70) cc_final: 0.8207 (m90) REVERT: D 4 LEU cc_start: 0.8341 (mt) cc_final: 0.7999 (tt) REVERT: E 39 GLN cc_start: 0.4568 (mm110) cc_final: 0.4283 (mm110) REVERT: H 60 ARG cc_start: 0.4995 (mmt90) cc_final: 0.4753 (mmt90) outliers start: 141 outliers final: 99 residues processed: 773 average time/residue: 0.1972 time to fit residues: 240.1097 Evaluate side-chains 774 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 659 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 190 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 chunk 230 optimal weight: 0.0050 chunk 289 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 312 optimal weight: 0.3980 chunk 288 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 365 optimal weight: 0.0070 chunk 243 optimal weight: 0.6980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 613 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN C 122 ASN C 542 ASN C 913 GLN C 955 ASN C 957 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.173039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128753 restraints weight = 56167.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132805 restraints weight = 25011.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135269 restraints weight = 14045.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136802 restraints weight = 9396.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137697 restraints weight = 7225.202| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 29905 Z= 0.105 Angle : 0.578 11.970 40768 Z= 0.287 Chirality : 0.043 0.195 4657 Planarity : 0.004 0.049 5239 Dihedral : 4.999 60.737 4107 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.22 % Allowed : 18.72 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.23 (0.13), residues: 3713 helix: 1.07 (0.21), residues: 664 sheet: -1.39 (0.17), residues: 792 loop : -2.45 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.023 0.001 TYR C 674 PHE 0.036 0.001 PHE A 592 TRP 0.024 0.001 TRP A 104 HIS 0.014 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00242 (29860) covalent geometry : angle 0.57317 (40678) SS BOND : bond 0.00346 ( 45) SS BOND : angle 1.61603 ( 90) hydrogen bonds : bond 0.03533 ( 849) hydrogen bonds : angle 5.01617 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 667 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6241 (m) cc_final: 0.5761 (p) REVERT: A 41 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8060 (mtpt) REVERT: A 188 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6763 (mmt180) REVERT: A 233 ILE cc_start: 0.8169 (tt) cc_final: 0.7856 (pt) REVERT: A 276 LEU cc_start: 0.8259 (tp) cc_final: 0.8048 (tp) REVERT: A 281 GLU cc_start: 0.7347 (pp20) cc_final: 0.6979 (pp20) REVERT: A 297 SER cc_start: 0.8284 (m) cc_final: 0.7965 (p) REVERT: A 299 THR cc_start: 0.8078 (m) cc_final: 0.7759 (m) REVERT: A 436 TRP cc_start: 0.7066 (p-90) cc_final: 0.6704 (p90) REVERT: A 542 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 547 LYS cc_start: 0.8331 (mttp) cc_final: 0.8094 (mppt) REVERT: A 599 THR cc_start: 0.8330 (m) cc_final: 0.8093 (t) REVERT: A 615 VAL cc_start: 0.8424 (t) cc_final: 0.8209 (m) REVERT: A 654 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 674 TYR cc_start: 0.8169 (t80) cc_final: 0.7798 (t80) REVERT: A 698 SER cc_start: 0.8449 (t) cc_final: 0.7859 (p) REVERT: A 737 ASP cc_start: 0.7328 (t70) cc_final: 0.6798 (t70) REVERT: A 759 PHE cc_start: 0.6823 (m-80) cc_final: 0.6258 (m-80) REVERT: A 763 LEU cc_start: 0.8374 (mt) cc_final: 0.8171 (mt) REVERT: A 773 GLU cc_start: 0.6750 (tm-30) cc_final: 0.5948 (tm-30) REVERT: A 803 SER cc_start: 0.8678 (m) cc_final: 0.8205 (p) REVERT: A 825 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8307 (mmtt) REVERT: A 854 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7934 (tmtt) REVERT: A 868 GLU cc_start: 0.7368 (tp30) cc_final: 0.7067 (tp30) REVERT: A 869 MET cc_start: 0.8189 (mtt) cc_final: 0.7960 (mtm) REVERT: A 902 MET cc_start: 0.8010 (tpp) cc_final: 0.7734 (tpp) REVERT: A 921 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8107 (mmmm) REVERT: A 925 ASN cc_start: 0.8421 (m-40) cc_final: 0.7839 (m-40) REVERT: A 949 GLN cc_start: 0.8376 (mm110) cc_final: 0.7463 (mm-40) REVERT: A 953 ASN cc_start: 0.8268 (m-40) cc_final: 0.7794 (m110) REVERT: A 966 LEU cc_start: 0.8690 (tp) cc_final: 0.8459 (tp) REVERT: A 979 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7130 (t0) REVERT: A 988 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7062 (tm-30) REVERT: A 1029 MET cc_start: 0.8216 (tpp) cc_final: 0.7643 (ttm) REVERT: A 1050 MET cc_start: 0.6804 (ttm) cc_final: 0.6553 (ttm) REVERT: A 1117 THR cc_start: 0.8440 (p) cc_final: 0.8146 (t) REVERT: A 1141 LEU cc_start: 0.8253 (tp) cc_final: 0.7982 (tt) REVERT: B 105 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7539 (mm) REVERT: B 106 PHE cc_start: 0.7407 (m-80) cc_final: 0.6993 (m-80) REVERT: B 189 GLU cc_start: 0.6850 (pm20) cc_final: 0.6451 (pm20) REVERT: B 200 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7483 (mmmm) REVERT: B 224 GLU cc_start: 0.8012 (pm20) cc_final: 0.7620 (pm20) REVERT: B 278 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8284 (ttmm) REVERT: B 343 ASN cc_start: 0.6521 (t0) cc_final: 0.6167 (t0) REVERT: B 354 ASN cc_start: 0.7900 (t0) cc_final: 0.7637 (m110) REVERT: B 380 TYR cc_start: 0.6727 (m-80) cc_final: 0.6377 (m-80) REVERT: B 392 PHE cc_start: 0.7011 (m-80) cc_final: 0.6680 (m-80) REVERT: B 394 ASN cc_start: 0.7795 (p0) cc_final: 0.7221 (p0) REVERT: B 439 ASN cc_start: 0.8024 (t0) cc_final: 0.7709 (t0) REVERT: B 528 LYS cc_start: 0.6934 (mmmt) cc_final: 0.6585 (ptpp) REVERT: B 542 ASN cc_start: 0.7937 (t0) cc_final: 0.7707 (t0) REVERT: B 564 GLN cc_start: 0.7999 (pm20) cc_final: 0.7155 (pm20) REVERT: B 602 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 643 PHE cc_start: 0.8298 (t80) cc_final: 0.8055 (t80) REVERT: B 645 THR cc_start: 0.8185 (p) cc_final: 0.6765 (m) REVERT: B 651 ILE cc_start: 0.8352 (mt) cc_final: 0.8149 (pt) REVERT: B 659 SER cc_start: 0.8660 (m) cc_final: 0.8237 (p) REVERT: B 725 GLU cc_start: 0.7535 (tt0) cc_final: 0.6876 (tp30) REVERT: B 759 PHE cc_start: 0.7335 (t80) cc_final: 0.6449 (t80) REVERT: B 773 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6937 (tp30) REVERT: B 776 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7844 (ttpp) REVERT: B 820 ASP cc_start: 0.7834 (t0) cc_final: 0.7409 (m-30) REVERT: B 850 ILE cc_start: 0.8333 (mm) cc_final: 0.7981 (tp) REVERT: B 851 CYS cc_start: 0.8237 (t) cc_final: 0.7555 (m) REVERT: B 854 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7917 (tttp) REVERT: B 856 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8417 (mmmm) REVERT: B 895 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6551 (mt0) REVERT: B 911 VAL cc_start: 0.8487 (t) cc_final: 0.8176 (m) REVERT: B 913 GLN cc_start: 0.7859 (pt0) cc_final: 0.7432 (pm20) REVERT: B 921 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8454 (mmmm) REVERT: B 933 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7986 (ttmm) REVERT: B 934 ILE cc_start: 0.8437 (tp) cc_final: 0.8157 (tt) REVERT: B 950 ASP cc_start: 0.7562 (t70) cc_final: 0.6900 (t70) REVERT: B 969 LYS cc_start: 0.7992 (pttm) cc_final: 0.7751 (pttm) REVERT: B 1002 GLN cc_start: 0.7802 (tp40) cc_final: 0.7386 (tm-30) REVERT: B 1003 SER cc_start: 0.8702 (m) cc_final: 0.8004 (t) REVERT: B 1005 GLN cc_start: 0.8342 (tp40) cc_final: 0.7799 (tp40) REVERT: B 1028 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8267 (mttt) REVERT: B 1061 VAL cc_start: 0.8688 (t) cc_final: 0.8272 (p) REVERT: B 1086 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8022 (ptpp) REVERT: B 1097 SER cc_start: 0.8499 (t) cc_final: 0.7899 (p) REVERT: C 41 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7157 (mtpp) REVERT: C 43 PHE cc_start: 0.8268 (t80) cc_final: 0.7943 (t80) REVERT: C 53 ASP cc_start: 0.7292 (t0) cc_final: 0.6934 (m-30) REVERT: C 65 PHE cc_start: 0.6963 (m-80) cc_final: 0.6696 (m-80) REVERT: C 199 PHE cc_start: 0.7835 (t80) cc_final: 0.7349 (t80) REVERT: C 201 ILE cc_start: 0.8857 (mt) cc_final: 0.8580 (mp) REVERT: C 224 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6767 (mm-30) REVERT: C 297 SER cc_start: 0.7799 (m) cc_final: 0.7129 (p) REVERT: C 301 CYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5603 (m) REVERT: C 308 VAL cc_start: 0.8501 (t) cc_final: 0.8199 (p) REVERT: C 326 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6709 (pt) REVERT: C 332 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6222 (pp) REVERT: C 436 TRP cc_start: 0.7488 (p-90) cc_final: 0.6763 (p-90) REVERT: C 619 GLU cc_start: 0.7036 (mp0) cc_final: 0.6549 (mp0) REVERT: C 644 GLN cc_start: 0.7650 (tp40) cc_final: 0.6898 (tp40) REVERT: C 705 VAL cc_start: 0.7988 (t) cc_final: 0.7711 (m) REVERT: C 725 GLU cc_start: 0.7148 (tt0) cc_final: 0.6899 (tt0) REVERT: C 759 PHE cc_start: 0.6692 (t80) cc_final: 0.6291 (m-80) REVERT: C 764 LYS cc_start: 0.8257 (tttm) cc_final: 0.7725 (ttpp) REVERT: C 765 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7709 (ttm-80) REVERT: C 768 THR cc_start: 0.8538 (m) cc_final: 0.8321 (p) REVERT: C 776 LYS cc_start: 0.8440 (tptp) cc_final: 0.8019 (tptp) REVERT: C 801 ASN cc_start: 0.5541 (t0) cc_final: 0.5294 (t0) REVERT: C 917 TYR cc_start: 0.7856 (m-10) cc_final: 0.7562 (m-10) REVERT: C 921 LYS cc_start: 0.8377 (tptp) cc_final: 0.8077 (tptp) REVERT: C 950 ASP cc_start: 0.7685 (t70) cc_final: 0.7012 (t0) REVERT: C 955 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7819 (t0) REVERT: C 964 LYS cc_start: 0.8631 (tppt) cc_final: 0.8182 (ttmm) REVERT: C 980 ILE cc_start: 0.8471 (mt) cc_final: 0.8190 (mt) REVERT: C 990 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 1005 GLN cc_start: 0.8043 (tp40) cc_final: 0.7600 (tp40) REVERT: C 1014 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7521 (ttm110) REVERT: D 4 LEU cc_start: 0.8533 (mt) cc_final: 0.7667 (tt) outliers start: 137 outliers final: 102 residues processed: 759 average time/residue: 0.1954 time to fit residues: 233.7779 Evaluate side-chains 769 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 652 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 280 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 217 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 330 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 616 ASN A 774 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN C 913 GLN C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.172726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128767 restraints weight = 56176.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132797 restraints weight = 24977.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135250 restraints weight = 14050.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136752 restraints weight = 9384.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137725 restraints weight = 7220.824| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29905 Z= 0.112 Angle : 0.581 14.287 40768 Z= 0.289 Chirality : 0.043 0.200 4657 Planarity : 0.004 0.060 5239 Dihedral : 5.000 60.517 4103 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.10 % Allowed : 19.30 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.15 (0.13), residues: 3713 helix: 1.18 (0.21), residues: 652 sheet: -1.35 (0.17), residues: 806 loop : -2.39 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 765 TYR 0.023 0.001 TYR C 655 PHE 0.035 0.001 PHE C 541 TRP 0.049 0.002 TRP B 353 HIS 0.010 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00256 (29860) covalent geometry : angle 0.57798 (40678) SS BOND : bond 0.00341 ( 45) SS BOND : angle 1.35108 ( 90) hydrogen bonds : bond 0.03544 ( 849) hydrogen bonds : angle 4.95486 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 666 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6290 (m) cc_final: 0.5814 (p) REVERT: A 41 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8072 (mtpt) REVERT: A 276 LEU cc_start: 0.8288 (tp) cc_final: 0.8070 (tp) REVERT: A 281 GLU cc_start: 0.7352 (pp20) cc_final: 0.6984 (pp20) REVERT: A 297 SER cc_start: 0.8338 (m) cc_final: 0.8038 (p) REVERT: A 403 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7060 (mmm-85) REVERT: A 436 TRP cc_start: 0.7038 (p-90) cc_final: 0.6715 (p90) REVERT: A 542 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: A 565 PHE cc_start: 0.6825 (m-80) cc_final: 0.6558 (m-80) REVERT: A 599 THR cc_start: 0.8346 (m) cc_final: 0.8112 (t) REVERT: A 654 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 660 TYR cc_start: 0.7434 (m-10) cc_final: 0.7186 (m-10) REVERT: A 674 TYR cc_start: 0.8200 (t80) cc_final: 0.7804 (t80) REVERT: A 698 SER cc_start: 0.8448 (t) cc_final: 0.7856 (p) REVERT: A 737 ASP cc_start: 0.7327 (t70) cc_final: 0.6792 (t70) REVERT: A 759 PHE cc_start: 0.6831 (m-80) cc_final: 0.6305 (m-80) REVERT: A 773 GLU cc_start: 0.6756 (tm-30) cc_final: 0.5899 (tm-30) REVERT: A 803 SER cc_start: 0.8701 (m) cc_final: 0.8238 (p) REVERT: A 825 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8305 (mmtt) REVERT: A 854 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7939 (tmtt) REVERT: A 868 GLU cc_start: 0.7388 (tp30) cc_final: 0.7098 (tp30) REVERT: A 869 MET cc_start: 0.8188 (mtt) cc_final: 0.7967 (mtm) REVERT: A 902 MET cc_start: 0.8018 (tpp) cc_final: 0.7756 (tpp) REVERT: A 921 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8151 (mmmm) REVERT: A 925 ASN cc_start: 0.8420 (m-40) cc_final: 0.8027 (m-40) REVERT: A 949 GLN cc_start: 0.8393 (mm110) cc_final: 0.7444 (mm-40) REVERT: A 953 ASN cc_start: 0.8266 (m-40) cc_final: 0.7772 (m110) REVERT: A 966 LEU cc_start: 0.8656 (tp) cc_final: 0.8433 (tp) REVERT: A 979 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7072 (t70) REVERT: A 988 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7056 (tm-30) REVERT: A 1029 MET cc_start: 0.8235 (tpp) cc_final: 0.7606 (ttm) REVERT: A 1050 MET cc_start: 0.6860 (ttm) cc_final: 0.6653 (ttm) REVERT: A 1117 THR cc_start: 0.8499 (p) cc_final: 0.8187 (t) REVERT: A 1141 LEU cc_start: 0.8283 (tp) cc_final: 0.8000 (tt) REVERT: B 105 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7551 (mm) REVERT: B 106 PHE cc_start: 0.7439 (m-80) cc_final: 0.7032 (m-80) REVERT: B 189 GLU cc_start: 0.6901 (pm20) cc_final: 0.6535 (pm20) REVERT: B 193 LYS cc_start: 0.7885 (mttt) cc_final: 0.7519 (mttp) REVERT: B 200 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7483 (mmmm) REVERT: B 224 GLU cc_start: 0.8032 (pm20) cc_final: 0.7656 (pm20) REVERT: B 278 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8238 (ttmm) REVERT: B 319 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7031 (ttm110) REVERT: B 354 ASN cc_start: 0.7941 (t0) cc_final: 0.7692 (m110) REVERT: B 380 TYR cc_start: 0.6761 (m-80) cc_final: 0.6416 (m-80) REVERT: B 392 PHE cc_start: 0.7104 (m-80) cc_final: 0.6806 (m-80) REVERT: B 394 ASN cc_start: 0.7758 (p0) cc_final: 0.7213 (p0) REVERT: B 439 ASN cc_start: 0.8005 (t0) cc_final: 0.7727 (t0) REVERT: B 528 LYS cc_start: 0.7016 (mmmt) cc_final: 0.6760 (ptpp) REVERT: B 542 ASN cc_start: 0.7938 (t0) cc_final: 0.7687 (t0) REVERT: B 564 GLN cc_start: 0.8069 (pm20) cc_final: 0.7861 (pm20) REVERT: B 602 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 643 PHE cc_start: 0.8270 (t80) cc_final: 0.8063 (t80) REVERT: B 645 THR cc_start: 0.8186 (p) cc_final: 0.6763 (m) REVERT: B 651 ILE cc_start: 0.8375 (mt) cc_final: 0.8156 (pt) REVERT: B 656 VAL cc_start: 0.8305 (m) cc_final: 0.8063 (p) REVERT: B 658 ASN cc_start: 0.7370 (t0) cc_final: 0.7043 (t0) REVERT: B 659 SER cc_start: 0.8666 (m) cc_final: 0.7798 (p) REVERT: B 663 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: B 698 SER cc_start: 0.8651 (t) cc_final: 0.8386 (p) REVERT: B 725 GLU cc_start: 0.7521 (tt0) cc_final: 0.6889 (tp30) REVERT: B 742 ILE cc_start: 0.8412 (mm) cc_final: 0.8184 (mt) REVERT: B 759 PHE cc_start: 0.7334 (t80) cc_final: 0.6412 (t80) REVERT: B 773 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: B 776 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7843 (ttpp) REVERT: B 820 ASP cc_start: 0.7733 (t0) cc_final: 0.7317 (m-30) REVERT: B 850 ILE cc_start: 0.8357 (mm) cc_final: 0.8115 (tp) REVERT: B 851 CYS cc_start: 0.8258 (t) cc_final: 0.7528 (m) REVERT: B 854 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7935 (tttp) REVERT: B 856 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8411 (mmmm) REVERT: B 911 VAL cc_start: 0.8493 (t) cc_final: 0.8188 (m) REVERT: B 913 GLN cc_start: 0.7852 (pt0) cc_final: 0.7470 (pm20) REVERT: B 921 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8448 (mmmm) REVERT: B 933 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7997 (ttmm) REVERT: B 934 ILE cc_start: 0.8380 (tp) cc_final: 0.8146 (tt) REVERT: B 950 ASP cc_start: 0.7566 (t70) cc_final: 0.6914 (t70) REVERT: B 969 LYS cc_start: 0.8008 (pttm) cc_final: 0.7770 (pttm) REVERT: B 1002 GLN cc_start: 0.7772 (tp40) cc_final: 0.7381 (tm-30) REVERT: B 1003 SER cc_start: 0.8699 (m) cc_final: 0.7933 (t) REVERT: B 1005 GLN cc_start: 0.8315 (tp40) cc_final: 0.7552 (tp40) REVERT: B 1028 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8290 (mttt) REVERT: B 1061 VAL cc_start: 0.8675 (t) cc_final: 0.8283 (p) REVERT: B 1086 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8010 (ptpp) REVERT: B 1097 SER cc_start: 0.8501 (t) cc_final: 0.7921 (p) REVERT: C 40 ASP cc_start: 0.7693 (t70) cc_final: 0.7363 (m-30) REVERT: C 41 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7028 (mtpp) REVERT: C 43 PHE cc_start: 0.8252 (t80) cc_final: 0.7933 (t80) REVERT: C 65 PHE cc_start: 0.6974 (m-80) cc_final: 0.6706 (m-80) REVERT: C 199 PHE cc_start: 0.7828 (t80) cc_final: 0.7340 (t80) REVERT: C 201 ILE cc_start: 0.8815 (mt) cc_final: 0.8511 (mp) REVERT: C 224 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 297 SER cc_start: 0.7848 (m) cc_final: 0.7266 (p) REVERT: C 301 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5610 (m) REVERT: C 308 VAL cc_start: 0.8502 (t) cc_final: 0.8296 (m) REVERT: C 332 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6204 (pp) REVERT: C 436 TRP cc_start: 0.7544 (p-90) cc_final: 0.6833 (p-90) REVERT: C 558 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7205 (mmmm) REVERT: C 619 GLU cc_start: 0.7042 (mp0) cc_final: 0.6572 (mp0) REVERT: C 644 GLN cc_start: 0.7728 (tp40) cc_final: 0.6970 (tp40) REVERT: C 705 VAL cc_start: 0.8021 (t) cc_final: 0.7619 (m) REVERT: C 725 GLU cc_start: 0.7145 (tt0) cc_final: 0.6908 (tt0) REVERT: C 754 LEU cc_start: 0.8552 (mt) cc_final: 0.8315 (mp) REVERT: C 759 PHE cc_start: 0.6690 (t80) cc_final: 0.6350 (m-80) REVERT: C 764 LYS cc_start: 0.8266 (tttm) cc_final: 0.7743 (ttpp) REVERT: C 765 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7719 (ttm-80) REVERT: C 768 THR cc_start: 0.8571 (m) cc_final: 0.8330 (p) REVERT: C 776 LYS cc_start: 0.8443 (tptp) cc_final: 0.8016 (tptp) REVERT: C 917 TYR cc_start: 0.7888 (m-10) cc_final: 0.7611 (m-10) REVERT: C 921 LYS cc_start: 0.8389 (tptp) cc_final: 0.8112 (tptp) REVERT: C 950 ASP cc_start: 0.7695 (t70) cc_final: 0.7032 (t0) REVERT: C 955 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7879 (t0) REVERT: C 964 LYS cc_start: 0.8675 (tppt) cc_final: 0.8184 (ttmm) REVERT: C 980 ILE cc_start: 0.8465 (mt) cc_final: 0.8176 (mt) REVERT: C 990 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7254 (mm-30) REVERT: C 1005 GLN cc_start: 0.8003 (tp40) cc_final: 0.7630 (tp40) REVERT: C 1010 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7781 (mm-40) REVERT: C 1014 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7526 (ttm110) REVERT: C 1101 HIS cc_start: 0.8659 (m-70) cc_final: 0.8382 (m90) REVERT: E 49 MET cc_start: 0.4005 (ptp) cc_final: 0.2497 (ptt) outliers start: 133 outliers final: 105 residues processed: 756 average time/residue: 0.1843 time to fit residues: 219.8534 Evaluate side-chains 768 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 650 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 142 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 307 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN B 935 GLN C 122 ASN C 913 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.172028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127721 restraints weight = 55533.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131767 restraints weight = 24803.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134207 restraints weight = 13980.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135716 restraints weight = 9397.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136650 restraints weight = 7238.697| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29905 Z= 0.124 Angle : 0.588 14.958 40768 Z= 0.293 Chirality : 0.043 0.190 4657 Planarity : 0.004 0.078 5239 Dihedral : 5.038 60.361 4103 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.01 % Allowed : 19.61 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.08 (0.13), residues: 3713 helix: 1.22 (0.21), residues: 652 sheet: -1.31 (0.17), residues: 822 loop : -2.34 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.023 0.001 TYR C 655 PHE 0.032 0.001 PHE B 190 TRP 0.053 0.002 TRP D 110 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00281 (29860) covalent geometry : angle 0.58500 (40678) SS BOND : bond 0.00308 ( 45) SS BOND : angle 1.34321 ( 90) hydrogen bonds : bond 0.03561 ( 849) hydrogen bonds : angle 4.92954 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 650 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6383 (m) cc_final: 0.5892 (p) REVERT: A 276 LEU cc_start: 0.8338 (tp) cc_final: 0.8101 (tp) REVERT: A 281 GLU cc_start: 0.7394 (pp20) cc_final: 0.7018 (pp20) REVERT: A 297 SER cc_start: 0.8313 (m) cc_final: 0.8048 (p) REVERT: A 403 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.7226 (mmm-85) REVERT: A 436 TRP cc_start: 0.7036 (p-90) cc_final: 0.6747 (p90) REVERT: A 542 ASN cc_start: 0.8217 (t0) cc_final: 0.7754 (m-40) REVERT: A 565 PHE cc_start: 0.6920 (m-80) cc_final: 0.6708 (m-80) REVERT: A 599 THR cc_start: 0.8363 (m) cc_final: 0.8138 (t) REVERT: A 644 GLN cc_start: 0.7364 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 654 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 660 TYR cc_start: 0.7504 (m-10) cc_final: 0.7296 (m-10) REVERT: A 674 TYR cc_start: 0.8221 (t80) cc_final: 0.7813 (t80) REVERT: A 698 SER cc_start: 0.8451 (t) cc_final: 0.7853 (p) REVERT: A 737 ASP cc_start: 0.7342 (t70) cc_final: 0.6821 (t70) REVERT: A 759 PHE cc_start: 0.6830 (m-80) cc_final: 0.6429 (m-80) REVERT: A 776 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8129 (tmmt) REVERT: A 803 SER cc_start: 0.8756 (m) cc_final: 0.8239 (p) REVERT: A 825 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8275 (mmtt) REVERT: A 854 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7931 (tttt) REVERT: A 868 GLU cc_start: 0.7393 (tp30) cc_final: 0.7087 (tp30) REVERT: A 869 MET cc_start: 0.8196 (mtt) cc_final: 0.7968 (mtm) REVERT: A 921 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8162 (mmmm) REVERT: A 925 ASN cc_start: 0.8430 (m-40) cc_final: 0.8036 (m-40) REVERT: A 949 GLN cc_start: 0.8410 (mm110) cc_final: 0.7463 (mm-40) REVERT: A 953 ASN cc_start: 0.8277 (m-40) cc_final: 0.7809 (m110) REVERT: A 979 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7125 (t70) REVERT: A 988 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7064 (tm-30) REVERT: A 1029 MET cc_start: 0.8236 (tpp) cc_final: 0.7597 (ttm) REVERT: A 1050 MET cc_start: 0.6940 (ttm) cc_final: 0.6603 (mtp) REVERT: A 1117 THR cc_start: 0.8523 (p) cc_final: 0.8207 (t) REVERT: A 1141 LEU cc_start: 0.8318 (tp) cc_final: 0.8033 (tt) REVERT: B 105 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7604 (mm) REVERT: B 106 PHE cc_start: 0.7458 (m-80) cc_final: 0.7002 (m-80) REVERT: B 170 TYR cc_start: 0.8033 (t80) cc_final: 0.7557 (t80) REVERT: B 200 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7472 (mmmm) REVERT: B 224 GLU cc_start: 0.8031 (pm20) cc_final: 0.7659 (pm20) REVERT: B 278 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8205 (ttmm) REVERT: B 319 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7041 (ttm110) REVERT: B 354 ASN cc_start: 0.7914 (t0) cc_final: 0.7697 (m110) REVERT: B 380 TYR cc_start: 0.6781 (m-80) cc_final: 0.6415 (m-80) REVERT: B 394 ASN cc_start: 0.7847 (p0) cc_final: 0.7296 (p0) REVERT: B 439 ASN cc_start: 0.8001 (t0) cc_final: 0.7774 (t0) REVERT: B 481 ASN cc_start: 0.8134 (t0) cc_final: 0.7870 (t0) REVERT: B 542 ASN cc_start: 0.7907 (t0) cc_final: 0.7639 (t0) REVERT: B 564 GLN cc_start: 0.8150 (pm20) cc_final: 0.7898 (pm20) REVERT: B 602 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 645 THR cc_start: 0.8216 (p) cc_final: 0.6957 (m) REVERT: B 651 ILE cc_start: 0.8390 (mt) cc_final: 0.8149 (pt) REVERT: B 656 VAL cc_start: 0.8314 (m) cc_final: 0.8086 (p) REVERT: B 658 ASN cc_start: 0.7358 (t0) cc_final: 0.7058 (t0) REVERT: B 659 SER cc_start: 0.8670 (m) cc_final: 0.7873 (p) REVERT: B 663 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: B 698 SER cc_start: 0.8640 (t) cc_final: 0.8375 (p) REVERT: B 725 GLU cc_start: 0.7507 (tt0) cc_final: 0.6843 (tp30) REVERT: B 759 PHE cc_start: 0.7336 (t80) cc_final: 0.6459 (t80) REVERT: B 773 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: B 776 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7857 (ttpp) REVERT: B 820 ASP cc_start: 0.7750 (t0) cc_final: 0.7310 (m-30) REVERT: B 850 ILE cc_start: 0.8373 (mm) cc_final: 0.8129 (tp) REVERT: B 851 CYS cc_start: 0.8279 (t) cc_final: 0.7525 (m) REVERT: B 854 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7964 (tttp) REVERT: B 856 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8421 (mmmm) REVERT: B 895 GLN cc_start: 0.6916 (mt0) cc_final: 0.6416 (mt0) REVERT: B 911 VAL cc_start: 0.8510 (t) cc_final: 0.8217 (m) REVERT: B 921 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8433 (mmmm) REVERT: B 934 ILE cc_start: 0.8367 (tp) cc_final: 0.8148 (tt) REVERT: B 950 ASP cc_start: 0.7583 (t70) cc_final: 0.6916 (t70) REVERT: B 969 LYS cc_start: 0.8054 (pttm) cc_final: 0.7813 (pttm) REVERT: B 1002 GLN cc_start: 0.7808 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 1003 SER cc_start: 0.8738 (m) cc_final: 0.7984 (t) REVERT: B 1005 GLN cc_start: 0.8323 (tp40) cc_final: 0.7744 (tp40) REVERT: B 1028 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8320 (mttt) REVERT: B 1061 VAL cc_start: 0.8681 (t) cc_final: 0.8253 (p) REVERT: B 1086 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8037 (ptpp) REVERT: C 41 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7232 (mtpp) REVERT: C 43 PHE cc_start: 0.8239 (t80) cc_final: 0.7933 (t80) REVERT: C 65 PHE cc_start: 0.7047 (m-80) cc_final: 0.6750 (m-80) REVERT: C 199 PHE cc_start: 0.7838 (t80) cc_final: 0.7274 (t80) REVERT: C 201 ILE cc_start: 0.8796 (mt) cc_final: 0.8476 (mp) REVERT: C 224 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6805 (mm-30) REVERT: C 297 SER cc_start: 0.7841 (m) cc_final: 0.7245 (p) REVERT: C 301 CYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5589 (m) REVERT: C 308 VAL cc_start: 0.8499 (t) cc_final: 0.8290 (m) REVERT: C 332 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6211 (pp) REVERT: C 436 TRP cc_start: 0.7492 (p-90) cc_final: 0.6772 (p-90) REVERT: C 558 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7181 (mmmm) REVERT: C 619 GLU cc_start: 0.7123 (mp0) cc_final: 0.6635 (mp0) REVERT: C 644 GLN cc_start: 0.7774 (tp40) cc_final: 0.6993 (tp40) REVERT: C 705 VAL cc_start: 0.7981 (t) cc_final: 0.7621 (m) REVERT: C 725 GLU cc_start: 0.7151 (tt0) cc_final: 0.6933 (tt0) REVERT: C 754 LEU cc_start: 0.8588 (mt) cc_final: 0.8377 (mm) REVERT: C 759 PHE cc_start: 0.6748 (t80) cc_final: 0.6453 (m-80) REVERT: C 764 LYS cc_start: 0.8266 (tttm) cc_final: 0.7759 (ttpp) REVERT: C 765 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7737 (ttm-80) REVERT: C 768 THR cc_start: 0.8592 (m) cc_final: 0.8335 (p) REVERT: C 776 LYS cc_start: 0.8478 (tptp) cc_final: 0.8032 (tptp) REVERT: C 917 TYR cc_start: 0.7907 (m-10) cc_final: 0.7607 (m-80) REVERT: C 921 LYS cc_start: 0.8413 (tptp) cc_final: 0.8143 (tptp) REVERT: C 950 ASP cc_start: 0.7724 (t70) cc_final: 0.7066 (t0) REVERT: C 955 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 964 LYS cc_start: 0.8618 (tppt) cc_final: 0.8158 (ttmm) REVERT: C 980 ILE cc_start: 0.8444 (mt) cc_final: 0.8170 (mt) REVERT: C 990 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 1005 GLN cc_start: 0.8023 (tp40) cc_final: 0.7721 (tp40) REVERT: C 1010 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7772 (mm-40) REVERT: C 1014 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7503 (ttm110) REVERT: C 1101 HIS cc_start: 0.8707 (m-70) cc_final: 0.8445 (m90) REVERT: D 84 MET cc_start: 0.2811 (mpp) cc_final: 0.2444 (mpp) REVERT: E 49 MET cc_start: 0.4124 (ptp) cc_final: 0.2653 (ptt) REVERT: H 82 LEU cc_start: 0.8178 (tp) cc_final: 0.7976 (mm) outliers start: 130 outliers final: 105 residues processed: 741 average time/residue: 0.1799 time to fit residues: 210.6021 Evaluate side-chains 757 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 641 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 275 optimal weight: 2.9990 chunk 354 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 333 optimal weight: 0.0070 chunk 187 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 299 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 774 GLN A 949 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 913 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.172127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128329 restraints weight = 55842.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132374 restraints weight = 24922.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134839 restraints weight = 14011.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136362 restraints weight = 9354.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137315 restraints weight = 7182.321| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29905 Z= 0.116 Angle : 0.593 15.055 40768 Z= 0.295 Chirality : 0.043 0.192 4657 Planarity : 0.005 0.107 5239 Dihedral : 4.991 60.244 4100 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.76 % Allowed : 19.89 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.03 (0.13), residues: 3713 helix: 1.22 (0.21), residues: 652 sheet: -1.24 (0.17), residues: 838 loop : -2.31 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.025 0.001 TYR B 495 PHE 0.030 0.001 PHE C 541 TRP 0.043 0.002 TRP B 353 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00266 (29860) covalent geometry : angle 0.59063 (40678) SS BOND : bond 0.00293 ( 45) SS BOND : angle 1.37039 ( 90) hydrogen bonds : bond 0.03517 ( 849) hydrogen bonds : angle 4.92377 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 652 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6399 (m) cc_final: 0.5924 (p) REVERT: A 92 PHE cc_start: 0.6897 (t80) cc_final: 0.6623 (t80) REVERT: A 94 SER cc_start: 0.7351 (OUTLIER) cc_final: 0.7142 (m) REVERT: A 276 LEU cc_start: 0.8348 (tp) cc_final: 0.8117 (tp) REVERT: A 281 GLU cc_start: 0.7395 (pp20) cc_final: 0.7017 (pp20) REVERT: A 297 SER cc_start: 0.8279 (m) cc_final: 0.8072 (p) REVERT: A 436 TRP cc_start: 0.7049 (p-90) cc_final: 0.6797 (p90) REVERT: A 542 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7760 (m-40) REVERT: A 599 THR cc_start: 0.8376 (m) cc_final: 0.8164 (t) REVERT: A 654 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 660 TYR cc_start: 0.7517 (m-10) cc_final: 0.7315 (m-10) REVERT: A 674 TYR cc_start: 0.8216 (t80) cc_final: 0.7786 (t80) REVERT: A 698 SER cc_start: 0.8458 (t) cc_final: 0.7855 (p) REVERT: A 737 ASP cc_start: 0.7342 (t70) cc_final: 0.6845 (t70) REVERT: A 759 PHE cc_start: 0.6829 (m-80) cc_final: 0.6405 (m-80) REVERT: A 776 LYS cc_start: 0.8368 (tmmt) cc_final: 0.8135 (tmmt) REVERT: A 803 SER cc_start: 0.8753 (m) cc_final: 0.8237 (p) REVERT: A 825 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8279 (mmtt) REVERT: A 854 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7925 (tttt) REVERT: A 868 GLU cc_start: 0.7382 (tp30) cc_final: 0.7086 (tp30) REVERT: A 869 MET cc_start: 0.8196 (mtt) cc_final: 0.7975 (mtm) REVERT: A 921 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8154 (mmmm) REVERT: A 925 ASN cc_start: 0.8423 (m-40) cc_final: 0.8024 (m-40) REVERT: A 945 LEU cc_start: 0.8605 (mm) cc_final: 0.8320 (mp) REVERT: A 953 ASN cc_start: 0.8306 (m-40) cc_final: 0.7916 (m110) REVERT: A 979 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7171 (t70) REVERT: A 988 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7068 (tm-30) REVERT: A 1029 MET cc_start: 0.8223 (tpp) cc_final: 0.7536 (ttm) REVERT: A 1050 MET cc_start: 0.6921 (ttm) cc_final: 0.6558 (mtp) REVERT: A 1117 THR cc_start: 0.8533 (p) cc_final: 0.8213 (t) REVERT: A 1141 LEU cc_start: 0.8311 (tp) cc_final: 0.8043 (tt) REVERT: B 105 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7645 (mm) REVERT: B 106 PHE cc_start: 0.7469 (m-80) cc_final: 0.7016 (m-80) REVERT: B 170 TYR cc_start: 0.7964 (t80) cc_final: 0.7490 (t80) REVERT: B 189 GLU cc_start: 0.6941 (pm20) cc_final: 0.6446 (pm20) REVERT: B 200 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7459 (mmmm) REVERT: B 224 GLU cc_start: 0.8032 (pm20) cc_final: 0.7671 (pm20) REVERT: B 278 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8203 (ttmt) REVERT: B 380 TYR cc_start: 0.6777 (m-80) cc_final: 0.6413 (m-80) REVERT: B 394 ASN cc_start: 0.7945 (p0) cc_final: 0.7446 (p0) REVERT: B 439 ASN cc_start: 0.7976 (t0) cc_final: 0.7753 (t0) REVERT: B 465 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 481 ASN cc_start: 0.8157 (t0) cc_final: 0.7882 (t0) REVERT: B 542 ASN cc_start: 0.7896 (t0) cc_final: 0.7679 (t0) REVERT: B 564 GLN cc_start: 0.8230 (pm20) cc_final: 0.7956 (pm20) REVERT: B 602 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 645 THR cc_start: 0.8207 (p) cc_final: 0.6947 (m) REVERT: B 651 ILE cc_start: 0.8383 (mt) cc_final: 0.8140 (pt) REVERT: B 656 VAL cc_start: 0.8295 (m) cc_final: 0.8081 (p) REVERT: B 658 ASN cc_start: 0.7361 (t0) cc_final: 0.7067 (t0) REVERT: B 659 SER cc_start: 0.8665 (m) cc_final: 0.7861 (p) REVERT: B 663 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: B 698 SER cc_start: 0.8638 (t) cc_final: 0.8366 (p) REVERT: B 725 GLU cc_start: 0.7459 (tt0) cc_final: 0.6878 (tp30) REVERT: B 759 PHE cc_start: 0.7327 (t80) cc_final: 0.6455 (t80) REVERT: B 776 LYS cc_start: 0.8298 (tmmt) cc_final: 0.7894 (ttpp) REVERT: B 820 ASP cc_start: 0.7733 (t0) cc_final: 0.7250 (m-30) REVERT: B 850 ILE cc_start: 0.8374 (mm) cc_final: 0.8141 (tp) REVERT: B 851 CYS cc_start: 0.8285 (t) cc_final: 0.7526 (m) REVERT: B 854 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7942 (tttp) REVERT: B 856 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8413 (mmmm) REVERT: B 895 GLN cc_start: 0.6871 (mt0) cc_final: 0.6426 (mt0) REVERT: B 911 VAL cc_start: 0.8518 (t) cc_final: 0.8209 (m) REVERT: B 921 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8429 (mmmm) REVERT: B 934 ILE cc_start: 0.8393 (tp) cc_final: 0.8184 (tt) REVERT: B 950 ASP cc_start: 0.7576 (t70) cc_final: 0.6912 (t70) REVERT: B 961 THR cc_start: 0.8824 (p) cc_final: 0.8309 (t) REVERT: B 969 LYS cc_start: 0.8051 (pttm) cc_final: 0.7816 (pttm) REVERT: B 1002 GLN cc_start: 0.7782 (tp40) cc_final: 0.7393 (tm-30) REVERT: B 1003 SER cc_start: 0.8747 (m) cc_final: 0.7962 (t) REVERT: B 1005 GLN cc_start: 0.8329 (tp40) cc_final: 0.7552 (tp40) REVERT: B 1028 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8310 (mttt) REVERT: B 1086 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8024 (ptpp) REVERT: C 41 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7233 (mtpp) REVERT: C 43 PHE cc_start: 0.8229 (t80) cc_final: 0.7906 (t80) REVERT: C 116 SER cc_start: 0.6509 (t) cc_final: 0.6225 (m) REVERT: C 199 PHE cc_start: 0.7821 (t80) cc_final: 0.7267 (t80) REVERT: C 201 ILE cc_start: 0.8795 (mt) cc_final: 0.8470 (mp) REVERT: C 224 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6822 (mm-30) REVERT: C 297 SER cc_start: 0.7834 (m) cc_final: 0.7251 (p) REVERT: C 301 CYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5594 (m) REVERT: C 308 VAL cc_start: 0.8495 (t) cc_final: 0.8282 (m) REVERT: C 332 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6183 (pp) REVERT: C 436 TRP cc_start: 0.7565 (p-90) cc_final: 0.6835 (p-90) REVERT: C 558 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7190 (mmmm) REVERT: C 619 GLU cc_start: 0.7113 (mp0) cc_final: 0.6634 (mp0) REVERT: C 644 GLN cc_start: 0.7773 (tp40) cc_final: 0.6995 (tp40) REVERT: C 705 VAL cc_start: 0.8013 (t) cc_final: 0.7665 (m) REVERT: C 725 GLU cc_start: 0.7138 (tt0) cc_final: 0.6908 (tt0) REVERT: C 754 LEU cc_start: 0.8588 (mt) cc_final: 0.8378 (mm) REVERT: C 759 PHE cc_start: 0.6676 (t80) cc_final: 0.6413 (m-80) REVERT: C 764 LYS cc_start: 0.8260 (tttm) cc_final: 0.7750 (ttpp) REVERT: C 765 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7690 (ttm-80) REVERT: C 768 THR cc_start: 0.8581 (m) cc_final: 0.8316 (p) REVERT: C 776 LYS cc_start: 0.8478 (tptp) cc_final: 0.8023 (tptp) REVERT: C 868 GLU cc_start: 0.7681 (tp30) cc_final: 0.7403 (tp30) REVERT: C 917 TYR cc_start: 0.7901 (m-10) cc_final: 0.7599 (m-80) REVERT: C 921 LYS cc_start: 0.8423 (tptp) cc_final: 0.8134 (tptp) REVERT: C 950 ASP cc_start: 0.7692 (t70) cc_final: 0.7030 (t0) REVERT: C 957 GLN cc_start: 0.8202 (tt0) cc_final: 0.7749 (tp40) REVERT: C 964 LYS cc_start: 0.8632 (tppt) cc_final: 0.8227 (ttmm) REVERT: C 980 ILE cc_start: 0.8436 (mt) cc_final: 0.8152 (mt) REVERT: C 990 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7282 (mm-30) REVERT: C 1005 GLN cc_start: 0.8042 (tp40) cc_final: 0.7725 (tp40) REVERT: C 1010 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7766 (mm-40) REVERT: C 1014 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7513 (ttm110) REVERT: C 1101 HIS cc_start: 0.8712 (m-70) cc_final: 0.8449 (m90) REVERT: D 84 MET cc_start: 0.2813 (mpp) cc_final: 0.2491 (mpp) REVERT: E 49 MET cc_start: 0.4095 (ptp) cc_final: 0.2644 (ptt) outliers start: 122 outliers final: 103 residues processed: 735 average time/residue: 0.1801 time to fit residues: 209.8853 Evaluate side-chains 752 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 638 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 288 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 151 optimal weight: 0.0000 chunk 239 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 710 ASN A 774 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 164 ASN C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124275 restraints weight = 56025.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128309 restraints weight = 25051.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130757 restraints weight = 14078.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132281 restraints weight = 9408.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133205 restraints weight = 7223.775| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29905 Z= 0.227 Angle : 0.662 15.453 40768 Z= 0.337 Chirality : 0.046 0.243 4657 Planarity : 0.005 0.079 5239 Dihedral : 5.313 61.123 4100 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.76 % Allowed : 20.35 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.11 (0.13), residues: 3713 helix: 1.15 (0.21), residues: 628 sheet: -1.32 (0.17), residues: 820 loop : -2.30 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 403 TYR 0.033 0.002 TYR A 198 PHE 0.059 0.002 PHE B 643 TRP 0.044 0.003 TRP D 110 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00496 (29860) covalent geometry : angle 0.65768 (40678) SS BOND : bond 0.00485 ( 45) SS BOND : angle 1.72407 ( 90) hydrogen bonds : bond 0.04050 ( 849) hydrogen bonds : angle 5.15559 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7196.24 seconds wall clock time: 124 minutes 11.90 seconds (7451.90 seconds total)