Starting phenix.real_space_refine on Fri Mar 6 07:09:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ycy_33742/03_2026/7ycy_33742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ycy_33742/03_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_33742/03_2026/7ycy_33742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ycy_33742/03_2026/7ycy_33742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ycy_33742/03_2026/7ycy_33742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ycy_33742/03_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-dev-5986/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: 6.32, per 1000 atoms: 0.22 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: 2.25 Conformation dependent library (CDL) restraints added in 1.3 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: 1.21 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: 6.61 Time building geometry restraints manager: 2.99 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: 2.150 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.760 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- 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 : 0.971 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: 0.7358 (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: 0.7449 (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: 0.6038 (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: 0.8287 (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: 0.8065 (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: 0.6683 (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: 0.7990 (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: 0.8055 (tp40) cc_final: 0.7348 (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: 0.8151 (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: 0.6473 (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: 0.6401 (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 869 MET cc_start: 0.8271 (mtt) cc_final: 0.8071 (mtm) 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: 0.6642 (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: 0.7104 (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: 0.1860 time to fit residues: 299.6706 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 : 1.085 ------------------------------------------------------------------------------- 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 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: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128894 restraints weight = 56810.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133037 restraints weight = 24956.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135532 restraints weight = 13887.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137075 restraints weight = 9265.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137966 restraints weight = 7113.944| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29905 Z= 0.190 Angle : 0.638 12.511 40768 Z= 0.328 Chirality : 0.045 0.261 4657 Planarity : 0.005 0.069 5239 Dihedral : 5.792 61.697 4156 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.81 % Allowed : 12.18 % Favored : 83.01 % 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: -3.43 (0.12), residues: 3713 helix: 0.00 (0.20), residues: 656 sheet: -2.20 (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 0.025 0.001 TYR A 495 PHE 0.028 0.002 PHE C 55 TRP 0.024 0.001 TRP A 104 HIS 0.011 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00409 (29860) covalent geometry : angle 0.62979 (40678) SS BOND : bond 0.00648 ( 45) SS BOND : angle 2.22373 ( 90) hydrogen bonds : bond 0.04698 ( 849) hydrogen bonds : angle 6.19798 ( 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 913 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 757 time to evaluate : 0.848 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 87 ASN cc_start: 0.7326 (p0) cc_final: 0.7099 (p0) REVERT: A 111 ASP cc_start: 0.5269 (OUTLIER) cc_final: 0.4960 (p0) REVERT: A 190 PHE cc_start: 0.7218 (m-80) cc_final: 0.6820 (m-80) REVERT: A 233 ILE cc_start: 0.8490 (tt) cc_final: 0.8081 (pt) REVERT: A 281 GLU cc_start: 0.7363 (pp20) cc_final: 0.7080 (pp20) REVERT: A 297 SER cc_start: 0.8400 (m) cc_final: 0.8126 (p) REVERT: A 326 ILE cc_start: 0.7958 (mp) cc_final: 0.7690 (mt) REVERT: A 403 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7600 (ptp-110) REVERT: A 478 LYS cc_start: -0.0618 (OUTLIER) cc_final: -0.1917 (ptmt) REVERT: A 505 HIS cc_start: 0.7160 (t-90) cc_final: 0.6922 (t-90) REVERT: A 535 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8146 (mttp) REVERT: A 542 ASN cc_start: 0.8176 (t0) cc_final: 0.7942 (t0) REVERT: A 592 PHE cc_start: 0.7850 (p90) cc_final: 0.7358 (p90) REVERT: A 599 THR cc_start: 0.8437 (m) cc_final: 0.8213 (t) REVERT: A 615 VAL cc_start: 0.8420 (t) cc_final: 0.8198 (m) REVERT: A 671 CYS cc_start: 0.4918 (m) cc_final: 0.4695 (m) REVERT: A 674 TYR cc_start: 0.8231 (t80) cc_final: 0.7943 (t80) REVERT: A 697 MET cc_start: 0.7301 (ttp) cc_final: 0.6781 (mtp) REVERT: A 698 SER cc_start: 0.8627 (t) cc_final: 0.8222 (p) REVERT: A 737 ASP cc_start: 0.7556 (t70) cc_final: 0.7331 (t0) REVERT: A 745 ASP cc_start: 0.6529 (m-30) cc_final: 0.6004 (t0) REVERT: A 751 ASN cc_start: 0.7942 (m-40) cc_final: 0.7715 (m-40) REVERT: A 754 LEU cc_start: 0.8313 (mt) cc_final: 0.8091 (mt) REVERT: A 759 PHE cc_start: 0.6820 (m-80) cc_final: 0.6410 (m-80) REVERT: A 762 GLN cc_start: 0.7505 (pt0) cc_final: 0.7258 (pt0) REVERT: A 763 LEU cc_start: 0.8431 (mt) cc_final: 0.8142 (mt) REVERT: A 773 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5779 (tm-30) REVERT: A 803 SER cc_start: 0.8699 (m) cc_final: 0.8261 (p) REVERT: A 816 SER cc_start: 0.7850 (p) cc_final: 0.7404 (t) REVERT: A 825 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8112 (mmtm) REVERT: A 854 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8053 (tttt) REVERT: A 855 PHE cc_start: 0.8257 (m-80) cc_final: 0.7964 (m-80) REVERT: A 868 GLU cc_start: 0.7372 (tp30) cc_final: 0.7054 (tp30) REVERT: A 869 MET cc_start: 0.8211 (mtt) cc_final: 0.7973 (mtm) REVERT: A 878 LEU cc_start: 0.8255 (mt) cc_final: 0.7922 (mp) REVERT: A 896 ILE cc_start: 0.8202 (tt) cc_final: 0.7979 (tt) REVERT: A 902 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7444 (tpp) REVERT: A 921 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8181 (mmmm) REVERT: A 925 ASN cc_start: 0.8543 (m-40) cc_final: 0.8053 (m-40) REVERT: A 933 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7819 (mtmm) REVERT: A 945 LEU cc_start: 0.8695 (mm) cc_final: 0.8348 (mp) REVERT: A 953 ASN cc_start: 0.8332 (m-40) cc_final: 0.7960 (m110) REVERT: A 960 ASN cc_start: 0.8005 (m110) cc_final: 0.7700 (m-40) REVERT: A 961 THR cc_start: 0.8598 (t) cc_final: 0.8380 (p) REVERT: A 976 VAL cc_start: 0.9028 (m) cc_final: 0.8646 (p) REVERT: A 978 ASN cc_start: 0.7855 (m-40) cc_final: 0.7452 (m-40) REVERT: A 983 ARG cc_start: 0.8413 (mtm180) cc_final: 0.8059 (mtp180) REVERT: A 1019 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7316 (ttp80) REVERT: A 1029 MET cc_start: 0.8346 (tpp) cc_final: 0.7564 (ttm) REVERT: A 1038 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8242 (mttt) REVERT: A 1117 THR cc_start: 0.8465 (p) cc_final: 0.8207 (t) REVERT: A 1129 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8334 (m) REVERT: A 1141 LEU cc_start: 0.8264 (tp) cc_final: 0.7917 (tt) REVERT: B 104 TRP cc_start: 0.7072 (m-90) cc_final: 0.6668 (m-90) REVERT: B 105 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7519 (mm) REVERT: B 106 PHE cc_start: 0.7353 (m-80) cc_final: 0.6898 (m-80) REVERT: B 130 VAL cc_start: 0.5946 (OUTLIER) cc_final: 0.5543 (p) REVERT: B 187 LEU cc_start: 0.7900 (tp) cc_final: 0.7618 (tt) REVERT: B 190 PHE cc_start: 0.8017 (m-10) cc_final: 0.7798 (m-80) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7597 (pm20) REVERT: B 267 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 278 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8386 (ttmt) REVERT: B 286 THR cc_start: 0.7709 (p) cc_final: 0.7369 (p) REVERT: B 307 THR cc_start: 0.7259 (m) cc_final: 0.6861 (p) REVERT: B 317 ASN cc_start: 0.8323 (p0) cc_final: 0.8053 (p0) REVERT: B 329 PHE cc_start: 0.7906 (m-10) cc_final: 0.7583 (m-80) REVERT: B 353 TRP cc_start: 0.8295 (p-90) cc_final: 0.8009 (p-90) REVERT: B 354 ASN cc_start: 0.7993 (m110) cc_final: 0.7629 (m110) REVERT: B 380 TYR cc_start: 0.6771 (m-80) cc_final: 0.6362 (m-80) REVERT: B 394 ASN cc_start: 0.7332 (t0) cc_final: 0.6862 (t0) REVERT: B 402 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8237 (tp) REVERT: B 408 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7534 (ptm-80) REVERT: B 429 PHE cc_start: 0.8343 (t80) cc_final: 0.7958 (t80) REVERT: B 465 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 515 PHE cc_start: 0.7403 (m-80) cc_final: 0.7124 (m-80) REVERT: B 546 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7887 (tm) REVERT: B 547 LYS cc_start: 0.8470 (tptp) cc_final: 0.8227 (tttm) REVERT: B 589 PRO cc_start: 0.7891 (Cg_exo) cc_final: 0.7682 (Cg_endo) REVERT: B 651 ILE cc_start: 0.8287 (mt) cc_final: 0.8007 (mp) REVERT: B 659 SER cc_start: 0.8790 (m) cc_final: 0.8215 (p) REVERT: B 703 ASN cc_start: 0.8334 (t0) cc_final: 0.8107 (t0) REVERT: B 705 VAL cc_start: 0.8621 (t) cc_final: 0.8375 (p) REVERT: B 725 GLU cc_start: 0.7457 (tt0) cc_final: 0.6542 (tt0) REVERT: B 737 ASP cc_start: 0.7649 (t0) cc_final: 0.7298 (t70) REVERT: B 776 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7802 (ttpp) REVERT: B 797 PHE cc_start: 0.7661 (m-10) cc_final: 0.7341 (m-80) REVERT: B 850 ILE cc_start: 0.8265 (mm) cc_final: 0.7944 (tp) REVERT: B 851 CYS cc_start: 0.8066 (t) cc_final: 0.7605 (m) REVERT: B 854 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8155 (tttp) REVERT: B 921 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8481 (mmmm) REVERT: B 933 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7824 (mtmm) REVERT: B 950 ASP cc_start: 0.7382 (t70) cc_final: 0.6752 (t70) REVERT: B 961 THR cc_start: 0.8808 (m) cc_final: 0.8581 (m) REVERT: B 969 LYS cc_start: 0.7859 (pttm) cc_final: 0.7568 (pttm) REVERT: B 994 ASP cc_start: 0.7559 (m-30) cc_final: 0.7024 (m-30) REVERT: B 997 ILE cc_start: 0.8334 (tt) cc_final: 0.8027 (pt) REVERT: B 1002 GLN cc_start: 0.7961 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 1003 SER cc_start: 0.8678 (m) cc_final: 0.8039 (t) REVERT: B 1005 GLN cc_start: 0.8292 (tp40) cc_final: 0.8068 (tp40) REVERT: B 1010 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: B 1028 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8089 (mttt) REVERT: B 1041 ASP cc_start: 0.7197 (t70) cc_final: 0.6648 (t0) REVERT: B 1050 MET cc_start: 0.7254 (mtp) cc_final: 0.6925 (mtp) REVERT: B 1061 VAL cc_start: 0.8789 (t) cc_final: 0.8416 (p) REVERT: B 1072 GLU cc_start: 0.7920 (pm20) cc_final: 0.7599 (pm20) REVERT: B 1081 ILE cc_start: 0.8363 (pt) cc_final: 0.8118 (mt) REVERT: B 1086 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (ptpp) REVERT: B 1097 SER cc_start: 0.8485 (t) cc_final: 0.7894 (p) REVERT: C 41 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7178 (mtpp) REVERT: C 105 ILE cc_start: 0.8318 (mp) cc_final: 0.7664 (pt) REVERT: C 192 PHE cc_start: 0.8372 (m-80) cc_final: 0.8045 (m-80) REVERT: C 199 PHE cc_start: 0.7786 (t80) cc_final: 0.7348 (t80) REVERT: C 201 ILE cc_start: 0.8806 (mt) cc_final: 0.8510 (mp) REVERT: C 224 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6793 (mm-30) REVERT: C 271 GLN cc_start: 0.7334 (mt0) cc_final: 0.7095 (mt0) REVERT: C 297 SER cc_start: 0.7897 (m) cc_final: 0.6988 (p) REVERT: C 298 GLU cc_start: 0.7485 (tt0) cc_final: 0.7281 (tt0) REVERT: C 326 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6692 (pt) REVERT: C 531 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8294 (p) REVERT: C 542 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7360 (t0) REVERT: C 563 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6997 (mm-40) REVERT: C 576 VAL cc_start: 0.7169 (OUTLIER) cc_final: 0.6944 (m) REVERT: C 588 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 619 GLU cc_start: 0.6948 (mp0) cc_final: 0.6346 (mp0) REVERT: C 644 GLN cc_start: 0.7704 (tp40) cc_final: 0.6949 (tp40) REVERT: C 705 VAL cc_start: 0.8266 (t) cc_final: 0.8005 (m) REVERT: C 725 GLU cc_start: 0.7254 (tt0) cc_final: 0.7025 (tt0) REVERT: C 764 LYS cc_start: 0.8245 (tttm) cc_final: 0.7940 (ttpp) REVERT: C 765 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7560 (ttp-110) REVERT: C 776 LYS cc_start: 0.8450 (tptp) cc_final: 0.8152 (tptp) REVERT: C 801 ASN cc_start: 0.5590 (t0) cc_final: 0.5386 (t0) REVERT: C 811 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8136 (ttmm) REVERT: C 825 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8161 (ttmm) REVERT: C 854 LYS cc_start: 0.8393 (tmmt) cc_final: 0.8036 (tptp) REVERT: C 867 ASP cc_start: 0.7669 (m-30) cc_final: 0.7453 (m-30) REVERT: C 869 MET cc_start: 0.8326 (mtt) cc_final: 0.8100 (mtm) REVERT: C 902 MET cc_start: 0.8013 (mtp) cc_final: 0.7689 (mmm) REVERT: C 922 LEU cc_start: 0.8979 (tp) cc_final: 0.8746 (tt) REVERT: C 945 LEU cc_start: 0.8478 (mm) cc_final: 0.8212 (mt) REVERT: C 996 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 998 THR cc_start: 0.8320 (t) cc_final: 0.8101 (p) REVERT: C 1014 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7643 (ttm-80) REVERT: C 1081 ILE cc_start: 0.8559 (pt) cc_final: 0.8355 (mt) REVERT: C 1125 ASN cc_start: 0.7452 (p0) cc_final: 0.7231 (p0) REVERT: D 84 MET cc_start: 0.3515 (mpp) cc_final: 0.3290 (mpp) REVERT: F 55 TRP cc_start: 0.6289 (p-90) cc_final: 0.6030 (p-90) REVERT: G 49 MET cc_start: 0.2330 (OUTLIER) cc_final: 0.2090 (tpt) REVERT: H 54 TYR cc_start: 0.7125 (m-80) cc_final: 0.6883 (m-80) REVERT: H 60 ARG cc_start: 0.5433 (mmm160) cc_final: 0.4871 (mmt90) REVERT: H 78 ASN cc_start: 0.5587 (m110) cc_final: 0.5113 (t0) outliers start: 156 outliers final: 72 residues processed: 865 average time/residue: 0.1788 time to fit residues: 246.9600 Evaluate side-chains 799 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 705 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 996 LEU 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 G residue 49 MET 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: 0.9990 chunk 327 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 254 optimal weight: 0.0040 chunk 167 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 A 957 GLN A1010 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 762 GLN C 955 ASN ** 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 = 0.4237 r_free = 0.4237 target = 0.173307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129349 restraints weight = 56481.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133478 restraints weight = 24849.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135970 restraints weight = 13892.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137524 restraints weight = 9278.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138466 restraints weight = 7122.065| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29905 Z= 0.130 Angle : 0.595 13.272 40768 Z= 0.300 Chirality : 0.044 0.389 4657 Planarity : 0.004 0.066 5239 Dihedral : 5.407 60.634 4132 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.84 % Allowed : 15.29 % Favored : 79.86 % 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: -2.92 (0.13), residues: 3713 helix: 0.56 (0.21), residues: 652 sheet: -1.80 (0.17), residues: 784 loop : -2.92 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 188 TYR 0.030 0.001 TYR A 495 PHE 0.039 0.001 PHE C 106 TRP 0.028 0.001 TRP D 110 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00289 (29860) covalent geometry : angle 0.58802 (40678) SS BOND : bond 0.00403 ( 45) SS BOND : angle 2.01195 ( 90) hydrogen bonds : bond 0.04107 ( 849) hydrogen bonds : angle 5.66412 ( 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 888 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 731 time to evaluate : 1.120 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: 0.8543 (OUTLIER) cc_final: 0.7955 (mtpt) REVERT: A 87 ASN cc_start: 0.7236 (p0) cc_final: 0.7029 (p0) REVERT: A 111 ASP cc_start: 0.5425 (OUTLIER) cc_final: 0.5128 (p0) REVERT: A 190 PHE cc_start: 0.7376 (m-80) cc_final: 0.7104 (m-80) REVERT: A 228 ASP cc_start: 0.6725 (t0) cc_final: 0.6465 (t0) REVERT: A 233 ILE cc_start: 0.8419 (tt) cc_final: 0.8186 (mp) REVERT: A 276 LEU cc_start: 0.8277 (tp) cc_final: 0.7929 (tp) REVERT: A 281 GLU cc_start: 0.7348 (pp20) cc_final: 0.6973 (pp20) REVERT: A 297 SER cc_start: 0.8376 (m) cc_final: 0.8056 (p) REVERT: A 326 ILE cc_start: 0.7902 (mp) cc_final: 0.7629 (mt) REVERT: A 478 LYS cc_start: -0.0630 (OUTLIER) cc_final: -0.1301 (ptmt) REVERT: A 505 HIS cc_start: 0.7240 (t-90) cc_final: 0.6982 (t-90) REVERT: A 542 ASN cc_start: 0.8200 (t0) cc_final: 0.7862 (m-40) REVERT: A 592 PHE cc_start: 0.7831 (p90) cc_final: 0.7093 (p90) REVERT: A 616 ASN cc_start: 0.6898 (t0) cc_final: 0.6613 (t0) REVERT: A 618 THR cc_start: 0.8335 (p) cc_final: 0.7578 (p) REVERT: A 674 TYR cc_start: 0.8181 (t80) cc_final: 0.7887 (t80) REVERT: A 697 MET cc_start: 0.7340 (ttp) cc_final: 0.6945 (mtp) REVERT: A 698 SER cc_start: 0.8565 (t) cc_final: 0.8015 (p) REVERT: A 751 ASN cc_start: 0.7986 (m-40) cc_final: 0.7735 (m-40) REVERT: A 754 LEU cc_start: 0.8475 (mt) cc_final: 0.8235 (mt) REVERT: A 759 PHE cc_start: 0.6844 (m-80) cc_final: 0.6509 (m-80) REVERT: A 763 LEU cc_start: 0.8400 (mt) cc_final: 0.8178 (mt) REVERT: A 773 GLU cc_start: 0.6588 (tm-30) cc_final: 0.5721 (tm-30) REVERT: A 803 SER cc_start: 0.8744 (m) cc_final: 0.8224 (p) REVERT: A 816 SER cc_start: 0.7847 (p) cc_final: 0.7609 (t) REVERT: A 825 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8168 (mmtm) REVERT: A 854 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8031 (tttt) REVERT: A 868 GLU cc_start: 0.7389 (tp30) cc_final: 0.7059 (tp30) REVERT: A 869 MET cc_start: 0.8199 (mtt) cc_final: 0.7954 (mtm) REVERT: A 878 LEU cc_start: 0.8280 (mt) cc_final: 0.7942 (mp) REVERT: A 921 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8147 (mmmm) REVERT: A 925 ASN cc_start: 0.8470 (m-40) cc_final: 0.7935 (m-40) REVERT: A 933 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7711 (mtmm) REVERT: A 945 LEU cc_start: 0.8660 (mm) cc_final: 0.8395 (mp) REVERT: A 949 GLN cc_start: 0.8250 (mm110) cc_final: 0.7467 (mm-40) REVERT: A 953 ASN cc_start: 0.8335 (m-40) cc_final: 0.7913 (m110) REVERT: A 960 ASN cc_start: 0.8022 (m110) cc_final: 0.7696 (m-40) REVERT: A 961 THR cc_start: 0.8635 (t) cc_final: 0.8373 (p) REVERT: A 979 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7518 (t0) REVERT: A 994 ASP cc_start: 0.7088 (m-30) cc_final: 0.6837 (m-30) REVERT: A 1019 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7274 (ttp80) REVERT: A 1029 MET cc_start: 0.8272 (tpp) cc_final: 0.7572 (ttm) REVERT: A 1038 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8259 (mttt) REVERT: A 1117 THR cc_start: 0.8467 (p) cc_final: 0.8197 (t) REVERT: A 1129 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8335 (m) REVERT: A 1141 LEU cc_start: 0.8258 (tp) cc_final: 0.7940 (tt) REVERT: B 60 SER cc_start: 0.8552 (t) cc_final: 0.8298 (t) REVERT: B 104 TRP cc_start: 0.7169 (m-90) cc_final: 0.6718 (m-90) REVERT: B 106 PHE cc_start: 0.7343 (m-80) cc_final: 0.6928 (m-80) REVERT: B 187 LEU cc_start: 0.7900 (tp) cc_final: 0.7603 (tt) REVERT: B 200 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7726 (mmmm) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7641 (pm20) REVERT: B 278 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8394 (ttmt) REVERT: B 286 THR cc_start: 0.7625 (p) cc_final: 0.7328 (p) REVERT: B 307 THR cc_start: 0.7253 (m) cc_final: 0.7031 (p) REVERT: B 329 PHE cc_start: 0.7757 (m-10) cc_final: 0.7528 (m-80) REVERT: B 343 ASN cc_start: 0.6546 (t0) cc_final: 0.5991 (t0) REVERT: B 353 TRP cc_start: 0.8422 (p-90) cc_final: 0.8043 (p-90) REVERT: B 354 ASN cc_start: 0.7956 (m110) cc_final: 0.7467 (m110) REVERT: B 380 TYR cc_start: 0.6716 (m-80) cc_final: 0.6261 (m-80) REVERT: B 429 PHE cc_start: 0.8354 (t80) cc_final: 0.7982 (t80) REVERT: B 465 GLU cc_start: 0.8715 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 515 PHE cc_start: 0.7477 (m-80) cc_final: 0.7212 (m-80) REVERT: B 547 LYS cc_start: 0.8439 (tptp) cc_final: 0.8165 (tttm) REVERT: B 564 GLN cc_start: 0.8153 (pm20) cc_final: 0.7590 (pm20) REVERT: B 651 ILE cc_start: 0.8301 (mt) cc_final: 0.8011 (mm) REVERT: B 659 SER cc_start: 0.8754 (m) cc_final: 0.8231 (p) REVERT: B 705 VAL cc_start: 0.8660 (t) cc_final: 0.8415 (p) REVERT: B 737 ASP cc_start: 0.7569 (t0) cc_final: 0.7260 (t70) REVERT: B 773 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: B 776 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7830 (ttpp) REVERT: B 823 PHE cc_start: 0.7134 (m-10) cc_final: 0.6881 (m-10) REVERT: B 850 ILE cc_start: 0.8328 (mm) cc_final: 0.7995 (tp) REVERT: B 851 CYS cc_start: 0.8153 (t) cc_final: 0.7613 (m) REVERT: B 854 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7987 (tttp) REVERT: B 911 VAL cc_start: 0.8430 (t) cc_final: 0.8152 (m) REVERT: B 913 GLN cc_start: 0.7892 (pt0) cc_final: 0.7617 (pt0) REVERT: B 921 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8470 (mmmm) REVERT: B 933 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7932 (mtmm) REVERT: B 950 ASP cc_start: 0.7508 (t70) cc_final: 0.6869 (t70) REVERT: B 969 LYS cc_start: 0.7895 (pttm) cc_final: 0.7607 (pttm) REVERT: B 997 ILE cc_start: 0.8339 (tt) cc_final: 0.7952 (pt) REVERT: B 1002 GLN cc_start: 0.7884 (tp40) cc_final: 0.7346 (tm-30) REVERT: B 1003 SER cc_start: 0.8789 (m) cc_final: 0.8087 (t) REVERT: B 1005 GLN cc_start: 0.8316 (tp40) cc_final: 0.7978 (tp40) REVERT: B 1010 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: B 1061 VAL cc_start: 0.8759 (t) cc_final: 0.8339 (p) REVERT: B 1086 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8057 (ptpp) REVERT: B 1097 SER cc_start: 0.8478 (t) cc_final: 0.7890 (p) REVERT: C 41 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7315 (mttt) REVERT: C 53 ASP cc_start: 0.7370 (t0) cc_final: 0.7054 (m-30) REVERT: C 187 LEU cc_start: 0.7305 (tp) cc_final: 0.7077 (tp) REVERT: C 199 PHE cc_start: 0.7801 (t80) cc_final: 0.7341 (t80) REVERT: C 201 ILE cc_start: 0.8883 (mt) cc_final: 0.8654 (mp) REVERT: C 297 SER cc_start: 0.7957 (m) cc_final: 0.7208 (p) REVERT: C 298 GLU cc_start: 0.7458 (tt0) cc_final: 0.7241 (tt0) REVERT: C 301 CYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5505 (m) REVERT: C 324 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7195 (tm-30) REVERT: C 326 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6386 (pt) REVERT: C 332 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6289 (pp) REVERT: C 436 TRP cc_start: 0.7451 (p-90) cc_final: 0.6877 (p-90) REVERT: C 542 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7396 (t0) REVERT: C 563 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6970 (mm-40) REVERT: C 588 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7725 (p) REVERT: C 619 GLU cc_start: 0.6961 (mp0) cc_final: 0.6393 (mp0) REVERT: C 644 GLN cc_start: 0.7634 (tp40) cc_final: 0.6989 (tp40) REVERT: C 674 TYR cc_start: 0.7982 (t80) cc_final: 0.7585 (t80) REVERT: C 705 VAL cc_start: 0.8288 (t) cc_final: 0.8014 (m) REVERT: C 759 PHE cc_start: 0.6882 (t80) cc_final: 0.5973 (t80) REVERT: C 764 LYS cc_start: 0.8214 (tttm) cc_final: 0.7917 (ttpp) REVERT: C 776 LYS cc_start: 0.8457 (tptp) cc_final: 0.8084 (tptp) REVERT: C 801 ASN cc_start: 0.5467 (t0) cc_final: 0.5249 (t0) REVERT: C 825 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8161 (ttmm) REVERT: C 854 LYS cc_start: 0.8330 (tmmt) cc_final: 0.7896 (tptp) REVERT: C 869 MET cc_start: 0.8339 (mtt) cc_final: 0.8112 (mtm) REVERT: C 904 TYR cc_start: 0.7856 (m-10) cc_final: 0.7640 (m-10) REVERT: C 918 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6952 (tt0) REVERT: C 922 LEU cc_start: 0.8920 (tp) cc_final: 0.8689 (tt) REVERT: C 945 LEU cc_start: 0.8569 (mm) cc_final: 0.8293 (mt) REVERT: C 964 LYS cc_start: 0.8619 (tppt) cc_final: 0.8237 (ttmm) REVERT: C 990 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 1005 GLN cc_start: 0.8147 (tp40) cc_final: 0.6840 (tp-100) REVERT: C 1014 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7466 (ttm110) REVERT: C 1072 GLU cc_start: 0.8269 (pm20) cc_final: 0.7932 (pm20) REVERT: C 1081 ILE cc_start: 0.8567 (pt) cc_final: 0.8364 (mt) REVERT: C 1101 HIS cc_start: 0.8583 (m-70) cc_final: 0.8151 (m90) REVERT: D 87 MET cc_start: 0.0210 (mmp) cc_final: 0.0006 (mmm) REVERT: E 39 GLN cc_start: 0.3927 (mm110) cc_final: 0.2945 (mm110) REVERT: G 49 MET cc_start: 0.2765 (ppp) cc_final: 0.1995 (tpt) REVERT: H 60 ARG cc_start: 0.5496 (mmm160) cc_final: 0.5010 (mmt90) outliers start: 157 outliers final: 93 residues processed: 842 average time/residue: 0.1809 time to fit residues: 242.9505 Evaluate side-chains 792 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 685 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 111 ASP 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 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 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 724 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE 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 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 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 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 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 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 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 221 SER 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 931 ILE 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: 2.9990 chunk 154 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 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 186 ASN C 913 GLN C 955 ASN C 957 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.172065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127834 restraints weight = 56157.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131902 restraints weight = 24911.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134344 restraints weight = 13976.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135916 restraints weight = 9352.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136814 restraints weight = 7186.009| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3461 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= 0.127 Angle : 0.595 14.813 40768 Z= 0.297 Chirality : 0.044 0.287 4657 Planarity : 0.004 0.049 5239 Dihedral : 5.296 61.612 4121 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.63 % Allowed : 16.62 % Favored : 78.75 % 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: -2.65 (0.13), residues: 3713 helix: 0.81 (0.21), residues: 655 sheet: -1.63 (0.17), residues: 766 loop : -2.75 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 99 TYR 0.031 0.001 TYR A 495 PHE 0.030 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 0.00284 (29860) covalent geometry : angle 0.59045 (40678) SS BOND : bond 0.00387 ( 45) SS BOND : angle 1.63818 ( 90) hydrogen bonds : bond 0.03878 ( 849) hydrogen bonds : angle 5.43810 ( 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 : 1.199 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: 0.6341 (m) cc_final: 0.5853 (p) REVERT: A 41 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7983 (mtpt) REVERT: A 87 ASN cc_start: 0.7203 (p0) cc_final: 0.6988 (p0) REVERT: A 188 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6618 (mmt180) REVERT: A 281 GLU cc_start: 0.7348 (pp20) cc_final: 0.7039 (pp20) REVERT: A 297 SER cc_start: 0.8432 (m) cc_final: 0.8060 (p) REVERT: A 326 ILE cc_start: 0.7906 (mp) cc_final: 0.7629 (mt) REVERT: A 478 LYS cc_start: -0.0693 (OUTLIER) cc_final: -0.1256 (ptmt) REVERT: A 535 LYS cc_start: 0.8446 (mttp) cc_final: 0.8245 (mttp) REVERT: A 542 ASN cc_start: 0.8225 (t0) cc_final: 0.7863 (m-40) REVERT: A 592 PHE cc_start: 0.7799 (p90) cc_final: 0.7263 (p90) REVERT: A 654 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6980 (mm-30) REVERT: A 674 TYR cc_start: 0.8219 (t80) cc_final: 0.7661 (t80) REVERT: A 697 MET cc_start: 0.7386 (ttp) cc_final: 0.7129 (mtp) REVERT: A 698 SER cc_start: 0.8507 (t) cc_final: 0.7977 (p) REVERT: A 710 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7223 (p0) REVERT: A 754 LEU cc_start: 0.8438 (mt) cc_final: 0.8236 (mt) REVERT: A 759 PHE cc_start: 0.6910 (m-80) cc_final: 0.6455 (m-80) REVERT: A 763 LEU cc_start: 0.8439 (mt) cc_final: 0.8168 (mt) REVERT: A 773 GLU cc_start: 0.6694 (tm-30) cc_final: 0.5993 (tm-30) REVERT: A 774 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6876 (mm110) REVERT: A 803 SER cc_start: 0.8749 (m) cc_final: 0.8240 (p) REVERT: A 825 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8222 (mmtm) REVERT: A 854 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8036 (tttt) REVERT: A 868 GLU cc_start: 0.7398 (tp30) cc_final: 0.7040 (tp30) REVERT: A 869 MET cc_start: 0.8193 (mtt) cc_final: 0.7951 (mtm) REVERT: A 878 LEU cc_start: 0.8280 (mt) cc_final: 0.7949 (mp) REVERT: A 921 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8185 (mmmm) REVERT: A 925 ASN cc_start: 0.8472 (m-40) cc_final: 0.8118 (m-40) REVERT: A 945 LEU cc_start: 0.8658 (mm) cc_final: 0.8407 (mp) REVERT: A 949 GLN cc_start: 0.8316 (mm110) cc_final: 0.7500 (mm-40) REVERT: A 953 ASN cc_start: 0.8336 (m-40) cc_final: 0.7945 (m110) REVERT: A 960 ASN cc_start: 0.8041 (m110) cc_final: 0.7708 (m-40) REVERT: A 961 THR cc_start: 0.8637 (t) cc_final: 0.8403 (p) REVERT: A 979 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7301 (t0) REVERT: A 994 ASP cc_start: 0.7136 (m-30) cc_final: 0.6858 (m-30) REVERT: A 1002 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 1029 MET cc_start: 0.8270 (tpp) cc_final: 0.7626 (ttm) REVERT: A 1038 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8250 (mttt) REVERT: A 1117 THR cc_start: 0.8483 (p) cc_final: 0.8195 (t) REVERT: A 1129 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 1141 LEU cc_start: 0.8267 (tp) cc_final: 0.7959 (tt) REVERT: B 60 SER cc_start: 0.8583 (t) cc_final: 0.8352 (t) REVERT: B 104 TRP cc_start: 0.7304 (m-90) cc_final: 0.6897 (m-90) REVERT: B 105 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 106 PHE cc_start: 0.7429 (m-80) cc_final: 0.7044 (m-80) REVERT: B 170 TYR cc_start: 0.8021 (t80) cc_final: 0.7785 (t80) REVERT: B 199 PHE cc_start: 0.7837 (t80) cc_final: 0.7635 (t80) REVERT: B 200 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7676 (mmmm) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7656 (pm20) REVERT: B 278 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8340 (ttmt) REVERT: B 286 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7329 (p) REVERT: B 287 ASP cc_start: 0.7186 (p0) cc_final: 0.6973 (p0) REVERT: B 343 ASN cc_start: 0.6574 (t0) cc_final: 0.6004 (t0) REVERT: B 353 TRP cc_start: 0.8427 (p-90) cc_final: 0.8130 (p-90) REVERT: B 354 ASN cc_start: 0.7907 (m110) cc_final: 0.7392 (m110) REVERT: B 380 TYR cc_start: 0.6763 (m-80) cc_final: 0.6321 (m-80) REVERT: B 394 ASN cc_start: 0.7939 (p0) cc_final: 0.7361 (p0) REVERT: B 408 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7239 (ppp-140) REVERT: B 409 GLN cc_start: 0.8586 (mp10) cc_final: 0.8360 (mp10) REVERT: B 429 PHE cc_start: 0.8357 (t80) cc_final: 0.7903 (t80) REVERT: B 465 GLU cc_start: 0.8741 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 512 VAL cc_start: 0.8792 (m) cc_final: 0.8430 (p) REVERT: B 547 LYS cc_start: 0.8385 (tptp) cc_final: 0.8168 (tttm) REVERT: B 564 GLN cc_start: 0.8134 (pm20) cc_final: 0.7457 (pm20) REVERT: B 645 THR cc_start: 0.8284 (p) cc_final: 0.8048 (p) REVERT: B 651 ILE cc_start: 0.8349 (mt) cc_final: 0.8080 (mm) REVERT: B 659 SER cc_start: 0.8702 (m) cc_final: 0.8171 (p) REVERT: B 725 GLU cc_start: 0.7646 (tt0) cc_final: 0.6982 (tp30) REVERT: B 759 PHE cc_start: 0.7392 (t80) cc_final: 0.6986 (t80) REVERT: B 764 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8141 (ttpp) REVERT: B 773 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: B 776 LYS cc_start: 0.8259 (tmmt) cc_final: 0.7837 (ttpp) REVERT: B 823 PHE cc_start: 0.7093 (m-10) cc_final: 0.6760 (m-10) REVERT: B 850 ILE cc_start: 0.8339 (mm) cc_final: 0.8005 (tp) REVERT: B 851 CYS cc_start: 0.8189 (t) cc_final: 0.7586 (m) REVERT: B 854 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7957 (tttp) REVERT: B 856 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8466 (mmmm) REVERT: B 911 VAL cc_start: 0.8422 (t) cc_final: 0.8165 (m) REVERT: B 913 GLN cc_start: 0.7865 (pt0) cc_final: 0.7644 (pt0) REVERT: B 921 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8449 (mmmm) REVERT: B 933 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7921 (mtmm) REVERT: B 950 ASP cc_start: 0.7540 (t70) cc_final: 0.6635 (t70) REVERT: B 969 LYS cc_start: 0.7910 (pttm) cc_final: 0.7621 (pttm) REVERT: B 1002 GLN cc_start: 0.7894 (tp40) cc_final: 0.7400 (tm-30) REVERT: B 1003 SER cc_start: 0.8791 (m) cc_final: 0.8019 (t) REVERT: B 1005 GLN cc_start: 0.8325 (tp40) cc_final: 0.7985 (tp40) REVERT: B 1028 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8282 (mttt) REVERT: B 1061 VAL cc_start: 0.8764 (t) cc_final: 0.8349 (p) REVERT: B 1086 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8108 (ptpp) REVERT: B 1097 SER cc_start: 0.8490 (t) cc_final: 0.7918 (p) REVERT: C 41 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7252 (mtpp) REVERT: C 199 PHE cc_start: 0.7794 (t80) cc_final: 0.7341 (t80) REVERT: C 201 ILE cc_start: 0.8894 (mt) cc_final: 0.8574 (mp) REVERT: C 297 SER cc_start: 0.7878 (m) cc_final: 0.7069 (p) REVERT: C 298 GLU cc_start: 0.7437 (tt0) cc_final: 0.7195 (tt0) REVERT: C 301 CYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5614 (m) REVERT: C 324 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 332 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6295 (pp) REVERT: C 436 TRP cc_start: 0.7503 (p-90) cc_final: 0.6987 (p-90) REVERT: C 542 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7248 (t0) REVERT: C 563 GLN cc_start: 0.7231 (mm-40) cc_final: 0.7029 (mm-40) REVERT: C 588 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7770 (p) REVERT: C 615 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8133 (t) REVERT: C 619 GLU cc_start: 0.6983 (mp0) cc_final: 0.6474 (mp0) REVERT: C 644 GLN cc_start: 0.7690 (tp40) cc_final: 0.7037 (tp40) REVERT: C 674 TYR cc_start: 0.7944 (t80) cc_final: 0.7627 (t80) REVERT: C 705 VAL cc_start: 0.8287 (t) cc_final: 0.8007 (m) REVERT: C 725 GLU cc_start: 0.7237 (tt0) cc_final: 0.7001 (tt0) REVERT: C 740 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7179 (tpp) REVERT: C 759 PHE cc_start: 0.6815 (t80) cc_final: 0.6582 (t80) REVERT: C 764 LYS cc_start: 0.8274 (tttm) cc_final: 0.7903 (ttpp) REVERT: C 776 LYS cc_start: 0.8442 (tptp) cc_final: 0.8131 (tptp) REVERT: C 780 GLU cc_start: 0.7465 (pt0) cc_final: 0.7247 (pt0) REVERT: C 801 ASN cc_start: 0.5507 (t0) cc_final: 0.5272 (t0) REVERT: C 825 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8117 (ttmm) REVERT: C 854 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7853 (tptp) REVERT: C 869 MET cc_start: 0.8377 (mtt) cc_final: 0.8147 (mtm) REVERT: C 904 TYR cc_start: 0.7897 (m-10) cc_final: 0.7654 (m-10) REVERT: C 918 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6978 (tt0) REVERT: C 921 LYS cc_start: 0.8442 (tptp) cc_final: 0.8186 (tptp) REVERT: C 964 LYS cc_start: 0.8626 (tppt) cc_final: 0.8175 (ttmm) REVERT: C 990 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 1014 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7439 (ttm110) REVERT: C 1050 MET cc_start: 0.7197 (mtm) cc_final: 0.6993 (mtm) REVERT: C 1081 ILE cc_start: 0.8560 (pt) cc_final: 0.8354 (mt) REVERT: C 1101 HIS cc_start: 0.8573 (m-70) cc_final: 0.8168 (m90) REVERT: D 4 LEU cc_start: 0.8209 (mt) cc_final: 0.7500 (tt) REVERT: E 39 GLN cc_start: 0.4476 (mm110) cc_final: 0.3995 (mm110) REVERT: G 49 MET cc_start: 0.3142 (ppp) cc_final: 0.2214 (tpt) outliers start: 150 outliers final: 96 residues processed: 806 average time/residue: 0.1824 time to fit residues: 233.7254 Evaluate side-chains 794 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 678 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 560 LEU 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 710 ASN 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 901 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 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 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 752 LEU Chi-restraints excluded: chain B residue 764 LYS 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 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 130 VAL Chi-restraints excluded: chain C residue 206 THR 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 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 615 VAL 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 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 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: 2.9990 chunk 269 optimal weight: 0.4980 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 506 GLN B 542 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 164 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 = 0.4170 r_free = 0.4170 target = 0.170225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124975 restraints weight = 54542.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128939 restraints weight = 24728.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131337 restraints weight = 14179.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132894 restraints weight = 9683.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133808 restraints weight = 7495.647| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29905 Z= 0.257 Angle : 0.658 13.076 40768 Z= 0.338 Chirality : 0.046 0.214 4657 Planarity : 0.005 0.051 5239 Dihedral : 5.627 62.702 4117 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.03 % Allowed : 17.55 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.13), residues: 3713 helix: 0.65 (0.21), residues: 655 sheet: -1.69 (0.17), residues: 820 loop : -2.66 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 99 TYR 0.027 0.002 TYR C1067 PHE 0.029 0.002 PHE C 106 TRP 0.040 0.002 TRP D 110 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00550 (29860) covalent geometry : angle 0.65338 (40678) SS BOND : bond 0.00678 ( 45) SS BOND : angle 1.86172 ( 90) hydrogen bonds : bond 0.04413 ( 849) hydrogen bonds : angle 5.51960 ( 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 871 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 708 time to evaluate : 1.338 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: A 33 THR cc_start: 0.6837 (m) cc_final: 0.6388 (p) REVERT: A 87 ASN cc_start: 0.7213 (p0) cc_final: 0.7003 (p0) REVERT: A 226 LEU cc_start: 0.8023 (mt) cc_final: 0.7693 (mt) REVERT: A 281 GLU cc_start: 0.7441 (pp20) cc_final: 0.7106 (pp20) REVERT: A 297 SER cc_start: 0.8459 (m) cc_final: 0.8073 (p) REVERT: A 326 ILE cc_start: 0.7978 (mp) cc_final: 0.7762 (mt) REVERT: A 328 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6780 (mtm-85) REVERT: A 436 TRP cc_start: 0.7181 (p-90) cc_final: 0.6819 (p90) REVERT: A 478 LYS cc_start: -0.0972 (OUTLIER) cc_final: -0.1558 (ptmt) REVERT: A 542 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8106 (t0) REVERT: A 592 PHE cc_start: 0.7860 (p90) cc_final: 0.7224 (p90) REVERT: A 644 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 654 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 660 TYR cc_start: 0.8092 (m-10) cc_final: 0.7866 (m-10) REVERT: A 674 TYR cc_start: 0.8319 (t80) cc_final: 0.7835 (t80) REVERT: A 697 MET cc_start: 0.7417 (ttp) cc_final: 0.7114 (mtp) REVERT: A 698 SER cc_start: 0.8509 (t) cc_final: 0.7936 (p) REVERT: A 710 ASN cc_start: 0.7668 (p0) cc_final: 0.7341 (p0) REVERT: A 759 PHE cc_start: 0.6953 (m-80) cc_final: 0.6552 (m-80) REVERT: A 763 LEU cc_start: 0.8562 (mt) cc_final: 0.8355 (mt) REVERT: A 773 GLU cc_start: 0.6848 (tm-30) cc_final: 0.5850 (tm-30) REVERT: A 803 SER cc_start: 0.8887 (m) cc_final: 0.8373 (p) REVERT: A 825 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8239 (mmmt) REVERT: A 854 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8097 (tttm) REVERT: A 868 GLU cc_start: 0.7413 (tp30) cc_final: 0.7125 (tp30) REVERT: A 869 MET cc_start: 0.8211 (mtt) cc_final: 0.7974 (mtm) REVERT: A 878 LEU cc_start: 0.8401 (mt) cc_final: 0.7963 (mp) REVERT: A 904 TYR cc_start: 0.8066 (m-10) cc_final: 0.7740 (m-10) REVERT: A 921 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8216 (mmmm) REVERT: A 925 ASN cc_start: 0.8497 (m-40) cc_final: 0.8125 (m-40) REVERT: A 945 LEU cc_start: 0.8668 (mm) cc_final: 0.8404 (mp) REVERT: A 953 ASN cc_start: 0.8407 (m-40) cc_final: 0.8052 (m110) REVERT: A 957 GLN cc_start: 0.8263 (tt0) cc_final: 0.7989 (tt0) REVERT: A 961 THR cc_start: 0.8699 (t) cc_final: 0.8472 (p) REVERT: A 976 VAL cc_start: 0.9060 (m) cc_final: 0.8766 (p) REVERT: A 977 LEU cc_start: 0.8948 (mt) cc_final: 0.8727 (mt) REVERT: A 978 ASN cc_start: 0.7971 (m-40) cc_final: 0.7538 (m-40) REVERT: A 979 ASP cc_start: 0.7749 (t0) cc_final: 0.7395 (t0) REVERT: A 1002 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 1029 MET cc_start: 0.8329 (tpp) cc_final: 0.7523 (ttm) REVERT: A 1038 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8129 (mtpp) REVERT: A 1050 MET cc_start: 0.7171 (ttm) cc_final: 0.6775 (mtp) REVERT: A 1117 THR cc_start: 0.8622 (p) cc_final: 0.8338 (t) REVERT: A 1141 LEU cc_start: 0.8387 (tp) cc_final: 0.8095 (tt) REVERT: B 60 SER cc_start: 0.8730 (t) cc_final: 0.8465 (t) REVERT: B 81 ASN cc_start: 0.8384 (t0) cc_final: 0.8013 (t0) REVERT: B 104 TRP cc_start: 0.7749 (m-90) cc_final: 0.7425 (m-90) REVERT: B 106 PHE cc_start: 0.7524 (m-80) cc_final: 0.7033 (m-80) REVERT: B 200 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7797 (mmmm) REVERT: B 224 GLU cc_start: 0.8038 (pm20) cc_final: 0.7666 (pm20) REVERT: B 343 ASN cc_start: 0.6679 (t0) cc_final: 0.6070 (t0) REVERT: B 353 TRP cc_start: 0.8496 (p-90) cc_final: 0.8152 (p-90) REVERT: B 354 ASN cc_start: 0.7898 (m110) cc_final: 0.7433 (m110) REVERT: B 380 TYR cc_start: 0.6877 (m-80) cc_final: 0.6411 (m-80) REVERT: B 392 PHE cc_start: 0.7188 (m-80) cc_final: 0.6814 (m-80) REVERT: B 394 ASN cc_start: 0.8109 (p0) cc_final: 0.7370 (p0) REVERT: B 408 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7513 (ptm-80) REVERT: B 429 PHE cc_start: 0.8449 (t80) cc_final: 0.7960 (t80) REVERT: B 465 GLU cc_start: 0.8837 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 481 ASN cc_start: 0.8130 (t0) cc_final: 0.7920 (t0) REVERT: B 512 VAL cc_start: 0.8826 (m) cc_final: 0.8510 (p) REVERT: B 564 GLN cc_start: 0.8182 (pm20) cc_final: 0.7620 (pm20) REVERT: B 651 ILE cc_start: 0.8374 (mt) cc_final: 0.8128 (pt) REVERT: B 659 SER cc_start: 0.8734 (m) cc_final: 0.8204 (p) REVERT: B 663 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: B 703 ASN cc_start: 0.8415 (t0) cc_final: 0.7852 (t0) REVERT: B 725 GLU cc_start: 0.7443 (tt0) cc_final: 0.6802 (tp30) REVERT: B 759 PHE cc_start: 0.7501 (t80) cc_final: 0.6926 (t80) REVERT: B 765 ARG cc_start: 0.7355 (ttm110) cc_final: 0.7090 (ttm110) REVERT: B 773 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: B 776 LYS cc_start: 0.8294 (tmmt) cc_final: 0.7917 (ttpt) REVERT: B 850 ILE cc_start: 0.8369 (mm) cc_final: 0.8165 (tp) REVERT: B 851 CYS cc_start: 0.8278 (t) cc_final: 0.7593 (m) REVERT: B 854 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8107 (tttp) REVERT: B 856 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8492 (mmmm) REVERT: B 911 VAL cc_start: 0.8491 (t) cc_final: 0.8211 (m) REVERT: B 921 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8479 (mmmm) REVERT: B 933 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7976 (mtmm) REVERT: B 950 ASP cc_start: 0.7756 (t70) cc_final: 0.6647 (t70) REVERT: B 954 HIS cc_start: 0.7899 (m90) cc_final: 0.7329 (m-70) REVERT: B 969 LYS cc_start: 0.8039 (pttm) cc_final: 0.7716 (pttm) REVERT: B 1003 SER cc_start: 0.8866 (m) cc_final: 0.8576 (t) REVERT: B 1005 GLN cc_start: 0.8431 (tp40) cc_final: 0.7813 (tp40) REVERT: B 1028 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8374 (mttt) REVERT: B 1050 MET cc_start: 0.7660 (mtp) cc_final: 0.7424 (mtp) REVERT: B 1086 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8219 (ptpp) REVERT: B 1097 SER cc_start: 0.8453 (t) cc_final: 0.7889 (p) REVERT: B 1107 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7517 (mtt180) REVERT: C 41 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7397 (mtpp) REVERT: C 43 PHE cc_start: 0.8300 (t80) cc_final: 0.8013 (t80) REVERT: C 65 PHE cc_start: 0.7247 (m-80) cc_final: 0.6688 (m-80) REVERT: C 199 PHE cc_start: 0.7844 (t80) cc_final: 0.7216 (t80) REVERT: C 201 ILE cc_start: 0.8873 (mt) cc_final: 0.8529 (mp) REVERT: C 293 LEU cc_start: 0.8649 (tp) cc_final: 0.8336 (tp) REVERT: C 297 SER cc_start: 0.8020 (m) cc_final: 0.7317 (p) REVERT: C 298 GLU cc_start: 0.7527 (tt0) cc_final: 0.7290 (tt0) REVERT: C 301 CYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5738 (m) REVERT: C 308 VAL cc_start: 0.8575 (t) cc_final: 0.8333 (m) REVERT: C 326 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7119 (pt) REVERT: C 332 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6360 (pp) REVERT: C 436 TRP cc_start: 0.7607 (p-90) cc_final: 0.7049 (p-90) REVERT: C 542 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7422 (t0) REVERT: C 563 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7074 (mm-40) REVERT: C 615 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8279 (t) REVERT: C 619 GLU cc_start: 0.7087 (mp0) cc_final: 0.6570 (mp0) REVERT: C 644 GLN cc_start: 0.7954 (tp40) cc_final: 0.7337 (tp40) REVERT: C 674 TYR cc_start: 0.8021 (t80) cc_final: 0.7608 (t80) REVERT: C 705 VAL cc_start: 0.8415 (t) cc_final: 0.8165 (m) REVERT: C 725 GLU cc_start: 0.7283 (tt0) cc_final: 0.7065 (tt0) REVERT: C 759 PHE cc_start: 0.6928 (t80) cc_final: 0.6422 (t80) REVERT: C 764 LYS cc_start: 0.8246 (tttm) cc_final: 0.7908 (ttpp) REVERT: C 776 LYS cc_start: 0.8501 (tptp) cc_final: 0.8091 (tptp) REVERT: C 801 ASN cc_start: 0.5245 (t0) cc_final: 0.4916 (t0) REVERT: C 825 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8177 (ttmm) REVERT: C 854 LYS cc_start: 0.8402 (tmmt) cc_final: 0.7961 (tptp) REVERT: C 869 MET cc_start: 0.8397 (mtt) cc_final: 0.8134 (mtm) REVERT: C 904 TYR cc_start: 0.7981 (m-10) cc_final: 0.7758 (m-10) REVERT: C 918 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7240 (tt0) REVERT: C 964 LYS cc_start: 0.8559 (tppt) cc_final: 0.8168 (ttmm) REVERT: C 990 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 1005 GLN cc_start: 0.8254 (tp40) cc_final: 0.7867 (tp40) REVERT: C 1014 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7536 (ttm110) REVERT: C 1050 MET cc_start: 0.7289 (mtm) cc_final: 0.6983 (mtm) REVERT: C 1072 GLU cc_start: 0.8357 (pm20) cc_final: 0.8092 (pm20) REVERT: C 1101 HIS cc_start: 0.8562 (m-70) cc_final: 0.8168 (m90) REVERT: D 4 LEU cc_start: 0.8229 (mt) cc_final: 0.7564 (tt) REVERT: D 87 MET cc_start: 0.1021 (mmp) cc_final: 0.0649 (mmm) REVERT: D 96 TYR cc_start: 0.2522 (m-80) cc_final: 0.1526 (m-80) REVERT: H 60 ARG cc_start: 0.5357 (mmt90) cc_final: 0.5154 (mmt90) outliers start: 163 outliers final: 112 residues processed: 818 average time/residue: 0.1914 time to fit residues: 247.8373 Evaluate side-chains 808 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 682 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 169 GLU 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 328 ARG 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 542 ASN Chi-restraints excluded: chain A residue 560 LEU 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 724 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1060 VAL 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 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 305 SER 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 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL 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 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1001 LEU 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 50 SER Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR 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 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL 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 931 ILE Chi-restraints excluded: chain C residue 933 LYS 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 C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR 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 69 LEU 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 50 ILE Chi-restraints excluded: chain I residue 62 ASN 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: 0.7980 chunk 304 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 913 GLN C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125723 restraints weight = 55533.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129766 restraints weight = 24664.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132218 restraints weight = 13853.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133769 restraints weight = 9264.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134658 restraints weight = 7103.175| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29905 Z= 0.129 Angle : 0.607 12.327 40768 Z= 0.305 Chirality : 0.044 0.236 4657 Planarity : 0.004 0.058 5239 Dihedral : 5.313 61.842 4107 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.10 % Allowed : 19.49 % Favored : 76.41 % 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: -2.42 (0.13), residues: 3713 helix: 0.91 (0.21), residues: 647 sheet: -1.54 (0.17), residues: 827 loop : -2.54 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 328 TYR 0.026 0.001 TYR C 655 PHE 0.020 0.001 PHE C 190 TRP 0.019 0.001 TRP D 110 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (29860) covalent geometry : angle 0.60096 (40678) SS BOND : bond 0.00370 ( 45) SS BOND : angle 1.90632 ( 90) hydrogen bonds : bond 0.03801 ( 849) hydrogen bonds : angle 5.26157 ( 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 827 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 694 time to evaluate : 0.763 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: A 33 THR cc_start: 0.6736 (m) cc_final: 0.6250 (p) REVERT: A 41 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: A 87 ASN cc_start: 0.7239 (p0) cc_final: 0.7022 (p0) REVERT: A 281 GLU cc_start: 0.7446 (pp20) cc_final: 0.7143 (pp20) REVERT: A 297 SER cc_start: 0.8412 (m) cc_final: 0.8029 (p) REVERT: A 326 ILE cc_start: 0.7946 (mp) cc_final: 0.7700 (mt) REVERT: A 328 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7176 (ttm170) REVERT: A 436 TRP cc_start: 0.6980 (p-90) cc_final: 0.6609 (p90) REVERT: A 478 LYS cc_start: -0.0726 (OUTLIER) cc_final: -0.1840 (ptmt) REVERT: A 542 ASN cc_start: 0.8224 (t0) cc_final: 0.7894 (t0) REVERT: A 592 PHE cc_start: 0.7783 (p90) cc_final: 0.7359 (p90) REVERT: A 644 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 660 TYR cc_start: 0.8015 (m-10) cc_final: 0.7793 (m-10) REVERT: A 674 TYR cc_start: 0.8277 (t80) cc_final: 0.7725 (t80) REVERT: A 697 MET cc_start: 0.7409 (ttp) cc_final: 0.7188 (mtp) REVERT: A 698 SER cc_start: 0.8510 (t) cc_final: 0.7921 (p) REVERT: A 710 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7307 (p0) REVERT: A 759 PHE cc_start: 0.6923 (m-80) cc_final: 0.6525 (m-80) REVERT: A 763 LEU cc_start: 0.8454 (mt) cc_final: 0.8238 (mt) REVERT: A 774 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7425 (mm110) REVERT: A 803 SER cc_start: 0.8811 (m) cc_final: 0.8290 (p) REVERT: A 825 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8257 (mmtt) REVERT: A 854 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8017 (tttt) REVERT: A 868 GLU cc_start: 0.7394 (tp30) cc_final: 0.7068 (tp30) REVERT: A 869 MET cc_start: 0.8216 (mtt) cc_final: 0.7976 (mtm) REVERT: A 878 LEU cc_start: 0.8330 (mt) cc_final: 0.7930 (mp) REVERT: A 904 TYR cc_start: 0.8031 (m-10) cc_final: 0.7797 (m-10) REVERT: A 921 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8185 (mmmm) REVERT: A 925 ASN cc_start: 0.8448 (m-40) cc_final: 0.8069 (m-40) REVERT: A 945 LEU cc_start: 0.8661 (mm) cc_final: 0.8404 (mp) REVERT: A 953 ASN cc_start: 0.8393 (m-40) cc_final: 0.8032 (m110) REVERT: A 957 GLN cc_start: 0.8247 (tt0) cc_final: 0.7974 (tt0) REVERT: A 961 THR cc_start: 0.8671 (t) cc_final: 0.8419 (p) REVERT: A 977 LEU cc_start: 0.8905 (mt) cc_final: 0.8663 (mt) REVERT: A 979 ASP cc_start: 0.7660 (t0) cc_final: 0.7327 (t0) REVERT: A 988 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7078 (tm-30) REVERT: A 994 ASP cc_start: 0.7271 (m-30) cc_final: 0.6953 (t0) REVERT: A 1002 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 1029 MET cc_start: 0.8275 (tpp) cc_final: 0.7567 (ttm) REVERT: A 1038 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8188 (mttm) REVERT: A 1050 MET cc_start: 0.6945 (ttm) cc_final: 0.6614 (mtp) REVERT: A 1117 THR cc_start: 0.8609 (p) cc_final: 0.8310 (t) REVERT: A 1141 LEU cc_start: 0.8361 (tp) cc_final: 0.8100 (tt) REVERT: B 60 SER cc_start: 0.8712 (t) cc_final: 0.8461 (t) REVERT: B 170 TYR cc_start: 0.8070 (t80) cc_final: 0.7652 (t80) REVERT: B 200 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7842 (mmmm) REVERT: B 224 GLU cc_start: 0.8037 (pm20) cc_final: 0.7646 (pm20) REVERT: B 241 LEU cc_start: 0.7915 (mt) cc_final: 0.7693 (mt) REVERT: B 278 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8307 (ttmt) REVERT: B 343 ASN cc_start: 0.6666 (t0) cc_final: 0.6060 (t0) REVERT: B 353 TRP cc_start: 0.8467 (p-90) cc_final: 0.8198 (p-90) REVERT: B 354 ASN cc_start: 0.7845 (m110) cc_final: 0.7363 (m110) REVERT: B 380 TYR cc_start: 0.6869 (m-80) cc_final: 0.6332 (m-80) REVERT: B 392 PHE cc_start: 0.7241 (m-80) cc_final: 0.6887 (m-80) REVERT: B 394 ASN cc_start: 0.8035 (p0) cc_final: 0.7291 (p0) REVERT: B 429 PHE cc_start: 0.8432 (t80) cc_final: 0.7833 (t80) REVERT: B 465 GLU cc_start: 0.8805 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 481 ASN cc_start: 0.8165 (t0) cc_final: 0.7904 (t0) REVERT: B 512 VAL cc_start: 0.8755 (m) cc_final: 0.8406 (p) REVERT: B 528 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6910 (ptpp) REVERT: B 542 ASN cc_start: 0.7842 (t0) cc_final: 0.7521 (t0) REVERT: B 564 GLN cc_start: 0.8112 (pm20) cc_final: 0.7533 (pm20) REVERT: B 651 ILE cc_start: 0.8346 (mt) cc_final: 0.8107 (pt) REVERT: B 658 ASN cc_start: 0.7424 (t0) cc_final: 0.6992 (t0) REVERT: B 659 SER cc_start: 0.8600 (m) cc_final: 0.7828 (p) REVERT: B 663 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: B 725 GLU cc_start: 0.7392 (tt0) cc_final: 0.6720 (tp30) REVERT: B 737 ASP cc_start: 0.7512 (t0) cc_final: 0.7262 (p0) REVERT: B 759 PHE cc_start: 0.7591 (t80) cc_final: 0.6567 (t80) REVERT: B 773 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: B 776 LYS cc_start: 0.8278 (tmmt) cc_final: 0.7899 (ttpt) REVERT: B 850 ILE cc_start: 0.8327 (mm) cc_final: 0.8092 (tp) REVERT: B 851 CYS cc_start: 0.8249 (t) cc_final: 0.7583 (m) REVERT: B 854 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8025 (tttp) REVERT: B 911 VAL cc_start: 0.8458 (t) cc_final: 0.8164 (m) REVERT: B 921 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8427 (mmmt) REVERT: B 933 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8000 (ttmm) REVERT: B 934 ILE cc_start: 0.8528 (tp) cc_final: 0.8243 (tp) REVERT: B 935 GLN cc_start: 0.8056 (tt0) cc_final: 0.7729 (tt0) REVERT: B 950 ASP cc_start: 0.7646 (t70) cc_final: 0.7022 (t70) REVERT: B 962 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 969 LYS cc_start: 0.8003 (pttm) cc_final: 0.7691 (pttm) REVERT: B 1003 SER cc_start: 0.8868 (m) cc_final: 0.8501 (t) REVERT: B 1005 GLN cc_start: 0.8391 (tp40) cc_final: 0.7824 (tp40) REVERT: B 1028 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8306 (mttt) REVERT: B 1097 SER cc_start: 0.8455 (t) cc_final: 0.7874 (p) REVERT: B 1107 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7644 (mtt180) REVERT: C 41 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7102 (mttt) REVERT: C 43 PHE cc_start: 0.8247 (t80) cc_final: 0.7969 (t80) REVERT: C 65 PHE cc_start: 0.7187 (m-80) cc_final: 0.6670 (m-80) REVERT: C 199 PHE cc_start: 0.7785 (t80) cc_final: 0.7106 (t80) REVERT: C 201 ILE cc_start: 0.8911 (mt) cc_final: 0.8600 (mp) REVERT: C 293 LEU cc_start: 0.8599 (tp) cc_final: 0.8301 (tp) REVERT: C 297 SER cc_start: 0.7987 (m) cc_final: 0.7248 (p) REVERT: C 298 GLU cc_start: 0.7438 (tt0) cc_final: 0.7216 (tt0) REVERT: C 301 CYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5660 (m) REVERT: C 308 VAL cc_start: 0.8596 (t) cc_final: 0.8333 (m) REVERT: C 324 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7296 (tm-30) REVERT: C 332 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6287 (pp) REVERT: C 436 TRP cc_start: 0.7570 (p-90) cc_final: 0.6987 (p-90) REVERT: C 542 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7337 (t0) REVERT: C 615 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8348 (t) REVERT: C 619 GLU cc_start: 0.7088 (mp0) cc_final: 0.6548 (mp0) REVERT: C 644 GLN cc_start: 0.7878 (tp40) cc_final: 0.7194 (tp40) REVERT: C 674 TYR cc_start: 0.7984 (t80) cc_final: 0.7580 (t80) REVERT: C 705 VAL cc_start: 0.8373 (t) cc_final: 0.8105 (m) REVERT: C 725 GLU cc_start: 0.7248 (tt0) cc_final: 0.7020 (tt0) REVERT: C 764 LYS cc_start: 0.8378 (tttm) cc_final: 0.7932 (ttpp) REVERT: C 776 LYS cc_start: 0.8473 (tptp) cc_final: 0.8027 (tptp) REVERT: C 825 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8165 (ttmm) REVERT: C 854 LYS cc_start: 0.8311 (tmmt) cc_final: 0.7873 (tptp) REVERT: C 869 MET cc_start: 0.8389 (mtt) cc_final: 0.8093 (mtm) REVERT: C 918 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7188 (tt0) REVERT: C 957 GLN cc_start: 0.8100 (tt0) cc_final: 0.7492 (tp40) REVERT: C 964 LYS cc_start: 0.8528 (tppt) cc_final: 0.8250 (ttmm) REVERT: C 980 ILE cc_start: 0.8437 (mt) cc_final: 0.8147 (mt) REVERT: C 990 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 1014 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7474 (ttm110) REVERT: C 1072 GLU cc_start: 0.8345 (pm20) cc_final: 0.8056 (pm20) REVERT: C 1101 HIS cc_start: 0.8581 (m-70) cc_final: 0.8212 (m90) REVERT: D 4 LEU cc_start: 0.8402 (mt) cc_final: 0.7861 (tt) REVERT: D 87 MET cc_start: 0.1270 (mmp) cc_final: 0.0848 (mmm) REVERT: D 96 TYR cc_start: 0.2350 (m-80) cc_final: 0.1495 (m-80) REVERT: E 39 GLN cc_start: 0.4687 (mm110) cc_final: 0.3992 (mm110) REVERT: G 49 MET cc_start: 0.3200 (ppp) cc_final: 0.2238 (tpt) outliers start: 133 outliers final: 101 residues processed: 790 average time/residue: 0.1903 time to fit residues: 236.9198 Evaluate side-chains 794 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 680 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL 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 328 ARG 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 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 ASN 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 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 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 201 ILE 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 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 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 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 764 LYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE 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 122 ASN 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 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 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL 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 931 ILE Chi-restraints excluded: chain C residue 933 LYS 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 47 LEU Chi-restraints excluded: chain D residue 92 THR 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 70 THR Chi-restraints excluded: chain H residue 117 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 190 optimal weight: 2.9990 chunk 187 optimal weight: 0.0020 chunk 230 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 312 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126059 restraints weight = 55750.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130114 restraints weight = 24746.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132574 restraints weight = 13866.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134110 restraints weight = 9265.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135026 restraints weight = 7104.496| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29905 Z= 0.132 Angle : 0.623 13.434 40768 Z= 0.312 Chirality : 0.044 0.223 4657 Planarity : 0.005 0.155 5239 Dihedral : 5.315 61.513 4107 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.41 % Allowed : 19.55 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 3713 helix: 0.95 (0.21), residues: 660 sheet: -1.50 (0.17), residues: 837 loop : -2.45 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.031 0.001 TYR A 198 PHE 0.023 0.001 PHE A 220 TRP 0.017 0.001 TRP H 38 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (29860) covalent geometry : angle 0.61508 (40678) SS BOND : bond 0.00493 ( 45) SS BOND : angle 2.22361 ( 90) hydrogen bonds : bond 0.03752 ( 849) hydrogen bonds : angle 5.21780 ( 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 819 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 676 time to evaluate : 1.155 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: A 33 THR cc_start: 0.6756 (m) cc_final: 0.6283 (p) REVERT: A 41 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7821 (mtpt) REVERT: A 87 ASN cc_start: 0.7157 (p0) cc_final: 0.6940 (p0) REVERT: A 92 PHE cc_start: 0.7095 (t80) cc_final: 0.6872 (t80) REVERT: A 94 SER cc_start: 0.7416 (OUTLIER) cc_final: 0.7142 (m) REVERT: A 281 GLU cc_start: 0.7377 (pp20) cc_final: 0.7115 (pp20) REVERT: A 297 SER cc_start: 0.8401 (m) cc_final: 0.8029 (p) REVERT: A 319 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7945 (ptp-110) REVERT: A 326 ILE cc_start: 0.7919 (mp) cc_final: 0.7643 (mt) REVERT: A 436 TRP cc_start: 0.7051 (p-90) cc_final: 0.6692 (p90) REVERT: A 533 LEU cc_start: 0.7941 (tp) cc_final: 0.7395 (tp) REVERT: A 535 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8241 (mmtm) REVERT: A 542 ASN cc_start: 0.8155 (t0) cc_final: 0.7872 (t0) REVERT: A 547 LYS cc_start: 0.8428 (mttp) cc_final: 0.8211 (mppt) REVERT: A 592 PHE cc_start: 0.7779 (p90) cc_final: 0.7358 (p90) REVERT: A 644 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 660 TYR cc_start: 0.7783 (m-10) cc_final: 0.7530 (m-10) REVERT: A 674 TYR cc_start: 0.8211 (t80) cc_final: 0.7742 (t80) REVERT: A 697 MET cc_start: 0.7493 (ttp) cc_final: 0.7267 (mtp) REVERT: A 698 SER cc_start: 0.8488 (t) cc_final: 0.7834 (p) REVERT: A 710 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 759 PHE cc_start: 0.6896 (m-80) cc_final: 0.6507 (m-80) REVERT: A 763 LEU cc_start: 0.8466 (mt) cc_final: 0.8254 (mt) REVERT: A 774 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7369 (mm110) REVERT: A 803 SER cc_start: 0.8812 (m) cc_final: 0.8284 (p) REVERT: A 825 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8201 (mmmt) REVERT: A 854 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8012 (tttt) REVERT: A 868 GLU cc_start: 0.7414 (tp30) cc_final: 0.7099 (tp30) REVERT: A 869 MET cc_start: 0.8206 (mtt) cc_final: 0.7965 (mtm) REVERT: A 878 LEU cc_start: 0.8318 (mt) cc_final: 0.7915 (mp) REVERT: A 921 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8169 (mmmm) REVERT: A 925 ASN cc_start: 0.8444 (m-40) cc_final: 0.8054 (m-40) REVERT: A 945 LEU cc_start: 0.8661 (mm) cc_final: 0.8397 (mp) REVERT: A 953 ASN cc_start: 0.8378 (m-40) cc_final: 0.8033 (m110) REVERT: A 957 GLN cc_start: 0.8218 (tt0) cc_final: 0.7974 (tt0) REVERT: A 961 THR cc_start: 0.8663 (t) cc_final: 0.8429 (p) REVERT: A 977 LEU cc_start: 0.8900 (mt) cc_final: 0.8698 (mt) REVERT: A 979 ASP cc_start: 0.7434 (t0) cc_final: 0.7064 (t0) REVERT: A 988 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7065 (tm-30) REVERT: A 994 ASP cc_start: 0.7223 (m-30) cc_final: 0.6901 (t0) REVERT: A 1002 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 1029 MET cc_start: 0.8253 (tpp) cc_final: 0.7607 (ttm) REVERT: A 1038 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8191 (mttm) REVERT: A 1050 MET cc_start: 0.6967 (ttm) cc_final: 0.6610 (mtp) REVERT: A 1117 THR cc_start: 0.8572 (p) cc_final: 0.8279 (t) REVERT: A 1141 LEU cc_start: 0.8357 (tp) cc_final: 0.8100 (tt) REVERT: B 31 SER cc_start: 0.8092 (m) cc_final: 0.7824 (p) REVERT: B 60 SER cc_start: 0.8720 (t) cc_final: 0.8149 (t) REVERT: B 170 TYR cc_start: 0.8067 (t80) cc_final: 0.7593 (t80) REVERT: B 200 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7841 (mmmm) REVERT: B 224 GLU cc_start: 0.8014 (pm20) cc_final: 0.7653 (pm20) REVERT: B 327 VAL cc_start: 0.8282 (t) cc_final: 0.8004 (m) REVERT: B 341 VAL cc_start: 0.9049 (m) cc_final: 0.8802 (p) REVERT: B 343 ASN cc_start: 0.6666 (t0) cc_final: 0.6073 (t0) REVERT: B 353 TRP cc_start: 0.8482 (p-90) cc_final: 0.8202 (p-90) REVERT: B 354 ASN cc_start: 0.7818 (m110) cc_final: 0.7342 (m110) REVERT: B 380 TYR cc_start: 0.6863 (m-80) cc_final: 0.6333 (m-80) REVERT: B 394 ASN cc_start: 0.8031 (p0) cc_final: 0.7307 (p0) REVERT: B 408 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7304 (ptm-80) REVERT: B 429 PHE cc_start: 0.8426 (t80) cc_final: 0.7834 (t80) REVERT: B 439 ASN cc_start: 0.8193 (t0) cc_final: 0.7858 (t0) REVERT: B 465 GLU cc_start: 0.8834 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 481 ASN cc_start: 0.8194 (t0) cc_final: 0.7862 (t0) REVERT: B 512 VAL cc_start: 0.8771 (m) cc_final: 0.8420 (p) REVERT: B 542 ASN cc_start: 0.7826 (t0) cc_final: 0.7456 (t0) REVERT: B 557 LYS cc_start: 0.7475 (mmmm) cc_final: 0.7207 (mmmm) REVERT: B 602 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8305 (p) REVERT: B 607 GLN cc_start: 0.7799 (mp10) cc_final: 0.7299 (mp10) REVERT: B 651 ILE cc_start: 0.8356 (mt) cc_final: 0.8119 (pt) REVERT: B 658 ASN cc_start: 0.7440 (t0) cc_final: 0.7013 (t0) REVERT: B 659 SER cc_start: 0.8625 (m) cc_final: 0.7836 (p) REVERT: B 663 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: B 670 ILE cc_start: 0.8633 (mm) cc_final: 0.8288 (mt) REVERT: B 703 ASN cc_start: 0.8399 (t0) cc_final: 0.7836 (t0) REVERT: B 725 GLU cc_start: 0.7454 (tt0) cc_final: 0.6819 (tp30) REVERT: B 759 PHE cc_start: 0.7372 (t80) cc_final: 0.6658 (t80) REVERT: B 776 LYS cc_start: 0.8287 (tmmt) cc_final: 0.7873 (ttpp) REVERT: B 820 ASP cc_start: 0.7850 (t0) cc_final: 0.7436 (m-30) REVERT: B 850 ILE cc_start: 0.8324 (mm) cc_final: 0.8081 (tp) REVERT: B 851 CYS cc_start: 0.8277 (t) cc_final: 0.7576 (m) REVERT: B 854 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8049 (tttp) REVERT: B 856 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8403 (mmmm) REVERT: B 869 MET cc_start: 0.8334 (mtp) cc_final: 0.8125 (mtt) REVERT: B 900 MET cc_start: 0.7721 (mtp) cc_final: 0.7520 (mtt) REVERT: B 911 VAL cc_start: 0.8466 (t) cc_final: 0.8179 (m) REVERT: B 921 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8416 (mmmm) REVERT: B 933 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7991 (ttmm) REVERT: B 934 ILE cc_start: 0.8484 (tp) cc_final: 0.8225 (tp) REVERT: B 950 ASP cc_start: 0.7626 (t70) cc_final: 0.6228 (t70) REVERT: B 954 HIS cc_start: 0.7843 (m90) cc_final: 0.7015 (m-70) REVERT: B 962 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8656 (tp) REVERT: B 969 LYS cc_start: 0.8008 (pttm) cc_final: 0.7733 (pttm) REVERT: B 1003 SER cc_start: 0.8841 (m) cc_final: 0.8470 (t) REVERT: B 1005 GLN cc_start: 0.8379 (tp40) cc_final: 0.7785 (tp40) REVERT: B 1028 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8294 (mttt) REVERT: B 1061 VAL cc_start: 0.8615 (t) cc_final: 0.8132 (p) REVERT: B 1097 SER cc_start: 0.8449 (t) cc_final: 0.7885 (p) REVERT: B 1107 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7199 (mtt180) REVERT: C 41 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7359 (mtpp) REVERT: C 43 PHE cc_start: 0.8249 (t80) cc_final: 0.7971 (t80) REVERT: C 65 PHE cc_start: 0.7162 (m-80) cc_final: 0.6780 (m-80) REVERT: C 102 ARG cc_start: 0.7023 (ptp-110) cc_final: 0.6814 (ptp-110) REVERT: C 199 PHE cc_start: 0.7735 (t80) cc_final: 0.7459 (t80) REVERT: C 293 LEU cc_start: 0.8608 (tp) cc_final: 0.8315 (tp) REVERT: C 297 SER cc_start: 0.7999 (m) cc_final: 0.7227 (p) REVERT: C 298 GLU cc_start: 0.7436 (tt0) cc_final: 0.7195 (tt0) REVERT: C 301 CYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5649 (m) REVERT: C 308 VAL cc_start: 0.8597 (t) cc_final: 0.8334 (m) REVERT: C 324 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 332 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.6187 (pp) REVERT: C 436 TRP cc_start: 0.7585 (p-90) cc_final: 0.7014 (p-90) REVERT: C 542 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7419 (t0) REVERT: C 615 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8364 (t) REVERT: C 619 GLU cc_start: 0.7098 (mp0) cc_final: 0.6561 (mp0) REVERT: C 644 GLN cc_start: 0.7884 (tp40) cc_final: 0.7173 (tp40) REVERT: C 666 ILE cc_start: 0.8576 (mt) cc_final: 0.8356 (mp) REVERT: C 674 TYR cc_start: 0.7985 (t80) cc_final: 0.7592 (t80) REVERT: C 705 VAL cc_start: 0.8356 (t) cc_final: 0.8083 (m) REVERT: C 725 GLU cc_start: 0.7231 (tt0) cc_final: 0.7022 (tt0) REVERT: C 764 LYS cc_start: 0.8285 (tttm) cc_final: 0.7752 (ttpp) REVERT: C 765 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: C 768 THR cc_start: 0.8618 (m) cc_final: 0.8394 (p) REVERT: C 776 LYS cc_start: 0.8456 (tptp) cc_final: 0.8034 (tptp) REVERT: C 854 LYS cc_start: 0.8294 (tmmt) cc_final: 0.7865 (tptp) REVERT: C 869 MET cc_start: 0.8365 (mtt) cc_final: 0.8083 (mtm) REVERT: C 904 TYR cc_start: 0.7942 (m-10) cc_final: 0.7728 (m-10) REVERT: C 918 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7103 (tt0) REVERT: C 921 LYS cc_start: 0.8453 (tptp) cc_final: 0.8158 (tptp) REVERT: C 950 ASP cc_start: 0.7757 (t70) cc_final: 0.7062 (t0) REVERT: C 957 GLN cc_start: 0.8084 (tt0) cc_final: 0.7489 (tp40) REVERT: C 964 LYS cc_start: 0.8559 (tppt) cc_final: 0.8181 (ttmm) REVERT: C 980 ILE cc_start: 0.8500 (mt) cc_final: 0.8233 (mt) REVERT: C 990 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7322 (mm-30) REVERT: C 994 ASP cc_start: 0.8043 (p0) cc_final: 0.7842 (p0) REVERT: C 1014 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7445 (ttm110) REVERT: C 1050 MET cc_start: 0.7179 (mtm) cc_final: 0.6967 (mtp) REVERT: C 1051 SER cc_start: 0.8258 (m) cc_final: 0.8035 (m) REVERT: C 1072 GLU cc_start: 0.8362 (pm20) cc_final: 0.8053 (pm20) REVERT: D 4 LEU cc_start: 0.7992 (mt) cc_final: 0.7500 (tt) REVERT: G 49 MET cc_start: 0.3421 (ppp) cc_final: 0.2239 (tpt) outliers start: 143 outliers final: 105 residues processed: 780 average time/residue: 0.1949 time to fit residues: 240.0159 Evaluate side-chains 790 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 672 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL 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 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 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR 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 850 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR 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 203 SER 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 318 PHE Chi-restraints excluded: chain B residue 362 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 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL 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 764 LYS 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 962 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE 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 122 ASN Chi-restraints excluded: chain C residue 206 THR 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 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL 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 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR 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 F residue 94 THR Chi-restraints excluded: chain G residue 47 LYS 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 H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 280 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 145 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 122 ASN C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS G 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124440 restraints weight = 55690.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128460 restraints weight = 24700.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130908 restraints weight = 13854.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132434 restraints weight = 9267.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133290 restraints weight = 7116.840| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29905 Z= 0.176 Angle : 0.639 12.405 40768 Z= 0.322 Chirality : 0.045 0.204 4657 Planarity : 0.005 0.126 5239 Dihedral : 5.396 61.615 4103 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.07 % Allowed : 20.35 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.13), residues: 3713 helix: 1.02 (0.21), residues: 644 sheet: -1.41 (0.17), residues: 827 loop : -2.45 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.034 0.002 TYR B 396 PHE 0.039 0.002 PHE A 192 TRP 0.018 0.002 TRP H 38 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00388 (29860) covalent geometry : angle 0.63292 (40678) SS BOND : bond 0.00467 ( 45) SS BOND : angle 2.03231 ( 90) hydrogen bonds : bond 0.03880 ( 849) hydrogen bonds : angle 5.24740 ( 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 811 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 679 time to evaluate : 1.192 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: 0.6886 (m) cc_final: 0.6415 (p) REVERT: A 41 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8107 (mtmm) REVERT: A 95 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8407 (tp) REVERT: A 281 GLU cc_start: 0.7402 (pp20) cc_final: 0.7106 (pp20) REVERT: A 297 SER cc_start: 0.8435 (m) cc_final: 0.8080 (p) REVERT: A 319 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7957 (ptp-110) REVERT: A 326 ILE cc_start: 0.7830 (mp) cc_final: 0.7608 (mt) REVERT: A 436 TRP cc_start: 0.7102 (p-90) cc_final: 0.6766 (p90) REVERT: A 533 LEU cc_start: 0.7892 (tp) cc_final: 0.7234 (tp) REVERT: A 542 ASN cc_start: 0.8237 (t0) cc_final: 0.7951 (t0) REVERT: A 547 LYS cc_start: 0.8471 (mttp) cc_final: 0.8225 (mppt) REVERT: A 565 PHE cc_start: 0.7033 (m-80) cc_final: 0.5973 (m-80) REVERT: A 592 PHE cc_start: 0.7851 (p90) cc_final: 0.7435 (p90) REVERT: A 644 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 660 TYR cc_start: 0.7684 (m-10) cc_final: 0.7437 (m-10) REVERT: A 674 TYR cc_start: 0.8297 (t80) cc_final: 0.7749 (t80) REVERT: A 697 MET cc_start: 0.7538 (ttp) cc_final: 0.7235 (mtp) REVERT: A 698 SER cc_start: 0.8493 (t) cc_final: 0.7819 (p) REVERT: A 710 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7347 (p0) REVERT: A 759 PHE cc_start: 0.6807 (m-80) cc_final: 0.6236 (m-80) REVERT: A 763 LEU cc_start: 0.8461 (mt) cc_final: 0.8241 (mt) REVERT: A 774 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7338 (mm110) REVERT: A 775 ASP cc_start: 0.8025 (m-30) cc_final: 0.7804 (m-30) REVERT: A 803 SER cc_start: 0.8841 (m) cc_final: 0.8348 (p) REVERT: A 825 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8184 (mmmt) REVERT: A 854 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8041 (tttt) REVERT: A 868 GLU cc_start: 0.7414 (tp30) cc_final: 0.7107 (tp30) REVERT: A 869 MET cc_start: 0.8202 (mtt) cc_final: 0.7992 (mtm) REVERT: A 878 LEU cc_start: 0.8341 (mt) cc_final: 0.7972 (mp) REVERT: A 902 MET cc_start: 0.8090 (tpp) cc_final: 0.7766 (tpp) REVERT: A 921 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8182 (mmmm) REVERT: A 925 ASN cc_start: 0.8441 (m-40) cc_final: 0.8069 (m-40) REVERT: A 945 LEU cc_start: 0.8665 (mm) cc_final: 0.8411 (mp) REVERT: A 949 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: A 953 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m110) REVERT: A 961 THR cc_start: 0.8661 (t) cc_final: 0.8437 (p) REVERT: A 977 LEU cc_start: 0.8929 (mt) cc_final: 0.8724 (mt) REVERT: A 979 ASP cc_start: 0.7443 (t0) cc_final: 0.7110 (t0) REVERT: A 988 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7076 (tm-30) REVERT: A 994 ASP cc_start: 0.7271 (m-30) cc_final: 0.7050 (t0) REVERT: A 1002 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 1029 MET cc_start: 0.8305 (tpp) cc_final: 0.7525 (ttm) REVERT: A 1038 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8172 (mttm) REVERT: A 1096 VAL cc_start: 0.8558 (m) cc_final: 0.8277 (p) REVERT: A 1117 THR cc_start: 0.8634 (p) cc_final: 0.8322 (t) REVERT: A 1141 LEU cc_start: 0.8363 (tp) cc_final: 0.8106 (tt) REVERT: B 31 SER cc_start: 0.8120 (m) cc_final: 0.7881 (p) REVERT: B 60 SER cc_start: 0.8734 (t) cc_final: 0.8150 (t) REVERT: B 106 PHE cc_start: 0.7483 (m-80) cc_final: 0.7245 (m-10) REVERT: B 202 TYR cc_start: 0.7893 (m-80) cc_final: 0.7671 (m-80) REVERT: B 278 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8328 (ttmt) REVERT: B 341 VAL cc_start: 0.9069 (m) cc_final: 0.8830 (p) REVERT: B 353 TRP cc_start: 0.8416 (p-90) cc_final: 0.8065 (p-90) REVERT: B 354 ASN cc_start: 0.7719 (m110) cc_final: 0.7210 (m110) REVERT: B 380 TYR cc_start: 0.6884 (m-80) cc_final: 0.6345 (m-80) REVERT: B 394 ASN cc_start: 0.8014 (p0) cc_final: 0.7290 (p0) REVERT: B 429 PHE cc_start: 0.8423 (t80) cc_final: 0.7820 (t80) REVERT: B 439 ASN cc_start: 0.8216 (t0) cc_final: 0.7881 (t0) REVERT: B 465 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 481 ASN cc_start: 0.8242 (t0) cc_final: 0.7866 (t0) REVERT: B 512 VAL cc_start: 0.8797 (m) cc_final: 0.8436 (p) REVERT: B 564 GLN cc_start: 0.8060 (pm20) cc_final: 0.7675 (pt0) REVERT: B 607 GLN cc_start: 0.7936 (mp10) cc_final: 0.7429 (mp10) REVERT: B 651 ILE cc_start: 0.8390 (mt) cc_final: 0.8127 (pt) REVERT: B 659 SER cc_start: 0.8661 (m) cc_final: 0.8222 (p) REVERT: B 663 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: B 703 ASN cc_start: 0.8363 (t0) cc_final: 0.7811 (t0) REVERT: B 725 GLU cc_start: 0.7450 (tt0) cc_final: 0.6840 (tp30) REVERT: B 759 PHE cc_start: 0.7357 (t80) cc_final: 0.6790 (t80) REVERT: B 776 LYS cc_start: 0.8281 (tmmt) cc_final: 0.7893 (ttpp) REVERT: B 788 ILE cc_start: 0.8457 (mm) cc_final: 0.8254 (mt) REVERT: B 820 ASP cc_start: 0.7876 (t0) cc_final: 0.7469 (m-30) REVERT: B 850 ILE cc_start: 0.8363 (mm) cc_final: 0.8133 (tp) REVERT: B 851 CYS cc_start: 0.8323 (t) cc_final: 0.7578 (m) REVERT: B 854 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8077 (tttp) REVERT: B 856 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8353 (mmmm) REVERT: B 911 VAL cc_start: 0.8482 (t) cc_final: 0.8192 (m) REVERT: B 921 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8414 (mmmm) REVERT: B 933 LYS cc_start: 0.8268 (mtpt) cc_final: 0.8026 (ttmm) REVERT: B 935 GLN cc_start: 0.8020 (tt0) cc_final: 0.7672 (tt0) REVERT: B 950 ASP cc_start: 0.7700 (t70) cc_final: 0.6457 (t70) REVERT: B 954 HIS cc_start: 0.7851 (m90) cc_final: 0.7132 (m-70) REVERT: B 969 LYS cc_start: 0.8075 (pttm) cc_final: 0.7748 (pttm) REVERT: B 1003 SER cc_start: 0.8879 (m) cc_final: 0.8482 (t) REVERT: B 1005 GLN cc_start: 0.8396 (tp40) cc_final: 0.8090 (tp40) REVERT: B 1028 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8319 (mttt) REVERT: B 1061 VAL cc_start: 0.8605 (t) cc_final: 0.8133 (p) REVERT: B 1107 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7241 (mtt180) REVERT: C 41 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7399 (mtpp) REVERT: C 43 PHE cc_start: 0.8242 (t80) cc_final: 0.7963 (t80) REVERT: C 65 PHE cc_start: 0.7201 (m-80) cc_final: 0.6709 (m-80) REVERT: C 102 ARG cc_start: 0.6905 (ptp-110) cc_final: 0.6672 (ptp-110) REVERT: C 293 LEU cc_start: 0.8626 (tp) cc_final: 0.8337 (tp) REVERT: C 297 SER cc_start: 0.8038 (m) cc_final: 0.7300 (p) REVERT: C 298 GLU cc_start: 0.7470 (tt0) cc_final: 0.7231 (tt0) REVERT: C 301 CYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5655 (m) REVERT: C 308 VAL cc_start: 0.8592 (t) cc_final: 0.8346 (m) REVERT: C 332 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6193 (pp) REVERT: C 436 TRP cc_start: 0.7569 (p-90) cc_final: 0.6968 (p-90) REVERT: C 542 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7445 (t0) REVERT: C 563 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7102 (mm-40) REVERT: C 615 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 619 GLU cc_start: 0.7079 (mp0) cc_final: 0.6556 (mp0) REVERT: C 644 GLN cc_start: 0.7955 (tp40) cc_final: 0.7282 (tp40) REVERT: C 674 TYR cc_start: 0.8005 (t80) cc_final: 0.7616 (t80) REVERT: C 705 VAL cc_start: 0.8390 (t) cc_final: 0.8111 (m) REVERT: C 725 GLU cc_start: 0.7269 (tt0) cc_final: 0.7069 (tt0) REVERT: C 764 LYS cc_start: 0.8296 (tttm) cc_final: 0.7873 (ttpp) REVERT: C 776 LYS cc_start: 0.8477 (tptp) cc_final: 0.8152 (tptp) REVERT: C 780 GLU cc_start: 0.7492 (pt0) cc_final: 0.7291 (pt0) REVERT: C 811 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8095 (ttpp) REVERT: C 854 LYS cc_start: 0.8341 (tmmt) cc_final: 0.7937 (tptp) REVERT: C 869 MET cc_start: 0.8363 (mtt) cc_final: 0.8085 (mtm) REVERT: C 904 TYR cc_start: 0.7964 (m-10) cc_final: 0.7751 (m-10) REVERT: C 918 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7124 (tt0) REVERT: C 950 ASP cc_start: 0.7755 (t70) cc_final: 0.7049 (t0) REVERT: C 957 GLN cc_start: 0.8013 (tt0) cc_final: 0.7453 (tp40) REVERT: C 964 LYS cc_start: 0.8601 (tppt) cc_final: 0.8199 (ttmm) REVERT: C 980 ILE cc_start: 0.8473 (mt) cc_final: 0.8219 (mt) REVERT: C 990 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 1014 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7439 (ttm110) REVERT: C 1050 MET cc_start: 0.7224 (mtm) cc_final: 0.7008 (mtp) REVERT: C 1072 GLU cc_start: 0.8366 (pm20) cc_final: 0.8098 (pm20) REVERT: C 1101 HIS cc_start: 0.8712 (m-70) cc_final: 0.8436 (m90) REVERT: D 4 LEU cc_start: 0.7846 (mt) cc_final: 0.7325 (tt) REVERT: G 49 MET cc_start: 0.3367 (ppp) cc_final: 0.2269 (tpt) outliers start: 132 outliers final: 106 residues processed: 774 average time/residue: 0.1933 time to fit residues: 237.2703 Evaluate side-chains 782 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 665 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL 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 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 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 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 850 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 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 203 SER 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 318 PHE Chi-restraints excluded: chain B residue 362 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 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL 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 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 1002 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1073 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 122 ASN Chi-restraints excluded: chain C residue 206 THR 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 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 92 THR 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 F residue 94 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 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 143 optimal weight: 0.0670 chunk 202 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 307 optimal weight: 0.0770 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 949 GLN A1048 HIS B1036 GLN C 121 ASN C 122 ASN C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125666 restraints weight = 54981.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129693 restraints weight = 24618.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132156 restraints weight = 13946.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133624 restraints weight = 9409.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134575 restraints weight = 7301.767| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29905 Z= 0.124 Angle : 0.626 11.344 40768 Z= 0.314 Chirality : 0.044 0.196 4657 Planarity : 0.005 0.134 5239 Dihedral : 5.304 61.051 4101 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.98 % Allowed : 20.75 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.13), residues: 3713 helix: 1.12 (0.21), residues: 644 sheet: -1.32 (0.17), residues: 822 loop : -2.37 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.024 0.001 TYR C 655 PHE 0.028 0.001 PHE C 190 TRP 0.047 0.002 TRP D 110 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (29860) covalent geometry : angle 0.62043 (40678) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.81891 ( 90) hydrogen bonds : bond 0.03682 ( 849) hydrogen bonds : angle 5.16369 ( 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 797 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 668 time to evaluate : 1.110 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: A 33 THR cc_start: 0.6806 (m) cc_final: 0.6344 (p) REVERT: A 41 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: A 92 PHE cc_start: 0.7240 (t80) cc_final: 0.6967 (t80) REVERT: A 95 ILE cc_start: 0.8557 (mm) cc_final: 0.8282 (tp) REVERT: A 281 GLU cc_start: 0.7398 (pp20) cc_final: 0.7093 (pp20) REVERT: A 297 SER cc_start: 0.8401 (m) cc_final: 0.8040 (p) REVERT: A 319 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7922 (ptp-110) REVERT: A 326 ILE cc_start: 0.7831 (mp) cc_final: 0.7593 (mt) REVERT: A 436 TRP cc_start: 0.7051 (p-90) cc_final: 0.6753 (p90) REVERT: A 533 LEU cc_start: 0.7603 (tp) cc_final: 0.7394 (tp) REVERT: A 542 ASN cc_start: 0.8201 (t0) cc_final: 0.7557 (t0) REVERT: A 547 LYS cc_start: 0.8151 (mttp) cc_final: 0.7869 (mttp) REVERT: A 558 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7604 (ptmt) REVERT: A 644 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7097 (tm-30) REVERT: A 674 TYR cc_start: 0.8255 (t80) cc_final: 0.7706 (t80) REVERT: A 698 SER cc_start: 0.8471 (t) cc_final: 0.7770 (p) REVERT: A 710 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7308 (p0) REVERT: A 759 PHE cc_start: 0.6572 (m-80) cc_final: 0.6029 (m-80) REVERT: A 763 LEU cc_start: 0.8464 (mt) cc_final: 0.8238 (mt) REVERT: A 773 GLU cc_start: 0.6896 (tm-30) cc_final: 0.5823 (tm-30) REVERT: A 774 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7127 (mm110) REVERT: A 784 GLN cc_start: 0.8086 (mt0) cc_final: 0.7881 (mt0) REVERT: A 803 SER cc_start: 0.8813 (m) cc_final: 0.8302 (p) REVERT: A 854 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7983 (tttm) REVERT: A 868 GLU cc_start: 0.7401 (tp30) cc_final: 0.7095 (tp30) REVERT: A 869 MET cc_start: 0.8201 (mtt) cc_final: 0.7993 (mtm) REVERT: A 878 LEU cc_start: 0.8310 (mt) cc_final: 0.7945 (mp) REVERT: A 902 MET cc_start: 0.8047 (tpp) cc_final: 0.7712 (tpp) REVERT: A 907 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7982 (t0) REVERT: A 921 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8165 (mmmm) REVERT: A 925 ASN cc_start: 0.8438 (m-40) cc_final: 0.8055 (m-40) REVERT: A 945 LEU cc_start: 0.8658 (mm) cc_final: 0.8393 (mp) REVERT: A 953 ASN cc_start: 0.8445 (m-40) cc_final: 0.8092 (m110) REVERT: A 961 THR cc_start: 0.8688 (t) cc_final: 0.8453 (p) REVERT: A 979 ASP cc_start: 0.7389 (t0) cc_final: 0.7070 (t0) REVERT: A 988 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7067 (tm-30) REVERT: A 1002 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 1029 MET cc_start: 0.8240 (tpp) cc_final: 0.7544 (ttm) REVERT: A 1086 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7589 (ptpt) REVERT: A 1117 THR cc_start: 0.8574 (p) cc_final: 0.8287 (t) REVERT: A 1141 LEU cc_start: 0.8341 (tp) cc_final: 0.8099 (tt) REVERT: B 31 SER cc_start: 0.8032 (m) cc_final: 0.7764 (p) REVERT: B 60 SER cc_start: 0.8725 (t) cc_final: 0.8120 (t) REVERT: B 170 TYR cc_start: 0.8002 (t80) cc_final: 0.7640 (t80) REVERT: B 189 GLU cc_start: 0.6986 (pm20) cc_final: 0.6620 (pm20) REVERT: B 202 TYR cc_start: 0.7977 (m-80) cc_final: 0.7592 (m-80) REVERT: B 278 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8244 (ttmt) REVERT: B 327 VAL cc_start: 0.8337 (t) cc_final: 0.8109 (m) REVERT: B 341 VAL cc_start: 0.9021 (m) cc_final: 0.8798 (p) REVERT: B 353 TRP cc_start: 0.8492 (p-90) cc_final: 0.8171 (p-90) REVERT: B 380 TYR cc_start: 0.6871 (m-80) cc_final: 0.6277 (m-80) REVERT: B 394 ASN cc_start: 0.7946 (p0) cc_final: 0.7278 (p0) REVERT: B 429 PHE cc_start: 0.8378 (t80) cc_final: 0.7807 (t80) REVERT: B 436 TRP cc_start: 0.7984 (p90) cc_final: 0.7743 (p90) REVERT: B 439 ASN cc_start: 0.8172 (t0) cc_final: 0.7879 (t0) REVERT: B 465 GLU cc_start: 0.8854 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 481 ASN cc_start: 0.8329 (t0) cc_final: 0.7930 (t0) REVERT: B 512 VAL cc_start: 0.8777 (m) cc_final: 0.8406 (p) REVERT: B 542 ASN cc_start: 0.7811 (t0) cc_final: 0.7390 (t0) REVERT: B 564 GLN cc_start: 0.8133 (pm20) cc_final: 0.7643 (pt0) REVERT: B 607 GLN cc_start: 0.7943 (mp10) cc_final: 0.7620 (mp10) REVERT: B 645 THR cc_start: 0.8432 (p) cc_final: 0.7073 (m) REVERT: B 651 ILE cc_start: 0.8373 (mt) cc_final: 0.8119 (pt) REVERT: B 658 ASN cc_start: 0.7416 (t0) cc_final: 0.7000 (t0) REVERT: B 659 SER cc_start: 0.8673 (m) cc_final: 0.7853 (p) REVERT: B 663 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: B 703 ASN cc_start: 0.8380 (t0) cc_final: 0.7795 (t0) REVERT: B 725 GLU cc_start: 0.7493 (tt0) cc_final: 0.6866 (tp30) REVERT: B 759 PHE cc_start: 0.7363 (t80) cc_final: 0.6788 (t80) REVERT: B 776 LYS cc_start: 0.8264 (tmmt) cc_final: 0.7904 (ttpt) REVERT: B 820 ASP cc_start: 0.7781 (t0) cc_final: 0.7369 (m-30) REVERT: B 850 ILE cc_start: 0.8331 (mm) cc_final: 0.8080 (tp) REVERT: B 854 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8090 (tttp) REVERT: B 856 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8381 (mmmm) REVERT: B 911 VAL cc_start: 0.8478 (t) cc_final: 0.8170 (m) REVERT: B 933 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7995 (ttmm) REVERT: B 935 GLN cc_start: 0.7953 (tt0) cc_final: 0.7604 (tt0) REVERT: B 950 ASP cc_start: 0.7622 (t70) cc_final: 0.6193 (t70) REVERT: B 954 HIS cc_start: 0.7820 (m90) cc_final: 0.6981 (m-70) REVERT: B 969 LYS cc_start: 0.8088 (pttm) cc_final: 0.7812 (pttm) REVERT: B 1003 SER cc_start: 0.8790 (m) cc_final: 0.8395 (t) REVERT: B 1005 GLN cc_start: 0.8362 (tp40) cc_final: 0.8051 (tp40) REVERT: B 1028 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8314 (mttt) REVERT: B 1061 VAL cc_start: 0.8601 (t) cc_final: 0.8160 (p) REVERT: B 1107 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7228 (mtt180) REVERT: C 41 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7371 (mtpp) REVERT: C 43 PHE cc_start: 0.8204 (t80) cc_final: 0.7916 (t80) REVERT: C 65 PHE cc_start: 0.7161 (m-80) cc_final: 0.6790 (m-80) REVERT: C 102 ARG cc_start: 0.6864 (ptp-110) cc_final: 0.6636 (ptp-110) REVERT: C 293 LEU cc_start: 0.8581 (tp) cc_final: 0.8283 (tp) REVERT: C 297 SER cc_start: 0.7958 (m) cc_final: 0.7100 (p) REVERT: C 298 GLU cc_start: 0.7423 (tt0) cc_final: 0.7191 (tt0) REVERT: C 301 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5635 (m) REVERT: C 308 VAL cc_start: 0.8607 (t) cc_final: 0.8360 (m) REVERT: C 332 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.6134 (pp) REVERT: C 436 TRP cc_start: 0.7537 (p-90) cc_final: 0.6940 (p-90) REVERT: C 542 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7254 (t0) REVERT: C 563 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7173 (mm-40) REVERT: C 615 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8376 (t) REVERT: C 619 GLU cc_start: 0.7074 (mp0) cc_final: 0.6546 (mp0) REVERT: C 644 GLN cc_start: 0.7772 (tp40) cc_final: 0.7065 (tp40) REVERT: C 674 TYR cc_start: 0.7992 (t80) cc_final: 0.7610 (t80) REVERT: C 705 VAL cc_start: 0.8397 (t) cc_final: 0.8099 (m) REVERT: C 725 GLU cc_start: 0.7171 (tt0) cc_final: 0.6966 (tt0) REVERT: C 764 LYS cc_start: 0.8302 (tttm) cc_final: 0.7875 (ttpp) REVERT: C 776 LYS cc_start: 0.8452 (tptp) cc_final: 0.8014 (tptp) REVERT: C 811 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8095 (ttpp) REVERT: C 864 LEU cc_start: 0.8765 (tp) cc_final: 0.8552 (tt) REVERT: C 950 ASP cc_start: 0.7714 (t70) cc_final: 0.7040 (t0) REVERT: C 957 GLN cc_start: 0.7946 (tt0) cc_final: 0.7378 (tp40) REVERT: C 964 LYS cc_start: 0.8595 (tppt) cc_final: 0.8208 (ttmm) REVERT: C 980 ILE cc_start: 0.8508 (mt) cc_final: 0.8236 (mt) REVERT: C 990 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7326 (mm-30) REVERT: C 1014 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7401 (ttm110) REVERT: C 1072 GLU cc_start: 0.8374 (pm20) cc_final: 0.8097 (pm20) REVERT: C 1101 HIS cc_start: 0.8729 (m-70) cc_final: 0.8458 (m90) REVERT: D 4 LEU cc_start: 0.7872 (mt) cc_final: 0.7228 (tt) REVERT: D 87 MET cc_start: 0.1351 (mmp) cc_final: 0.0692 (mmm) outliers start: 129 outliers final: 99 residues processed: 760 average time/residue: 0.1948 time to fit residues: 233.2552 Evaluate side-chains 761 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 651 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 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 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR 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 850 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR 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 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 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 538 CYS Chi-restraints excluded: chain B residue 551 VAL 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 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 1018 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1073 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 95 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 206 THR 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 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS 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 F residue 94 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 39 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 62 ASN 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: 0.0060 chunk 354 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 333 optimal weight: 0.0970 chunk 187 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 299 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 965 GLN A1125 ASN B 506 GLN B 853 GLN C 122 ASN C 690 GLN C 751 ASN C 913 GLN C 935 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN I 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.170487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126506 restraints weight = 55715.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130556 restraints weight = 24848.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133036 restraints weight = 13964.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134558 restraints weight = 9342.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135435 restraints weight = 7183.116| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29905 Z= 0.114 Angle : 0.622 10.890 40768 Z= 0.312 Chirality : 0.044 0.194 4657 Planarity : 0.005 0.132 5239 Dihedral : 5.217 61.139 4097 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.70 % Allowed : 21.40 % Favored : 74.90 % 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: -2.07 (0.13), residues: 3713 helix: 1.16 (0.21), residues: 648 sheet: -1.24 (0.17), residues: 838 loop : -2.33 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.031 0.001 TYR I 51 PHE 0.044 0.001 PHE A 192 TRP 0.031 0.001 TRP D 110 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (29860) covalent geometry : angle 0.61854 (40678) SS BOND : bond 0.00404 ( 45) SS BOND : angle 1.60062 ( 90) hydrogen bonds : bond 0.03607 ( 849) hydrogen bonds : angle 5.08839 ( 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 789 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 669 time to evaluate : 1.068 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: A 33 THR cc_start: 0.6819 (m) cc_final: 0.6409 (p) REVERT: A 95 ILE cc_start: 0.8668 (mm) cc_final: 0.8411 (tp) REVERT: A 201 ILE cc_start: 0.8196 (mm) cc_final: 0.7993 (mm) REVERT: A 281 GLU cc_start: 0.7397 (pp20) cc_final: 0.7091 (pp20) REVERT: A 297 SER cc_start: 0.8360 (m) cc_final: 0.8000 (p) REVERT: A 319 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7930 (ptp-110) REVERT: A 326 ILE cc_start: 0.7803 (mp) cc_final: 0.7565 (mt) REVERT: A 436 TRP cc_start: 0.7027 (p-90) cc_final: 0.6738 (p90) REVERT: A 533 LEU cc_start: 0.7553 (tp) cc_final: 0.7344 (tp) REVERT: A 542 ASN cc_start: 0.8215 (t0) cc_final: 0.8015 (t0) REVERT: A 558 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7709 (ptmt) REVERT: A 644 GLN cc_start: 0.7428 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 660 TYR cc_start: 0.7206 (m-10) cc_final: 0.6931 (m-10) REVERT: A 674 TYR cc_start: 0.8237 (t80) cc_final: 0.7676 (t80) REVERT: A 698 SER cc_start: 0.8436 (t) cc_final: 0.7706 (p) REVERT: A 710 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7310 (p0) REVERT: A 759 PHE cc_start: 0.6550 (m-80) cc_final: 0.5998 (m-80) REVERT: A 763 LEU cc_start: 0.8389 (mt) cc_final: 0.8173 (mt) REVERT: A 773 GLU cc_start: 0.6862 (tm-30) cc_final: 0.5597 (tm-30) REVERT: A 774 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7180 (mm110) REVERT: A 803 SER cc_start: 0.8808 (m) cc_final: 0.8263 (p) REVERT: A 825 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8076 (mtpt) REVERT: A 854 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7917 (tttm) REVERT: A 868 GLU cc_start: 0.7385 (tp30) cc_final: 0.7080 (tp30) REVERT: A 869 MET cc_start: 0.8194 (mtt) cc_final: 0.7985 (mtm) REVERT: A 878 LEU cc_start: 0.8336 (mt) cc_final: 0.7976 (mp) REVERT: A 902 MET cc_start: 0.8036 (tpp) cc_final: 0.7779 (tpp) REVERT: A 921 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8074 (mmmm) REVERT: A 925 ASN cc_start: 0.8416 (m-40) cc_final: 0.7846 (m-40) REVERT: A 945 LEU cc_start: 0.8672 (mm) cc_final: 0.8380 (mp) REVERT: A 953 ASN cc_start: 0.8456 (m-40) cc_final: 0.8102 (m110) REVERT: A 961 THR cc_start: 0.8659 (t) cc_final: 0.8455 (p) REVERT: A 979 ASP cc_start: 0.7313 (t0) cc_final: 0.7004 (t0) REVERT: A 988 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7131 (tm-30) REVERT: A 1029 MET cc_start: 0.8232 (tpp) cc_final: 0.7580 (ttm) REVERT: A 1048 HIS cc_start: 0.8052 (t-90) cc_final: 0.7194 (t-170) REVERT: A 1050 MET cc_start: 0.7007 (ttm) cc_final: 0.6516 (ttp) REVERT: A 1117 THR cc_start: 0.8567 (p) cc_final: 0.8251 (t) REVERT: A 1141 LEU cc_start: 0.8312 (tp) cc_final: 0.8085 (tt) REVERT: B 31 SER cc_start: 0.7996 (m) cc_final: 0.7703 (p) REVERT: B 60 SER cc_start: 0.8697 (t) cc_final: 0.8062 (t) REVERT: B 106 PHE cc_start: 0.7449 (m-80) cc_final: 0.6968 (m-80) REVERT: B 170 TYR cc_start: 0.7977 (t80) cc_final: 0.7616 (t80) REVERT: B 189 GLU cc_start: 0.7037 (pm20) cc_final: 0.6656 (pm20) REVERT: B 202 TYR cc_start: 0.7946 (m-80) cc_final: 0.7520 (m-80) REVERT: B 278 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8340 (ttmt) REVERT: B 327 VAL cc_start: 0.8412 (t) cc_final: 0.8153 (m) REVERT: B 353 TRP cc_start: 0.8464 (p-90) cc_final: 0.8169 (p-90) REVERT: B 380 TYR cc_start: 0.6871 (m-80) cc_final: 0.6283 (m-80) REVERT: B 394 ASN cc_start: 0.7927 (p0) cc_final: 0.7270 (p0) REVERT: B 429 PHE cc_start: 0.8373 (t80) cc_final: 0.7802 (t80) REVERT: B 436 TRP cc_start: 0.7947 (p90) cc_final: 0.7733 (p90) REVERT: B 439 ASN cc_start: 0.8092 (t0) cc_final: 0.7801 (t0) REVERT: B 465 GLU cc_start: 0.8769 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 481 ASN cc_start: 0.8339 (t0) cc_final: 0.7931 (t0) REVERT: B 512 VAL cc_start: 0.8760 (m) cc_final: 0.8382 (p) REVERT: B 571 ASP cc_start: 0.7396 (t0) cc_final: 0.7073 (p0) REVERT: B 607 GLN cc_start: 0.8019 (mp10) cc_final: 0.7617 (mp10) REVERT: B 645 THR cc_start: 0.8381 (p) cc_final: 0.6945 (m) REVERT: B 651 ILE cc_start: 0.8362 (mt) cc_final: 0.8141 (pt) REVERT: B 656 VAL cc_start: 0.8248 (p) cc_final: 0.8039 (m) REVERT: B 658 ASN cc_start: 0.7411 (t0) cc_final: 0.6971 (t0) REVERT: B 659 SER cc_start: 0.8711 (m) cc_final: 0.7960 (p) REVERT: B 663 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: B 703 ASN cc_start: 0.8375 (t0) cc_final: 0.7816 (t0) REVERT: B 725 GLU cc_start: 0.7475 (tt0) cc_final: 0.6839 (tp30) REVERT: B 759 PHE cc_start: 0.7381 (t80) cc_final: 0.6652 (t80) REVERT: B 776 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7882 (ttpt) REVERT: B 804 GLN cc_start: 0.7901 (mt0) cc_final: 0.7596 (mm-40) REVERT: B 820 ASP cc_start: 0.7712 (t0) cc_final: 0.7176 (m-30) REVERT: B 850 ILE cc_start: 0.8376 (mm) cc_final: 0.8111 (tp) REVERT: B 854 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8069 (tttp) REVERT: B 856 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8406 (mmmm) REVERT: B 911 VAL cc_start: 0.8457 (t) cc_final: 0.8147 (m) REVERT: B 935 GLN cc_start: 0.7827 (tt0) cc_final: 0.7597 (tt0) REVERT: B 950 ASP cc_start: 0.7604 (t70) cc_final: 0.6983 (t70) REVERT: B 961 THR cc_start: 0.8824 (p) cc_final: 0.8418 (t) REVERT: B 969 LYS cc_start: 0.8077 (pttm) cc_final: 0.7799 (pttm) REVERT: B 1003 SER cc_start: 0.8768 (m) cc_final: 0.8426 (t) REVERT: B 1005 GLN cc_start: 0.8290 (tp40) cc_final: 0.7706 (tp40) REVERT: B 1028 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8301 (mttt) REVERT: B 1115 ILE cc_start: 0.8999 (mt) cc_final: 0.8586 (tp) REVERT: C 41 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7309 (mtpp) REVERT: C 43 PHE cc_start: 0.8184 (t80) cc_final: 0.7926 (t80) REVERT: C 65 PHE cc_start: 0.7116 (m-80) cc_final: 0.6771 (m-80) REVERT: C 102 ARG cc_start: 0.6706 (ptp-110) cc_final: 0.6500 (ptp-110) REVERT: C 122 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7004 (p0) REVERT: C 201 ILE cc_start: 0.8786 (mt) cc_final: 0.8496 (mp) REVERT: C 293 LEU cc_start: 0.8541 (tp) cc_final: 0.8263 (tp) REVERT: C 297 SER cc_start: 0.7966 (m) cc_final: 0.7094 (p) REVERT: C 298 GLU cc_start: 0.7415 (tt0) cc_final: 0.7184 (tt0) REVERT: C 301 CYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5548 (m) REVERT: C 308 VAL cc_start: 0.8629 (t) cc_final: 0.8342 (m) REVERT: C 332 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6094 (pp) REVERT: C 436 TRP cc_start: 0.7561 (p-90) cc_final: 0.6968 (p-90) REVERT: C 563 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7200 (mm-40) REVERT: C 619 GLU cc_start: 0.7112 (mp0) cc_final: 0.6582 (mp0) REVERT: C 644 GLN cc_start: 0.7762 (tp40) cc_final: 0.7048 (tp40) REVERT: C 705 VAL cc_start: 0.8381 (t) cc_final: 0.8058 (m) REVERT: C 725 GLU cc_start: 0.7180 (tt0) cc_final: 0.6952 (tt0) REVERT: C 764 LYS cc_start: 0.8305 (tttm) cc_final: 0.7770 (ttpp) REVERT: C 768 THR cc_start: 0.8546 (m) cc_final: 0.8340 (p) REVERT: C 776 LYS cc_start: 0.8442 (tptp) cc_final: 0.8009 (tptp) REVERT: C 864 LEU cc_start: 0.8728 (tp) cc_final: 0.8397 (tt) REVERT: C 921 LYS cc_start: 0.8398 (tptp) cc_final: 0.8115 (tptp) REVERT: C 950 ASP cc_start: 0.7765 (t70) cc_final: 0.7040 (t0) REVERT: C 957 GLN cc_start: 0.7911 (tt0) cc_final: 0.7358 (tp40) REVERT: C 964 LYS cc_start: 0.8597 (tppt) cc_final: 0.8219 (ttmm) REVERT: C 980 ILE cc_start: 0.8494 (mt) cc_final: 0.8240 (mt) REVERT: C 990 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 1014 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7283 (ttm110) REVERT: C 1051 SER cc_start: 0.8060 (m) cc_final: 0.7845 (m) REVERT: C 1072 GLU cc_start: 0.8370 (pm20) cc_final: 0.8138 (pm20) REVERT: C 1101 HIS cc_start: 0.8738 (m-70) cc_final: 0.8467 (m90) REVERT: D 4 LEU cc_start: 0.7674 (mt) cc_final: 0.6920 (tt) REVERT: D 84 MET cc_start: 0.2967 (mpp) cc_final: 0.2608 (mpp) outliers start: 120 outliers final: 94 residues processed: 756 average time/residue: 0.1939 time to fit residues: 232.1668 Evaluate side-chains 754 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 653 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 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 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 666 ILE 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 775 ASP Chi-restraints excluded: chain A residue 850 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 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 362 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 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL 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 803 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 206 THR 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 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 933 LYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS 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 F residue 94 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 H residue 70 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 62 ASN 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: 0.8980 chunk 18 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN B 388 ASN B 506 GLN B 853 GLN B 957 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 542 ASN C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124371 restraints weight = 56003.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128381 restraints weight = 25001.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130858 restraints weight = 14109.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132380 restraints weight = 9430.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133297 restraints weight = 7251.325| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29905 Z= 0.173 Angle : 0.653 18.004 40768 Z= 0.328 Chirality : 0.045 0.206 4657 Planarity : 0.005 0.134 5239 Dihedral : 5.334 61.368 4095 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.36 % Allowed : 21.71 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3713 helix: 1.17 (0.21), residues: 635 sheet: -1.18 (0.17), residues: 816 loop : -2.25 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 273 TYR 0.031 0.002 TYR I 51 PHE 0.033 0.002 PHE A 592 TRP 0.033 0.002 TRP B 104 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00385 (29860) covalent geometry : angle 0.64784 (40678) SS BOND : bond 0.00437 ( 45) SS BOND : angle 1.78288 ( 90) hydrogen bonds : bond 0.03890 ( 849) hydrogen bonds : angle 5.14831 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7179.61 seconds wall clock time: 124 minutes 4.42 seconds (7444.42 seconds total)