Starting phenix.real_space_refine on Fri Sep 19 07:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxi_32180/09_2025/7vxi_32180.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.114 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 113 5.16 5 C 15677 2.51 5 N 4111 2.21 5 O 4669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24570 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7950 Classifications: {'peptide': 1020} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 50, 'TRANS': 969} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.44, per 1000 atoms: 0.26 Number of scatterers: 24570 At special positions: 0 Unit cell: (158.485, 158.485, 180.345, 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 113 16.00 O 4669 8.00 N 4111 7.00 C 15677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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 15 " - pdb=" SG CYS B 136 " 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 538 " - pdb=" SG CYS B 590 " 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=2.02 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 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 24.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.503A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.412A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.549A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.761A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.767A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.621A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.702A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.972A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.769A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.726A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.142A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.687A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.636A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.851A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.336A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.605A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.835A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.608A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.637A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.199A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.668A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.971A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.154A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.993A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.990A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.597A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.428A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.028A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.747A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.638A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.544A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.847A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.505A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.012A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.833A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.041A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.158A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.098A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.529A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.599A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.074A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.622A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.363A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.606A pdb=" N ALA A 348 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 401 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.606A pdb=" N ALA A 348 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 401 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.396A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.160A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.431A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.112A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.243A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.542A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.591A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 144 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.328A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 144 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.184A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.713A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.537A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.016A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.275A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.066A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.596A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.049A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.537A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.630A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.001A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.942A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.731A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.597A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 968 hydrogen bonds defined for protein. 2697 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: 6.30 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7948 1.35 - 1.47: 6161 1.47 - 1.59: 10883 1.59 - 1.71: 0 1.71 - 1.83: 143 Bond restraints: 25135 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.34e-02 1.83e+03 2.03e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.41e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.416 -0.082 2.34e-02 1.83e+03 1.24e+01 bond pdb=" C LYS C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.331 1.387 -0.056 2.07e-02 2.33e+03 7.26e+00 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.541 -0.024 9.30e-03 1.16e+04 6.81e+00 ... (remaining 25130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 32720 1.04 - 2.07: 1189 2.07 - 3.11: 182 3.11 - 4.14: 98 4.14 - 5.18: 7 Bond angle restraints: 34196 Sorted by residual: angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 116.63 111.59 5.04 1.16e+00 7.43e-01 1.89e+01 angle pdb=" C PRO B 986 " pdb=" N PRO B 987 " pdb=" CA PRO B 987 " ideal model delta sigma weight residual 118.85 122.36 -3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.34 111.95 4.39 1.40e+00 5.10e-01 9.82e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.31 -3.61 1.22e+00 6.72e-01 8.77e+00 angle pdb=" O LEU A 24 " pdb=" C LEU A 24 " pdb=" N PRO A 25 " ideal model delta sigma weight residual 121.88 123.88 -2.00 7.10e-01 1.98e+00 7.92e+00 ... (remaining 34191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 14670 16.60 - 33.21: 222 33.21 - 49.81: 79 49.81 - 66.42: 12 66.42 - 83.02: 5 Dihedral angle restraints: 14988 sinusoidal: 5841 harmonic: 9147 Sorted by residual: dihedral pdb=" CA THR B 19 " pdb=" C THR B 19 " pdb=" N THR B 20 " pdb=" CA THR B 20 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA B 352 " pdb=" C ALA B 352 " pdb=" N TRP B 353 " pdb=" CA TRP B 353 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 14985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2564 0.032 - 0.063: 833 0.063 - 0.095: 195 0.095 - 0.127: 261 0.127 - 0.158: 25 Chirality restraints: 3878 Sorted by residual: chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE C 896 " pdb=" N ILE C 896 " pdb=" C ILE C 896 " pdb=" CB ILE C 896 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 664 " pdb=" N ILE B 664 " pdb=" C ILE B 664 " pdb=" CB ILE B 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 3875 not shown) Planarity restraints: 4436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 24 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C LEU C 24 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 24 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO C 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C LEU A 24 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 24 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 985 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ASP B 985 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 985 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 986 " 0.013 2.00e-02 2.50e+03 ... (remaining 4433 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 431 2.68 - 3.23: 23442 3.23 - 3.79: 35558 3.79 - 4.34: 51187 4.34 - 4.90: 83401 Nonbonded interactions: 194019 Sorted by model distance: nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.125 3.040 nonbonded pdb=" OD1 ASN B 422 " pdb=" N TYR B 423 " model vdw 2.126 3.120 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.150 3.040 nonbonded pdb=" O GLN C 563 " pdb=" NH1 ARG C 577 " model vdw 2.186 3.120 ... (remaining 194014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 244 or resid 247 through 438 or resid 495 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 827 or resid 854 throu \ gh 1147)) selection = (chain 'C' and (resid 14 through 244 or resid 247 through 438 or resid 495 throu \ gh 1147)) } 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 individual isotropic 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: 2.750 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.100 Process input model: 25.660 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 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 0.105 25172 Z= 0.123 Angle : 0.489 5.176 34270 Z= 0.298 Chirality : 0.043 0.158 3878 Planarity : 0.003 0.046 4436 Dihedral : 7.294 83.023 8989 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -1.83 (0.12), residues: 3106 helix: -1.73 (0.17), residues: 649 sheet: -0.49 (0.16), residues: 710 loop : -1.29 (0.12), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.014 0.001 TYR A 495 PHE 0.016 0.001 PHE B 133 TRP 0.032 0.001 TRP B 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00221 (25135) covalent geometry : angle 0.48821 (34196) SS BOND : bond 0.00289 ( 37) SS BOND : angle 0.70730 ( 74) hydrogen bonds : bond 0.25649 ( 954) hydrogen bonds : angle 9.99195 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 0.918 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: A 300 LYS cc_start: 0.7698 (mttt) cc_final: 0.7367 (mtmm) REVERT: A 541 PHE cc_start: 0.6371 (p90) cc_final: 0.5886 (p90) REVERT: A 581 THR cc_start: 0.6716 (m) cc_final: 0.5759 (p) REVERT: A 605 SER cc_start: 0.7805 (t) cc_final: 0.7598 (p) REVERT: A 716 THR cc_start: 0.8076 (p) cc_final: 0.7830 (t) REVERT: A 725 GLU cc_start: 0.6073 (mt-10) cc_final: 0.5846 (mt-10) REVERT: A 863 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8326 (Cg_exo) REVERT: A 864 LEU cc_start: 0.7742 (tp) cc_final: 0.7032 (tp) REVERT: A 881 THR cc_start: 0.6459 (p) cc_final: 0.6218 (p) REVERT: A 886 TRP cc_start: 0.7740 (p90) cc_final: 0.7461 (p90) REVERT: A 912 THR cc_start: 0.7875 (m) cc_final: 0.7667 (p) REVERT: A 976 VAL cc_start: 0.7854 (t) cc_final: 0.7621 (t) REVERT: A 1052 PHE cc_start: 0.7173 (m-10) cc_final: 0.6630 (m-80) REVERT: A 1073 LYS cc_start: 0.7192 (tttt) cc_final: 0.6859 (ttpp) REVERT: B 45 SER cc_start: 0.6482 (p) cc_final: 0.6223 (t) REVERT: B 49 HIS cc_start: 0.7378 (t-90) cc_final: 0.7126 (t70) REVERT: B 129 LYS cc_start: 0.6274 (ttmt) cc_final: 0.5944 (tptt) REVERT: B 206 LYS cc_start: 0.6772 (tptt) cc_final: 0.6518 (tptp) REVERT: B 295 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7901 (Cg_endo) REVERT: B 300 LYS cc_start: 0.6935 (mttt) cc_final: 0.6724 (ptpt) REVERT: B 651 ILE cc_start: 0.7642 (pt) cc_final: 0.7195 (mp) REVERT: B 657 ASN cc_start: 0.7615 (m-40) cc_final: 0.7406 (m-40) REVERT: B 747 THR cc_start: 0.7109 (m) cc_final: 0.6323 (p) REVERT: B 780 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6777 (mt-10) REVERT: B 960 ASN cc_start: 0.7572 (t0) cc_final: 0.7090 (m-40) REVERT: B 1011 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7364 (mm110) REVERT: B 1028 LYS cc_start: 0.7288 (mttt) cc_final: 0.6630 (mmtp) REVERT: B 1036 GLN cc_start: 0.8208 (tt0) cc_final: 0.7016 (tt0) REVERT: B 1050 MET cc_start: 0.7636 (ptm) cc_final: 0.7276 (ptm) REVERT: B 1054 GLN cc_start: 0.6757 (mm-40) cc_final: 0.5623 (mt0) REVERT: B 1073 LYS cc_start: 0.7439 (mttt) cc_final: 0.7175 (mttt) REVERT: B 1122 VAL cc_start: 0.8306 (t) cc_final: 0.7911 (p) REVERT: C 56 LEU cc_start: 0.8173 (tp) cc_final: 0.7926 (tt) REVERT: C 59 PHE cc_start: 0.7135 (m-10) cc_final: 0.6875 (m-80) REVERT: C 92 PHE cc_start: 0.5727 (t80) cc_final: 0.5470 (t80) REVERT: C 177 MET cc_start: 0.3610 (tpp) cc_final: 0.3212 (tpp) REVERT: C 398 ASP cc_start: 0.5315 (m-30) cc_final: 0.4996 (m-30) REVERT: C 399 SER cc_start: 0.7076 (m) cc_final: 0.6254 (p) REVERT: C 400 PHE cc_start: 0.5507 (p90) cc_final: 0.5090 (p90) REVERT: C 615 VAL cc_start: 0.7278 (m) cc_final: 0.6954 (t) REVERT: C 775 ASP cc_start: 0.7492 (m-30) cc_final: 0.7117 (m-30) REVERT: C 780 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6829 (mt-10) REVERT: C 819 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 869 MET cc_start: 0.7435 (mtt) cc_final: 0.7200 (mtt) REVERT: C 884 SER cc_start: 0.7977 (m) cc_final: 0.7764 (m) REVERT: C 886 TRP cc_start: 0.8476 (p90) cc_final: 0.8175 (p90) REVERT: C 936 ASP cc_start: 0.7394 (m-30) cc_final: 0.7146 (m-30) REVERT: C 1033 VAL cc_start: 0.7754 (t) cc_final: 0.7509 (t) REVERT: C 1119 ASN cc_start: 0.6229 (m-40) cc_final: 0.5965 (p0) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.1935 time to fit residues: 194.0157 Evaluate side-chains 508 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 317 ASN A 498 GLN A 563 GLN A 762 GLN A 895 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 394 ASN B 519 HIS B 675 GLN B 751 ASN B 762 GLN B 872 GLN B 901 GLN B 955 ASN B1005 GLN B1101 HIS C 125 ASN C 239 GLN C 388 ASN C 544 ASN C 644 GLN C 655 HIS C 751 ASN C 764 ASN C 856 ASN C 901 GLN C 955 ASN C1071 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.211497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179259 restraints weight = 40752.726| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.40 r_work: 0.4083 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25172 Z= 0.164 Angle : 0.602 8.101 34270 Z= 0.324 Chirality : 0.047 0.178 3878 Planarity : 0.004 0.068 4436 Dihedral : 4.274 19.037 3365 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.13 % Rotamer: Outliers : 1.75 % Allowed : 5.90 % Favored : 92.35 % 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 aren not related in a simple way. whole: -0.46 (0.14), residues: 3106 helix: 0.88 (0.20), residues: 667 sheet: 0.04 (0.17), residues: 700 loop : -0.91 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 995 TYR 0.021 0.002 TYR B 279 PHE 0.024 0.002 PHE A 238 TRP 0.017 0.002 TRP B 64 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00363 (25135) covalent geometry : angle 0.59678 (34196) SS BOND : bond 0.00652 ( 37) SS BOND : angle 1.87991 ( 74) hydrogen bonds : bond 0.05185 ( 954) hydrogen bonds : angle 6.23327 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 533 time to evaluate : 0.896 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: A 190 ARG cc_start: 0.7336 (mmt180) cc_final: 0.7118 (mtp85) REVERT: A 239 GLN cc_start: 0.7266 (tt0) cc_final: 0.7018 (tt0) REVERT: A 287 ASP cc_start: 0.7948 (t70) cc_final: 0.7654 (t70) REVERT: A 300 LYS cc_start: 0.8611 (mttt) cc_final: 0.8008 (mmtp) REVERT: A 310 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7979 (ptmm) REVERT: A 605 SER cc_start: 0.8111 (t) cc_final: 0.7830 (m) REVERT: A 725 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6823 (mt-10) REVERT: A 748 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 772 VAL cc_start: 0.8231 (t) cc_final: 0.7963 (p) REVERT: A 855 PHE cc_start: 0.6148 (m-80) cc_final: 0.5892 (m-80) REVERT: A 864 LEU cc_start: 0.8365 (tp) cc_final: 0.7890 (tt) REVERT: A 886 TRP cc_start: 0.8099 (p90) cc_final: 0.7895 (p90) REVERT: A 900 MET cc_start: 0.6981 (mmm) cc_final: 0.6608 (mtm) REVERT: A 902 MET cc_start: 0.7918 (mmt) cc_final: 0.7607 (tpt) REVERT: A 934 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 1002 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: A 1013 ILE cc_start: 0.8042 (mm) cc_final: 0.7736 (mt) REVERT: A 1019 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: A 1057 PRO cc_start: 0.8591 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: B 33 THR cc_start: 0.7048 (p) cc_final: 0.5585 (m) REVERT: B 129 LYS cc_start: 0.7105 (ttmt) cc_final: 0.6827 (tptt) REVERT: B 300 LYS cc_start: 0.7759 (mttt) cc_final: 0.7518 (mttm) REVERT: B 531 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.6945 (m) REVERT: B 660 TYR cc_start: 0.7681 (m-80) cc_final: 0.7461 (m-80) REVERT: B 814 LYS cc_start: 0.7102 (mttt) cc_final: 0.6880 (mmmt) REVERT: B 917 TYR cc_start: 0.6186 (m-10) cc_final: 0.5085 (m-80) REVERT: B 957 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7987 (mm-40) REVERT: B 983 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: B 1028 LYS cc_start: 0.8143 (mttt) cc_final: 0.7828 (mttm) REVERT: B 1122 VAL cc_start: 0.8503 (t) cc_final: 0.8285 (p) REVERT: C 59 PHE cc_start: 0.7570 (m-10) cc_final: 0.7331 (m-10) REVERT: C 177 MET cc_start: 0.3551 (tpp) cc_final: 0.3187 (tpp) REVERT: C 396 TYR cc_start: 0.5997 (m-80) cc_final: 0.5021 (m-80) REVERT: C 399 SER cc_start: 0.7063 (m) cc_final: 0.6786 (m) REVERT: C 400 PHE cc_start: 0.5582 (p90) cc_final: 0.5256 (p90) REVERT: C 531 THR cc_start: 0.8051 (p) cc_final: 0.7826 (t) REVERT: C 615 VAL cc_start: 0.7917 (m) cc_final: 0.7125 (t) REVERT: C 655 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7244 (t70) REVERT: C 663 ASP cc_start: 0.7579 (m-30) cc_final: 0.7311 (m-30) REVERT: C 756 TYR cc_start: 0.8339 (m-80) cc_final: 0.7995 (m-80) REVERT: C 823 PHE cc_start: 0.6691 (m-10) cc_final: 0.6152 (m-80) REVERT: C 856 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7280 (m-40) REVERT: C 867 ASP cc_start: 0.7567 (m-30) cc_final: 0.7344 (t0) REVERT: C 884 SER cc_start: 0.8753 (m) cc_final: 0.8410 (p) REVERT: C 886 TRP cc_start: 0.8572 (p90) cc_final: 0.8297 (p90) REVERT: C 936 ASP cc_start: 0.7795 (m-30) cc_final: 0.7371 (m-30) REVERT: C 952 VAL cc_start: 0.8083 (t) cc_final: 0.7748 (m) REVERT: C 990 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7427 (mp0) REVERT: C 1010 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7714 (mm-40) REVERT: C 1052 PHE cc_start: 0.7785 (m-10) cc_final: 0.7582 (m-10) REVERT: C 1120 THR cc_start: 0.7995 (p) cc_final: 0.7741 (m) outliers start: 48 outliers final: 25 residues processed: 557 average time/residue: 0.1894 time to fit residues: 159.5294 Evaluate side-chains 514 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 484 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 206 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 644 GLN A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1048 HIS B 207 HIS B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN C 616 ASN C 644 GLN C 764 ASN C 856 ASN C1002 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.202677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.169916 restraints weight = 39236.116| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.41 r_work: 0.3993 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 25172 Z= 0.265 Angle : 0.676 12.759 34270 Z= 0.366 Chirality : 0.048 0.225 3878 Planarity : 0.005 0.072 4436 Dihedral : 4.824 21.182 3365 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.77 % Allowed : 7.72 % Favored : 89.51 % 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 aren not related in a simple way. whole: -0.32 (0.14), residues: 3106 helix: 1.05 (0.20), residues: 678 sheet: 0.28 (0.17), residues: 737 loop : -0.98 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 905 TYR 0.032 0.002 TYR C 279 PHE 0.035 0.003 PHE B 541 TRP 0.023 0.002 TRP A1102 HIS 0.035 0.002 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00602 (25135) covalent geometry : angle 0.67010 (34196) SS BOND : bond 0.00585 ( 37) SS BOND : angle 2.07107 ( 74) hydrogen bonds : bond 0.05748 ( 954) hydrogen bonds : angle 5.99291 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 531 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 300 LYS cc_start: 0.8667 (mttt) cc_final: 0.8451 (mttm) REVERT: A 315 THR cc_start: 0.8340 (m) cc_final: 0.8000 (p) REVERT: A 605 SER cc_start: 0.8431 (t) cc_final: 0.8021 (m) REVERT: A 690 GLN cc_start: 0.7236 (mm-40) cc_final: 0.7005 (mm110) REVERT: A 772 VAL cc_start: 0.8504 (t) cc_final: 0.8298 (p) REVERT: A 858 LEU cc_start: 0.8644 (mm) cc_final: 0.8432 (mt) REVERT: A 872 GLN cc_start: 0.7507 (tt0) cc_final: 0.7255 (tt0) REVERT: A 995 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7731 (mtt180) REVERT: A 1002 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: A 1013 ILE cc_start: 0.8127 (mm) cc_final: 0.7904 (mt) REVERT: A 1028 LYS cc_start: 0.8666 (mttt) cc_final: 0.8154 (mttp) REVERT: A 1137 VAL cc_start: 0.8671 (t) cc_final: 0.8402 (m) REVERT: B 129 LYS cc_start: 0.7226 (ttmt) cc_final: 0.7016 (tptt) REVERT: B 239 GLN cc_start: 0.6288 (tt0) cc_final: 0.5948 (tm-30) REVERT: B 725 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 726 ILE cc_start: 0.8838 (mp) cc_final: 0.8588 (mt) REVERT: B 765 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7396 (ttp-170) REVERT: B 804 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: B 817 PHE cc_start: 0.8346 (t80) cc_final: 0.8053 (t80) REVERT: B 859 THR cc_start: 0.8198 (m) cc_final: 0.7945 (p) REVERT: B 933 LYS cc_start: 0.8470 (mttt) cc_final: 0.8022 (mtmt) REVERT: B 934 ILE cc_start: 0.8473 (mm) cc_final: 0.8206 (tp) REVERT: B 957 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8005 (mm-40) REVERT: B 974 SER cc_start: 0.8636 (t) cc_final: 0.8423 (p) REVERT: C 102 ARG cc_start: 0.6909 (mmt-90) cc_final: 0.6674 (mmp-170) REVERT: C 310 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7838 (ttpp) REVERT: C 323 THR cc_start: 0.7360 (m) cc_final: 0.6879 (p) REVERT: C 364 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6542 (t0) REVERT: C 377 PHE cc_start: 0.7651 (t80) cc_final: 0.7243 (t80) REVERT: C 537 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7480 (mtpp) REVERT: C 567 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7227 (mtt-85) REVERT: C 581 THR cc_start: 0.8257 (t) cc_final: 0.7898 (p) REVERT: C 608 VAL cc_start: 0.8180 (m) cc_final: 0.7931 (t) REVERT: C 711 SER cc_start: 0.8348 (p) cc_final: 0.8083 (p) REVERT: C 780 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 823 PHE cc_start: 0.6881 (m-10) cc_final: 0.6221 (m-80) REVERT: C 856 ASN cc_start: 0.7832 (m110) cc_final: 0.7631 (m110) REVERT: C 936 ASP cc_start: 0.7947 (m-30) cc_final: 0.7620 (m-30) REVERT: C 990 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7508 (mp0) REVERT: C 1002 GLN cc_start: 0.7549 (mt0) cc_final: 0.7333 (mt0) REVERT: C 1010 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7787 (mm-40) REVERT: C 1072 GLU cc_start: 0.7612 (pm20) cc_final: 0.7335 (pm20) REVERT: C 1132 ILE cc_start: 0.8417 (tt) cc_final: 0.8209 (mt) outliers start: 76 outliers final: 48 residues processed: 567 average time/residue: 0.1787 time to fit residues: 154.2252 Evaluate side-chains 526 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 474 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 177 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 210 optimal weight: 0.0370 chunk 184 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 312 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 287 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 239 GLN A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 607 GLN B 779 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B1106 GLN C 394 ASN C 644 GLN C 655 HIS C 764 ASN C 856 ASN C 907 ASN C 913 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.202636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169783 restraints weight = 38984.656| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.39 r_work: 0.3978 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25172 Z= 0.150 Angle : 0.562 13.276 34270 Z= 0.296 Chirality : 0.045 0.309 3878 Planarity : 0.004 0.076 4436 Dihedral : 4.476 19.202 3365 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.33 % Allowed : 9.91 % Favored : 87.76 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 3106 helix: 1.46 (0.21), residues: 671 sheet: 0.38 (0.18), residues: 734 loop : -0.95 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.018 0.001 TYR C 380 PHE 0.022 0.002 PHE A 238 TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (25135) covalent geometry : angle 0.55700 (34196) SS BOND : bond 0.00465 ( 37) SS BOND : angle 1.73546 ( 74) hydrogen bonds : bond 0.04548 ( 954) hydrogen bonds : angle 5.61901 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 493 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 THR cc_start: 0.8326 (m) cc_final: 0.8018 (p) REVERT: A 583 GLU cc_start: 0.4974 (mm-30) cc_final: 0.4547 (tp30) REVERT: A 605 SER cc_start: 0.8382 (t) cc_final: 0.7975 (m) REVERT: A 772 VAL cc_start: 0.8557 (t) cc_final: 0.8319 (p) REVERT: A 858 LEU cc_start: 0.8575 (mm) cc_final: 0.8365 (mt) REVERT: A 882 ILE cc_start: 0.8523 (mm) cc_final: 0.8289 (mt) REVERT: A 900 MET cc_start: 0.7834 (mtt) cc_final: 0.7628 (mtm) REVERT: A 976 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8091 (t) REVERT: A 1002 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: A 1013 ILE cc_start: 0.8097 (mm) cc_final: 0.7769 (mt) REVERT: A 1017 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 1028 LYS cc_start: 0.8594 (mttt) cc_final: 0.8090 (mtpp) REVERT: A 1050 MET cc_start: 0.8452 (ptt) cc_final: 0.8238 (ptm) REVERT: A 1137 VAL cc_start: 0.8720 (t) cc_final: 0.8377 (m) REVERT: B 129 LYS cc_start: 0.7174 (ttmt) cc_final: 0.6871 (ttmt) REVERT: B 153 MET cc_start: -0.1466 (ttp) cc_final: -0.2376 (ttp) REVERT: B 194 PHE cc_start: 0.7580 (m-80) cc_final: 0.7314 (m-80) REVERT: B 239 GLN cc_start: 0.6375 (tt0) cc_final: 0.6033 (tm-30) REVERT: B 725 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 726 ILE cc_start: 0.8819 (mp) cc_final: 0.8564 (mt) REVERT: B 765 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7294 (ttp-170) REVERT: B 804 GLN cc_start: 0.8003 (tp40) cc_final: 0.7699 (mm-40) REVERT: B 817 PHE cc_start: 0.8336 (t80) cc_final: 0.7921 (t80) REVERT: B 825 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7770 (mmtp) REVERT: B 859 THR cc_start: 0.8153 (m) cc_final: 0.7936 (p) REVERT: B 933 LYS cc_start: 0.8393 (mttt) cc_final: 0.8107 (mttt) REVERT: B 934 ILE cc_start: 0.8322 (mm) cc_final: 0.8115 (tp) REVERT: B 957 GLN cc_start: 0.8238 (mm-40) cc_final: 0.8003 (mm-40) REVERT: B 974 SER cc_start: 0.8529 (t) cc_final: 0.8267 (p) REVERT: B 1019 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7502 (ttp-110) REVERT: B 1106 GLN cc_start: 0.7115 (mt0) cc_final: 0.6808 (mt0) REVERT: C 38 TYR cc_start: 0.7842 (m-10) cc_final: 0.6225 (m-10) REVERT: C 310 LYS cc_start: 0.7971 (ptmm) cc_final: 0.7722 (ttpp) REVERT: C 364 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6373 (t0) REVERT: C 377 PHE cc_start: 0.7504 (t80) cc_final: 0.7187 (t80) REVERT: C 532 ASN cc_start: 0.8253 (t0) cc_final: 0.8045 (t0) REVERT: C 608 VAL cc_start: 0.8197 (m) cc_final: 0.7981 (t) REVERT: C 936 ASP cc_start: 0.7845 (m-30) cc_final: 0.7436 (m-30) REVERT: C 1005 GLN cc_start: 0.7992 (mm110) cc_final: 0.7659 (mp10) REVERT: C 1010 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7560 (mt0) REVERT: C 1072 GLU cc_start: 0.7552 (pm20) cc_final: 0.7188 (pm20) outliers start: 64 outliers final: 45 residues processed: 529 average time/residue: 0.1942 time to fit residues: 155.7916 Evaluate side-chains 516 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 468 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 244 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 245 optimal weight: 0.0370 chunk 272 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN A 239 GLN A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 644 GLN C 655 HIS C 764 ASN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.202493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169024 restraints weight = 39033.479| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.56 r_work: 0.3978 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25172 Z= 0.125 Angle : 0.532 12.097 34270 Z= 0.280 Chirality : 0.044 0.170 3878 Planarity : 0.004 0.063 4436 Dihedral : 4.288 18.953 3365 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 2.91 % Allowed : 10.24 % Favored : 86.85 % 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 aren not related in a simple way. whole: 0.01 (0.14), residues: 3106 helix: 1.71 (0.21), residues: 672 sheet: 0.46 (0.18), residues: 744 loop : -0.93 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 466 TYR 0.020 0.001 TYR A 904 PHE 0.024 0.001 PHE B 92 TRP 0.019 0.001 TRP A 353 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00279 (25135) covalent geometry : angle 0.52709 (34196) SS BOND : bond 0.00378 ( 37) SS BOND : angle 1.69754 ( 74) hydrogen bonds : bond 0.04171 ( 954) hydrogen bonds : angle 5.43947 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 485 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7869 (mt) REVERT: A 353 TRP cc_start: 0.4097 (p90) cc_final: 0.3845 (p90) REVERT: A 605 SER cc_start: 0.8175 (t) cc_final: 0.7807 (m) REVERT: A 764 ASN cc_start: 0.7939 (m-40) cc_final: 0.7683 (m110) REVERT: A 772 VAL cc_start: 0.8428 (t) cc_final: 0.8145 (p) REVERT: A 806 LEU cc_start: 0.8175 (mt) cc_final: 0.7969 (mt) REVERT: A 858 LEU cc_start: 0.8567 (mm) cc_final: 0.8303 (mt) REVERT: A 882 ILE cc_start: 0.8440 (mm) cc_final: 0.8179 (mt) REVERT: A 886 TRP cc_start: 0.8301 (p90) cc_final: 0.7922 (p90) REVERT: A 900 MET cc_start: 0.7721 (mtt) cc_final: 0.7480 (mtm) REVERT: A 914 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7160 (m-40) REVERT: A 933 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7946 (ttmp) REVERT: A 976 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7950 (t) REVERT: A 1002 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: A 1013 ILE cc_start: 0.8009 (mm) cc_final: 0.7664 (mt) REVERT: A 1051 SER cc_start: 0.8201 (t) cc_final: 0.7756 (p) REVERT: A 1137 VAL cc_start: 0.8659 (t) cc_final: 0.8318 (m) REVERT: B 129 LYS cc_start: 0.6944 (ttmt) cc_final: 0.6547 (tppt) REVERT: B 153 MET cc_start: -0.1589 (ttp) cc_final: -0.2496 (ttp) REVERT: B 194 PHE cc_start: 0.7488 (m-80) cc_final: 0.7178 (m-80) REVERT: B 314 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6765 (tm-30) REVERT: B 531 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7013 (m) REVERT: B 726 ILE cc_start: 0.8811 (mp) cc_final: 0.8533 (mt) REVERT: B 747 THR cc_start: 0.7489 (p) cc_final: 0.7188 (t) REVERT: B 762 GLN cc_start: 0.7286 (mt0) cc_final: 0.7047 (mt0) REVERT: B 804 GLN cc_start: 0.7826 (tp40) cc_final: 0.7583 (mm-40) REVERT: B 817 PHE cc_start: 0.8172 (t80) cc_final: 0.7774 (t80) REVERT: B 933 LYS cc_start: 0.8222 (mttt) cc_final: 0.7976 (mttt) REVERT: B 957 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7636 (mm-40) REVERT: B 964 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7807 (mtmm) REVERT: B 974 SER cc_start: 0.8451 (t) cc_final: 0.8140 (p) REVERT: B 1106 GLN cc_start: 0.7127 (mt0) cc_final: 0.6916 (mt0) REVERT: C 38 TYR cc_start: 0.7701 (m-10) cc_final: 0.6796 (m-10) REVERT: C 323 THR cc_start: 0.7330 (m) cc_final: 0.7109 (p) REVERT: C 377 PHE cc_start: 0.7394 (t80) cc_final: 0.7073 (t80) REVERT: C 396 TYR cc_start: 0.6048 (m-10) cc_final: 0.5847 (m-10) REVERT: C 537 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7832 (mtpp) REVERT: C 608 VAL cc_start: 0.8174 (m) cc_final: 0.7942 (t) REVERT: C 655 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7191 (t70) REVERT: C 740 MET cc_start: 0.7270 (ttp) cc_final: 0.6914 (ttp) REVERT: C 776 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: C 777 ASN cc_start: 0.7998 (m-40) cc_final: 0.7781 (m-40) REVERT: C 790 LYS cc_start: 0.7531 (mtmm) cc_final: 0.7260 (mttm) REVERT: C 936 ASP cc_start: 0.7657 (m-30) cc_final: 0.7120 (m-30) REVERT: C 981 LEU cc_start: 0.8406 (mt) cc_final: 0.8189 (mp) REVERT: C 1005 GLN cc_start: 0.7862 (mm110) cc_final: 0.7485 (mp10) REVERT: C 1031 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: C 1072 GLU cc_start: 0.7460 (pm20) cc_final: 0.7091 (pm20) outliers start: 80 outliers final: 52 residues processed: 526 average time/residue: 0.1916 time to fit residues: 154.0938 Evaluate side-chains 529 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 469 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 214 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 252 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 80 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 146 HIS A 196 ASN A 239 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN C 644 GLN C 655 HIS C 764 ASN C 935 GLN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.203790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.171203 restraints weight = 39096.432| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.39 r_work: 0.4000 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25172 Z= 0.121 Angle : 0.523 11.104 34270 Z= 0.275 Chirality : 0.043 0.165 3878 Planarity : 0.004 0.044 4436 Dihedral : 4.219 19.062 3365 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 2.91 % Allowed : 11.22 % Favored : 85.87 % 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 aren not related in a simple way. whole: 0.08 (0.14), residues: 3106 helix: 1.77 (0.21), residues: 673 sheet: 0.55 (0.18), residues: 727 loop : -0.91 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.020 0.001 TYR A 904 PHE 0.028 0.001 PHE A 823 TRP 0.014 0.001 TRP C 64 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00273 (25135) covalent geometry : angle 0.51893 (34196) SS BOND : bond 0.00379 ( 37) SS BOND : angle 1.43754 ( 74) hydrogen bonds : bond 0.04028 ( 954) hydrogen bonds : angle 5.34942 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 479 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7882 (mt) REVERT: A 300 LYS cc_start: 0.8646 (mtmm) cc_final: 0.7933 (mttp) REVERT: A 605 SER cc_start: 0.8227 (t) cc_final: 0.7886 (m) REVERT: A 764 ASN cc_start: 0.8098 (m-40) cc_final: 0.7854 (m110) REVERT: A 772 VAL cc_start: 0.8562 (t) cc_final: 0.8288 (p) REVERT: A 858 LEU cc_start: 0.8608 (mm) cc_final: 0.8393 (mt) REVERT: A 882 ILE cc_start: 0.8505 (mm) cc_final: 0.8265 (mt) REVERT: A 886 TRP cc_start: 0.8391 (p90) cc_final: 0.8053 (p90) REVERT: A 900 MET cc_start: 0.8016 (mtt) cc_final: 0.7768 (mtm) REVERT: A 914 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7203 (m-40) REVERT: A 933 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8008 (ttmp) REVERT: A 957 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 976 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8031 (t) REVERT: A 1002 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: A 1013 ILE cc_start: 0.8109 (mm) cc_final: 0.7780 (mt) REVERT: A 1031 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 1051 SER cc_start: 0.8256 (t) cc_final: 0.7842 (p) REVERT: A 1137 VAL cc_start: 0.8736 (t) cc_final: 0.8400 (m) REVERT: B 153 MET cc_start: -0.1518 (ttp) cc_final: -0.2413 (ttp) REVERT: B 531 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7295 (m) REVERT: B 666 ILE cc_start: 0.7903 (mm) cc_final: 0.7588 (mt) REVERT: B 726 ILE cc_start: 0.8799 (mp) cc_final: 0.8547 (mt) REVERT: B 747 THR cc_start: 0.7643 (p) cc_final: 0.7406 (t) REVERT: B 762 GLN cc_start: 0.7428 (mt0) cc_final: 0.7222 (mt0) REVERT: B 776 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7720 (ttpp) REVERT: B 804 GLN cc_start: 0.7981 (tp40) cc_final: 0.7757 (mm-40) REVERT: B 817 PHE cc_start: 0.8291 (t80) cc_final: 0.7932 (t80) REVERT: B 933 LYS cc_start: 0.8330 (mttt) cc_final: 0.7789 (mtmm) REVERT: B 957 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7924 (mm-40) REVERT: B 964 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7992 (mtmm) REVERT: B 974 SER cc_start: 0.8465 (t) cc_final: 0.8193 (p) REVERT: B 1106 GLN cc_start: 0.7256 (mt0) cc_final: 0.6906 (mt0) REVERT: C 38 TYR cc_start: 0.7763 (m-10) cc_final: 0.6833 (m-10) REVERT: C 377 PHE cc_start: 0.7525 (t80) cc_final: 0.7226 (t80) REVERT: C 537 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7850 (mtpp) REVERT: C 608 VAL cc_start: 0.8148 (m) cc_final: 0.7929 (t) REVERT: C 740 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7419 (ttt) REVERT: C 773 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7183 (mm-30) REVERT: C 776 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8171 (ttpt) REVERT: C 777 ASN cc_start: 0.8000 (m-40) cc_final: 0.7773 (m-40) REVERT: C 936 ASP cc_start: 0.7848 (m-30) cc_final: 0.7292 (m-30) REVERT: C 1005 GLN cc_start: 0.8091 (mm110) cc_final: 0.7559 (mt0) REVERT: C 1031 GLU cc_start: 0.8028 (tt0) cc_final: 0.7535 (mt-10) REVERT: C 1072 GLU cc_start: 0.7542 (pm20) cc_final: 0.7242 (pm20) REVERT: C 1123 SER cc_start: 0.8183 (t) cc_final: 0.7830 (m) outliers start: 80 outliers final: 50 residues processed: 518 average time/residue: 0.1805 time to fit residues: 143.4592 Evaluate side-chains 527 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 467 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 118 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 134 optimal weight: 0.0470 chunk 131 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 978 ASN C 644 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.202864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169829 restraints weight = 38611.198| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.41 r_work: 0.3987 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25172 Z= 0.143 Angle : 0.551 10.530 34270 Z= 0.290 Chirality : 0.044 0.218 3878 Planarity : 0.004 0.042 4436 Dihedral : 4.293 21.178 3365 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 11.88 % Favored : 85.32 % 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 aren not related in a simple way. whole: 0.08 (0.15), residues: 3106 helix: 1.79 (0.21), residues: 676 sheet: 0.52 (0.18), residues: 731 loop : -0.90 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.023 0.001 TYR A 904 PHE 0.036 0.002 PHE C 541 TRP 0.012 0.001 TRP C 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00326 (25135) covalent geometry : angle 0.54765 (34196) SS BOND : bond 0.00370 ( 37) SS BOND : angle 1.47965 ( 74) hydrogen bonds : bond 0.04228 ( 954) hydrogen bonds : angle 5.36241 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 483 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 300 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8012 (mttp) REVERT: A 303 LEU cc_start: 0.8350 (tt) cc_final: 0.8128 (tp) REVERT: A 315 THR cc_start: 0.8348 (m) cc_final: 0.7996 (p) REVERT: A 605 SER cc_start: 0.8251 (t) cc_final: 0.7891 (m) REVERT: A 772 VAL cc_start: 0.8616 (t) cc_final: 0.8340 (p) REVERT: A 858 LEU cc_start: 0.8668 (mm) cc_final: 0.8419 (mt) REVERT: A 882 ILE cc_start: 0.8493 (mm) cc_final: 0.8251 (mt) REVERT: A 900 MET cc_start: 0.8114 (mtt) cc_final: 0.7891 (mtm) REVERT: A 933 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8080 (ttmp) REVERT: A 957 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 976 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8104 (t) REVERT: A 1002 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: A 1013 ILE cc_start: 0.8133 (mm) cc_final: 0.7810 (mt) REVERT: A 1031 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 1051 SER cc_start: 0.8275 (t) cc_final: 0.7897 (p) REVERT: A 1072 GLU cc_start: 0.7644 (pm20) cc_final: 0.7409 (pt0) REVERT: A 1137 VAL cc_start: 0.8748 (t) cc_final: 0.8436 (m) REVERT: B 153 MET cc_start: -0.1414 (ttp) cc_final: -0.2315 (ttp) REVERT: B 531 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7359 (m) REVERT: B 726 ILE cc_start: 0.8788 (mp) cc_final: 0.8534 (mt) REVERT: B 747 THR cc_start: 0.7695 (p) cc_final: 0.7421 (t) REVERT: B 762 GLN cc_start: 0.7485 (mt0) cc_final: 0.7236 (mt0) REVERT: B 804 GLN cc_start: 0.8022 (tp40) cc_final: 0.7705 (mm-40) REVERT: B 817 PHE cc_start: 0.8320 (t80) cc_final: 0.8012 (t80) REVERT: B 933 LYS cc_start: 0.8348 (mttt) cc_final: 0.8066 (mttt) REVERT: B 957 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7922 (mm-40) REVERT: B 964 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8049 (mtmm) REVERT: B 974 SER cc_start: 0.8459 (t) cc_final: 0.8209 (p) REVERT: B 1106 GLN cc_start: 0.7438 (mt0) cc_final: 0.7158 (mt0) REVERT: C 38 TYR cc_start: 0.7827 (m-10) cc_final: 0.6929 (m-10) REVERT: C 129 LYS cc_start: 0.6571 (mptt) cc_final: 0.6222 (mptt) REVERT: C 377 PHE cc_start: 0.7522 (t80) cc_final: 0.7286 (t80) REVERT: C 532 ASN cc_start: 0.8201 (t0) cc_final: 0.7891 (t0) REVERT: C 537 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7922 (mtpp) REVERT: C 608 VAL cc_start: 0.8147 (m) cc_final: 0.7925 (t) REVERT: C 740 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7676 (ttp) REVERT: C 773 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 777 ASN cc_start: 0.8056 (m-40) cc_final: 0.7850 (m-40) REVERT: C 936 ASP cc_start: 0.7904 (m-30) cc_final: 0.7326 (m-30) REVERT: C 1005 GLN cc_start: 0.8140 (mm110) cc_final: 0.7702 (mt0) REVERT: C 1072 GLU cc_start: 0.7571 (pm20) cc_final: 0.7194 (pm20) REVERT: C 1123 SER cc_start: 0.8178 (t) cc_final: 0.7960 (m) outliers start: 77 outliers final: 56 residues processed: 518 average time/residue: 0.1859 time to fit residues: 148.7620 Evaluate side-chains 550 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 488 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 123 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 978 ASN C 644 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.198564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166055 restraints weight = 38713.891| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.36 r_work: 0.3973 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25172 Z= 0.157 Angle : 0.567 9.971 34270 Z= 0.298 Chirality : 0.045 0.294 3878 Planarity : 0.004 0.043 4436 Dihedral : 4.376 21.581 3365 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.27 % Rotamer: Outliers : 2.81 % Allowed : 12.02 % Favored : 85.17 % 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 aren not related in a simple way. whole: 0.02 (0.15), residues: 3106 helix: 1.76 (0.21), residues: 675 sheet: 0.46 (0.18), residues: 730 loop : -0.93 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.024 0.002 TYR A 904 PHE 0.019 0.002 PHE B 541 TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00362 (25135) covalent geometry : angle 0.56383 (34196) SS BOND : bond 0.00393 ( 37) SS BOND : angle 1.46707 ( 74) hydrogen bonds : bond 0.04359 ( 954) hydrogen bonds : angle 5.36853 ( 2697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 482 time to evaluate : 0.863 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: A 226 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7885 (mt) REVERT: A 300 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8035 (mttm) REVERT: A 605 SER cc_start: 0.8286 (t) cc_final: 0.7909 (m) REVERT: A 764 ASN cc_start: 0.8242 (m110) cc_final: 0.7964 (m110) REVERT: A 772 VAL cc_start: 0.8621 (t) cc_final: 0.8365 (p) REVERT: A 858 LEU cc_start: 0.8678 (mm) cc_final: 0.8427 (mt) REVERT: A 882 ILE cc_start: 0.8491 (mm) cc_final: 0.8262 (mt) REVERT: A 900 MET cc_start: 0.8185 (mtt) cc_final: 0.7974 (mtm) REVERT: A 933 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (ttmp) REVERT: A 957 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 1002 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: A 1013 ILE cc_start: 0.8128 (mm) cc_final: 0.7799 (mt) REVERT: A 1031 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 1051 SER cc_start: 0.8365 (t) cc_final: 0.7989 (p) REVERT: A 1137 VAL cc_start: 0.8737 (t) cc_final: 0.8414 (m) REVERT: B 153 MET cc_start: -0.1298 (ttp) cc_final: -0.2249 (ttp) REVERT: B 531 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7429 (m) REVERT: B 696 THR cc_start: 0.8615 (m) cc_final: 0.8376 (t) REVERT: B 726 ILE cc_start: 0.8802 (mp) cc_final: 0.8574 (mt) REVERT: B 747 THR cc_start: 0.7581 (p) cc_final: 0.7296 (t) REVERT: B 776 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7829 (ttpp) REVERT: B 804 GLN cc_start: 0.8001 (tp40) cc_final: 0.7742 (mm-40) REVERT: B 825 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7732 (mmtp) REVERT: B 918 GLU cc_start: 0.7765 (mp0) cc_final: 0.7467 (mp0) REVERT: B 921 LYS cc_start: 0.8161 (mptt) cc_final: 0.7941 (mptt) REVERT: B 933 LYS cc_start: 0.8356 (mttt) cc_final: 0.8077 (mttt) REVERT: B 954 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7178 (mt0) REVERT: B 957 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7942 (mm-40) REVERT: B 964 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8073 (mtmm) REVERT: B 974 SER cc_start: 0.8421 (t) cc_final: 0.8167 (p) REVERT: C 38 TYR cc_start: 0.7872 (m-10) cc_final: 0.6982 (m-10) REVERT: C 44 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7656 (ptt-90) REVERT: C 317 ASN cc_start: 0.8344 (m-40) cc_final: 0.8093 (m-40) REVERT: C 377 PHE cc_start: 0.7485 (t80) cc_final: 0.7275 (t80) REVERT: C 532 ASN cc_start: 0.8187 (t0) cc_final: 0.7891 (t0) REVERT: C 537 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7994 (mtpp) REVERT: C 608 VAL cc_start: 0.8149 (m) cc_final: 0.7947 (t) REVERT: C 777 ASN cc_start: 0.8061 (m-40) cc_final: 0.7861 (m-40) REVERT: C 820 ASP cc_start: 0.8015 (m-30) cc_final: 0.7787 (m-30) REVERT: C 936 ASP cc_start: 0.7838 (m-30) cc_final: 0.7292 (m-30) REVERT: C 977 LEU cc_start: 0.8509 (mm) cc_final: 0.8166 (mt) REVERT: C 1005 GLN cc_start: 0.8156 (mm110) cc_final: 0.7645 (mt0) REVERT: C 1010 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7578 (mm-40) REVERT: C 1050 MET cc_start: 0.8218 (ptm) cc_final: 0.8005 (ptp) REVERT: C 1072 GLU cc_start: 0.7612 (pm20) cc_final: 0.7205 (pm20) REVERT: C 1123 SER cc_start: 0.8190 (t) cc_final: 0.7915 (m) outliers start: 77 outliers final: 61 residues processed: 518 average time/residue: 0.1896 time to fit residues: 150.4135 Evaluate side-chains 539 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 472 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 56 optimal weight: 5.9990 chunk 288 optimal weight: 0.2980 chunk 31 optimal weight: 0.0980 chunk 47 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 188 ASN A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN B 978 ASN C 644 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.209091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.180269 restraints weight = 40235.123| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.26 r_work: 0.3999 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25172 Z= 0.107 Angle : 0.533 10.142 34270 Z= 0.279 Chirality : 0.043 0.176 3878 Planarity : 0.004 0.068 4436 Dihedral : 4.187 20.218 3365 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 12.93 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3106 helix: 1.92 (0.21), residues: 666 sheet: 0.49 (0.18), residues: 717 loop : -0.90 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 190 TYR 0.025 0.001 TYR A 904 PHE 0.023 0.001 PHE B 927 TRP 0.017 0.001 TRP C 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00236 (25135) covalent geometry : angle 0.53045 (34196) SS BOND : bond 0.00326 ( 37) SS BOND : angle 1.25643 ( 74) hydrogen bonds : bond 0.03838 ( 954) hydrogen bonds : angle 5.23556 ( 2697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 479 time to evaluate : 0.899 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: A 127 VAL cc_start: 0.7840 (t) cc_final: 0.7605 (m) REVERT: A 226 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7883 (mt) REVERT: A 240 THR cc_start: 0.6512 (m) cc_final: 0.5751 (p) REVERT: A 300 LYS cc_start: 0.8613 (mtmm) cc_final: 0.7945 (mttm) REVERT: A 605 SER cc_start: 0.8238 (t) cc_final: 0.7871 (m) REVERT: A 764 ASN cc_start: 0.8138 (m-40) cc_final: 0.7827 (m110) REVERT: A 772 VAL cc_start: 0.8540 (t) cc_final: 0.8255 (p) REVERT: A 858 LEU cc_start: 0.8647 (mm) cc_final: 0.8402 (mt) REVERT: A 882 ILE cc_start: 0.8452 (mm) cc_final: 0.8191 (mt) REVERT: A 900 MET cc_start: 0.7999 (mtt) cc_final: 0.7765 (mtm) REVERT: A 933 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7905 (ttmp) REVERT: A 1002 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 1010 GLN cc_start: 0.7605 (mt0) cc_final: 0.7160 (mm110) REVERT: A 1013 ILE cc_start: 0.8049 (mm) cc_final: 0.7644 (mt) REVERT: A 1019 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7369 (ttp80) REVERT: A 1031 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 1051 SER cc_start: 0.8230 (t) cc_final: 0.7813 (p) REVERT: A 1137 VAL cc_start: 0.8743 (t) cc_final: 0.8407 (m) REVERT: B 153 MET cc_start: -0.1508 (ttp) cc_final: -0.2361 (ttp) REVERT: B 531 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7211 (m) REVERT: B 726 ILE cc_start: 0.8805 (mp) cc_final: 0.8529 (mt) REVERT: B 776 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7774 (ttpp) REVERT: B 804 GLN cc_start: 0.7913 (tp40) cc_final: 0.7639 (mm-40) REVERT: B 817 PHE cc_start: 0.8200 (t80) cc_final: 0.7926 (t80) REVERT: B 825 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7669 (mmtp) REVERT: B 933 LYS cc_start: 0.8044 (mttt) cc_final: 0.7714 (mttt) REVERT: B 954 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7034 (mt0) REVERT: B 957 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7734 (mm-40) REVERT: B 964 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7894 (mtmm) REVERT: B 974 SER cc_start: 0.8383 (t) cc_final: 0.8087 (p) REVERT: B 1101 HIS cc_start: 0.8108 (m90) cc_final: 0.7664 (m-70) REVERT: B 1122 VAL cc_start: 0.8727 (t) cc_final: 0.8406 (p) REVERT: C 38 TYR cc_start: 0.7741 (m-10) cc_final: 0.6906 (m-10) REVERT: C 44 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7509 (ptt-90) REVERT: C 129 LYS cc_start: 0.6221 (mptt) cc_final: 0.5992 (mptt) REVERT: C 239 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.6164 (mm-40) REVERT: C 377 PHE cc_start: 0.7439 (t80) cc_final: 0.7221 (t80) REVERT: C 532 ASN cc_start: 0.7993 (t0) cc_final: 0.7645 (t0) REVERT: C 537 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7911 (mtpp) REVERT: C 608 VAL cc_start: 0.8152 (m) cc_final: 0.7927 (t) REVERT: C 615 VAL cc_start: 0.8167 (m) cc_final: 0.7340 (t) REVERT: C 740 MET cc_start: 0.7198 (ttp) cc_final: 0.6728 (ttt) REVERT: C 777 ASN cc_start: 0.7807 (m-40) cc_final: 0.7556 (m-40) REVERT: C 820 ASP cc_start: 0.7864 (m-30) cc_final: 0.7636 (m-30) REVERT: C 936 ASP cc_start: 0.7682 (m-30) cc_final: 0.7082 (m-30) REVERT: C 977 LEU cc_start: 0.8382 (mm) cc_final: 0.8053 (mt) REVERT: C 1005 GLN cc_start: 0.8004 (mm110) cc_final: 0.7504 (mt0) REVERT: C 1050 MET cc_start: 0.8030 (ptm) cc_final: 0.7825 (ptp) REVERT: C 1123 SER cc_start: 0.8163 (t) cc_final: 0.7813 (m) outliers start: 59 outliers final: 46 residues processed: 505 average time/residue: 0.1913 time to fit residues: 147.6223 Evaluate side-chains 531 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 479 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 260 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 644 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.198841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165324 restraints weight = 38425.160| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.54 r_work: 0.3947 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25172 Z= 0.160 Angle : 0.582 9.225 34270 Z= 0.306 Chirality : 0.045 0.219 3878 Planarity : 0.004 0.059 4436 Dihedral : 4.369 19.594 3365 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 2.11 % Allowed : 13.48 % Favored : 84.41 % 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 aren not related in a simple way. whole: 0.00 (0.15), residues: 3106 helix: 1.72 (0.21), residues: 669 sheet: 0.43 (0.18), residues: 726 loop : -0.91 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 190 TYR 0.026 0.002 TYR A 904 PHE 0.032 0.002 PHE C 541 TRP 0.016 0.001 TRP C 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00370 (25135) covalent geometry : angle 0.57817 (34196) SS BOND : bond 0.00396 ( 37) SS BOND : angle 1.47014 ( 74) hydrogen bonds : bond 0.04337 ( 954) hydrogen bonds : angle 5.31071 ( 2697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6212 Ramachandran restraints generated. 3106 Oldfield, 0 Emsley, 3106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 486 time to evaluate : 0.886 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: A 127 VAL cc_start: 0.7921 (t) cc_final: 0.7630 (m) REVERT: A 226 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7961 (mt) REVERT: A 240 THR cc_start: 0.6379 (m) cc_final: 0.5656 (p) REVERT: A 300 LYS cc_start: 0.8632 (mtmm) cc_final: 0.7843 (mttm) REVERT: A 605 SER cc_start: 0.8251 (t) cc_final: 0.7867 (m) REVERT: A 764 ASN cc_start: 0.8141 (m-40) cc_final: 0.7721 (m110) REVERT: A 772 VAL cc_start: 0.8494 (t) cc_final: 0.8230 (p) REVERT: A 804 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: A 858 LEU cc_start: 0.8678 (mm) cc_final: 0.8447 (mt) REVERT: A 882 ILE cc_start: 0.8430 (mm) cc_final: 0.8153 (mt) REVERT: A 900 MET cc_start: 0.7950 (mtt) cc_final: 0.7712 (mtm) REVERT: A 933 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7884 (ttmp) REVERT: A 1013 ILE cc_start: 0.7977 (mm) cc_final: 0.7569 (mt) REVERT: A 1019 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7121 (ttp80) REVERT: A 1031 GLU cc_start: 0.7548 (mp0) cc_final: 0.7140 (mp0) REVERT: A 1051 SER cc_start: 0.8189 (t) cc_final: 0.7801 (p) REVERT: A 1137 VAL cc_start: 0.8699 (t) cc_final: 0.8391 (m) REVERT: B 153 MET cc_start: -0.1185 (ttp) cc_final: -0.2144 (ttp) REVERT: B 531 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7154 (m) REVERT: B 691 SER cc_start: 0.7538 (p) cc_final: 0.7287 (t) REVERT: B 726 ILE cc_start: 0.8821 (mp) cc_final: 0.8545 (mt) REVERT: B 762 GLN cc_start: 0.7180 (mt0) cc_final: 0.6956 (mt0) REVERT: B 776 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7667 (ttpp) REVERT: B 804 GLN cc_start: 0.7848 (tp40) cc_final: 0.7597 (mm-40) REVERT: B 811 LYS cc_start: 0.7872 (mtmt) cc_final: 0.5690 (mtmt) REVERT: B 817 PHE cc_start: 0.8122 (t80) cc_final: 0.7829 (t80) REVERT: B 933 LYS cc_start: 0.8138 (mttt) cc_final: 0.7803 (mttt) REVERT: B 957 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7621 (mm-40) REVERT: B 964 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7768 (mtmm) REVERT: B 974 SER cc_start: 0.8359 (t) cc_final: 0.8079 (p) REVERT: B 1101 HIS cc_start: 0.8055 (m90) cc_final: 0.7598 (m-70) REVERT: C 38 TYR cc_start: 0.7729 (m-10) cc_final: 0.6869 (m-10) REVERT: C 44 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7446 (ptt-90) REVERT: C 239 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.6018 (mm110) REVERT: C 317 ASN cc_start: 0.8124 (m-40) cc_final: 0.7814 (m-40) REVERT: C 323 THR cc_start: 0.7335 (m) cc_final: 0.7110 (p) REVERT: C 532 ASN cc_start: 0.7995 (t0) cc_final: 0.7661 (t0) REVERT: C 537 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7931 (mtpp) REVERT: C 608 VAL cc_start: 0.8121 (m) cc_final: 0.7901 (t) REVERT: C 655 HIS cc_start: 0.7745 (t70) cc_final: 0.7437 (t70) REVERT: C 820 ASP cc_start: 0.7826 (m-30) cc_final: 0.7607 (m-30) REVERT: C 936 ASP cc_start: 0.7602 (m-30) cc_final: 0.7021 (m-30) REVERT: C 1005 GLN cc_start: 0.7947 (mm110) cc_final: 0.7451 (mt0) REVERT: C 1031 GLU cc_start: 0.7955 (tt0) cc_final: 0.7624 (mt-10) REVERT: C 1050 MET cc_start: 0.7999 (ptm) cc_final: 0.7752 (ptp) REVERT: C 1123 SER cc_start: 0.8167 (t) cc_final: 0.7814 (m) outliers start: 58 outliers final: 46 residues processed: 509 average time/residue: 0.1863 time to fit residues: 144.7308 Evaluate side-chains 530 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 479 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 175 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 74 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 317 ASN A 439 ASN A 536 ASN B 978 ASN C 644 GLN C 764 ASN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165300 restraints weight = 38587.089| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.53 r_work: 0.3961 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25172 Z= 0.126 Angle : 0.560 11.959 34270 Z= 0.292 Chirality : 0.044 0.178 3878 Planarity : 0.004 0.053 4436 Dihedral : 4.289 20.543 3365 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 2.19 % Allowed : 13.19 % Favored : 84.63 % 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 aren not related in a simple way. whole: 0.03 (0.15), residues: 3106 helix: 1.75 (0.21), residues: 671 sheet: 0.47 (0.19), residues: 717 loop : -0.90 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.026 0.001 TYR A 904 PHE 0.029 0.001 PHE C 541 TRP 0.024 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00289 (25135) covalent geometry : angle 0.55773 (34196) SS BOND : bond 0.00350 ( 37) SS BOND : angle 1.32091 ( 74) hydrogen bonds : bond 0.03993 ( 954) hydrogen bonds : angle 5.24365 ( 2697) =============================================================================== Job complete usr+sys time: 7464.99 seconds wall clock time: 128 minutes 11.06 seconds (7691.06 seconds total)