Starting phenix.real_space_refine on Thu Mar 5 16:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwu_23557/03_2026/7lwu_23557.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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 102 5.16 5 C 15063 2.51 5 N 3880 2.21 5 O 4531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7696 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7708 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7682 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.34, per 1000 atoms: 0.23 Number of scatterers: 23576 At special positions: 0 Unit cell: (128.28, 138.97, 193.489, 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 102 16.00 O 4531 8.00 N 3880 7.00 C 15063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 343 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 903.3 milliseconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.2% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.635A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.969A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.526A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.097A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.531A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.716A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.644A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.523A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.509A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.501A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 removed outlier: 3.641A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.534A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.843A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.369A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.608A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.939A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.556A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.831A 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 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.756A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.273A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.759A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.536A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.299A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.833A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.850A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.873A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.511A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.511A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (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: 3.592A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.626A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.415A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.554A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.986A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.831A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.814A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.046A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.283A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.706A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.800A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.158A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.656A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.310A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.708A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.272A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.986A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.848A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.411A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.246A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.624A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.829A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.783A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.852A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.773A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.811A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.883A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.869A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.475A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.475A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.602A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2838 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: 5.45 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6199 1.33 - 1.46: 4602 1.46 - 1.58: 13163 1.58 - 1.70: 0 1.70 - 1.83: 126 Bond restraints: 24090 Sorted by residual: bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.541 -0.026 5.50e-03 3.31e+04 2.32e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 24085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 24226 1.97 - 3.94: 7744 3.94 - 5.91: 741 5.91 - 7.88: 62 7.88 - 9.85: 10 Bond angle restraints: 32783 Sorted by residual: angle pdb=" CA ASP C 570 " pdb=" CB ASP C 570 " pdb=" CG ASP C 570 " ideal model delta sigma weight residual 112.60 122.41 -9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" CA ASN A 188 " pdb=" CB ASN A 188 " pdb=" CG ASN A 188 " ideal model delta sigma weight residual 112.60 119.34 -6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.39 -6.59 1.00e+00 1.00e+00 4.35e+01 angle pdb=" N ASN C 710 " pdb=" CA ASN C 710 " pdb=" C ASN C 710 " ideal model delta sigma weight residual 113.38 120.10 -6.72 1.17e+00 7.31e-01 3.29e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 32778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13792 17.95 - 35.90: 755 35.90 - 53.85: 144 53.85 - 71.79: 38 71.79 - 89.74: 29 Dihedral angle restraints: 14758 sinusoidal: 6098 harmonic: 8660 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -169.24 83.24 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -152.61 66.61 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -141.95 55.95 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 14755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3844 0.270 - 0.540: 23 0.540 - 0.810: 0 0.810 - 1.080: 0 1.080 - 1.349: 1 Chirality restraints: 3868 Sorted by residual: chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA ASN C 710 " pdb=" N ASN C 710 " pdb=" C ASN C 710 " pdb=" CB ASN C 710 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3865 not shown) Planarity restraints: 4213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.267 2.00e-02 2.50e+03 1.52e-01 4.60e+02 pdb=" CG TYR C 904 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.128 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.097 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.209 2.00e-02 2.50e+03 1.06e-01 2.83e+02 pdb=" CG TRP C 886 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.094 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.143 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.129 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " -0.136 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" CG ASN B 657 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.211 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.167 2.00e-02 2.50e+03 ... (remaining 4210 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 11700 3.00 - 3.48: 22141 3.48 - 3.95: 38281 3.95 - 4.43: 42179 4.43 - 4.90: 72119 Nonbonded interactions: 186420 Sorted by model distance: nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.528 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.533 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.543 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.549 3.040 ... (remaining 186415 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 487 or (resid 488 and (name N or name CA or name C or name \ O or name CB )) or resid 489 through 527 or (resid 528 and (name N or name CA o \ r name C or name O or name CB )) or resid 529 through 810 or (resid 811 and (nam \ e N or name CA or name C or name O or name CB )) or resid 813 through 827 or res \ id 855 through 866 or (resid 867 through 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 1141 or (resid 1142 and (name N or na \ me CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 114 \ 5 through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1311)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 483 or resid 485 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 582 o \ r (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 84 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C or \ name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (resi \ d 745 and (name N or name CA or name C or name O or name CB )) or resid 746 thro \ ugh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) o \ r resid 749 through 810 or (resid 811 and (name N or name CA or name C or name O \ or name CB )) or resid 813 or (resid 814 and (name N or name CA or name C or na \ me O or name CB )) or resid 815 through 827 or resid 855 through 866 or (resid 8 \ 67 through 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 1091 or (resid 1092 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1311)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 through 215 and (name N or name CA or name C or name O \ or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) o \ r resid 481 through 483 or resid 485 through 487 or (resid 488 and (name N or na \ me CA or name C or name O or name CB )) or resid 489 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 582 or (resid 583 and (name N or name CA or name C or name O or nam \ e CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C \ or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 813 or (resid 814 a \ nd (name N or name CA or name C or name O or name CB )) or resid 815 through 109 \ 1 or (resid 1092 and (name N or name CA or name C or name O or name CB )) or res \ id 1093 through 1141 or (resid 1142 and (name N or name CA or name C or name O o \ r name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1311)) } 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: 1.840 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.013 0.077 24163 Z= 0.778 Angle : 1.786 13.039 32964 Z= 1.193 Chirality : 0.096 1.349 3868 Planarity : 0.013 0.168 4178 Dihedral : 12.679 89.743 9068 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.47 % Favored : 94.32 % Rotamer: Outliers : 0.94 % Allowed : 2.04 % Favored : 97.01 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 2924 helix: -1.10 (0.16), residues: 670 sheet: 1.00 (0.21), residues: 521 loop : -0.69 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 273 TYR 0.267 0.020 TYR C 904 PHE 0.071 0.011 PHE A 718 TRP 0.209 0.026 TRP C 886 HIS 0.014 0.003 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01344 (24090) covalent geometry : angle 1.76890 (32783) SS BOND : bond 0.01182 ( 38) SS BOND : angle 2.08783 ( 76) hydrogen bonds : bond 0.17621 ( 1012) hydrogen bonds : angle 8.41645 ( 2838) link_NAG-ASN : bond 0.01411 ( 35) link_NAG-ASN : angle 4.60140 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7385 (ttmt) cc_final: 0.6611 (tptt) REVERT: A 133 PHE cc_start: 0.7023 (m-80) cc_final: 0.6534 (t80) REVERT: A 201 PHE cc_start: 0.7833 (t80) cc_final: 0.7572 (t80) REVERT: A 284 THR cc_start: 0.8868 (m) cc_final: 0.8576 (p) REVERT: A 324 GLU cc_start: 0.7252 (mp0) cc_final: 0.6914 (mp0) REVERT: A 529 LYS cc_start: 0.7802 (mttt) cc_final: 0.7409 (mtmm) REVERT: B 525 CYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3375 (m) REVERT: B 565 PHE cc_start: 0.6947 (m-10) cc_final: 0.6527 (m-80) REVERT: C 239 GLN cc_start: 0.7863 (pt0) cc_final: 0.7091 (tt0) REVERT: C 360 ASN cc_start: 0.6967 (m110) cc_final: 0.6566 (t0) REVERT: C 619 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.5978 (mp0) outliers start: 24 outliers final: 5 residues processed: 332 average time/residue: 0.1713 time to fit residues: 88.3038 Evaluate side-chains 189 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 188 ASN A 317 ASN B 370 ASN B1088 HIS C 81 ASN C 165 ASN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122485 restraints weight = 31758.713| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.30 r_work: 0.3226 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24163 Z= 0.177 Angle : 0.671 11.720 32964 Z= 0.353 Chirality : 0.047 0.219 3868 Planarity : 0.004 0.053 4178 Dihedral : 7.142 62.177 3925 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.61 % Allowed : 5.78 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2924 helix: 1.12 (0.20), residues: 673 sheet: 0.63 (0.18), residues: 704 loop : -0.46 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.025 0.002 TYR C 170 PHE 0.014 0.002 PHE C 759 TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00409 (24090) covalent geometry : angle 0.64541 (32783) SS BOND : bond 0.00854 ( 38) SS BOND : angle 1.95264 ( 76) hydrogen bonds : bond 0.05134 ( 1012) hydrogen bonds : angle 6.26994 ( 2838) link_NAG-ASN : bond 0.00440 ( 35) link_NAG-ASN : angle 2.88681 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7429 (ttmt) cc_final: 0.6741 (tttp) REVERT: A 190 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7814 (mtt-85) REVERT: A 392 PHE cc_start: 0.7398 (m-80) cc_final: 0.6761 (m-80) REVERT: A 529 LYS cc_start: 0.7756 (mttt) cc_final: 0.7312 (mtmm) REVERT: A 985 ASP cc_start: 0.7104 (t0) cc_final: 0.6884 (t0) REVERT: A 994 ASP cc_start: 0.8676 (t0) cc_final: 0.8329 (m-30) REVERT: B 129 LYS cc_start: 0.6670 (tttt) cc_final: 0.5940 (tptp) REVERT: B 316 SER cc_start: 0.9038 (t) cc_final: 0.8765 (m) REVERT: B 525 CYS cc_start: 0.3289 (OUTLIER) cc_final: 0.2796 (m) REVERT: B 1002 GLN cc_start: 0.8711 (tt0) cc_final: 0.8461 (tt0) REVERT: C 237 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7613 (mtp-110) REVERT: C 305 SER cc_start: 0.9084 (t) cc_final: 0.8839 (p) REVERT: C 360 ASN cc_start: 0.6925 (m110) cc_final: 0.6646 (t0) REVERT: C 1010 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8098 (mm110) outliers start: 41 outliers final: 23 residues processed: 233 average time/residue: 0.1427 time to fit residues: 54.9336 Evaluate side-chains 179 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 290 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 123 optimal weight: 0.0070 chunk 223 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN C 81 ASN C 207 HIS ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138932 restraints weight = 31396.554| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.56 r_work: 0.3284 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24163 Z= 0.136 Angle : 0.574 11.450 32964 Z= 0.300 Chirality : 0.045 0.213 3868 Planarity : 0.004 0.065 4178 Dihedral : 6.433 58.944 3919 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.61 % Allowed : 7.31 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2924 helix: 1.75 (0.21), residues: 662 sheet: 0.64 (0.18), residues: 686 loop : -0.28 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 357 TYR 0.023 0.001 TYR B 200 PHE 0.014 0.001 PHE C 565 TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00317 (24090) covalent geometry : angle 0.55585 (32783) SS BOND : bond 0.00314 ( 38) SS BOND : angle 1.39894 ( 76) hydrogen bonds : bond 0.04412 ( 1012) hydrogen bonds : angle 5.76496 ( 2838) link_NAG-ASN : bond 0.00344 ( 35) link_NAG-ASN : angle 2.36765 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7425 (ttmt) cc_final: 0.6692 (tttp) REVERT: A 269 TYR cc_start: 0.8982 (m-10) cc_final: 0.8740 (m-10) REVERT: A 390 LEU cc_start: 0.8337 (mp) cc_final: 0.8079 (mt) REVERT: A 392 PHE cc_start: 0.7684 (m-80) cc_final: 0.7261 (m-80) REVERT: A 529 LYS cc_start: 0.7699 (mttt) cc_final: 0.7308 (mtmm) REVERT: A 985 ASP cc_start: 0.7362 (t0) cc_final: 0.7059 (t0) REVERT: A 994 ASP cc_start: 0.8607 (t0) cc_final: 0.8301 (m-30) REVERT: B 129 LYS cc_start: 0.6816 (tttt) cc_final: 0.6181 (tptp) REVERT: B 284 THR cc_start: 0.8330 (m) cc_final: 0.7963 (p) REVERT: B 525 CYS cc_start: 0.3256 (OUTLIER) cc_final: 0.2769 (m) REVERT: B 544 ASN cc_start: 0.7968 (m-40) cc_final: 0.7730 (t0) REVERT: B 804 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8079 (mp10) REVERT: B 950 ASP cc_start: 0.8931 (t0) cc_final: 0.8637 (m-30) REVERT: B 1002 GLN cc_start: 0.8713 (tt0) cc_final: 0.8472 (tt0) REVERT: C 237 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7648 (mtp-110) REVERT: C 360 ASN cc_start: 0.6964 (m110) cc_final: 0.6592 (t0) REVERT: C 697 MET cc_start: 0.8539 (ptt) cc_final: 0.8292 (ptt) REVERT: C 1010 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8130 (mm110) outliers start: 41 outliers final: 29 residues processed: 209 average time/residue: 0.1371 time to fit residues: 47.9100 Evaluate side-chains 182 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 157 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 140 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 580 GLN B 762 GLN C 207 HIS C 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.184993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118820 restraints weight = 31592.400| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.47 r_work: 0.3261 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24163 Z= 0.156 Angle : 0.559 8.748 32964 Z= 0.289 Chirality : 0.045 0.224 3868 Planarity : 0.004 0.047 4178 Dihedral : 6.249 59.287 3917 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 7.67 % Favored : 90.17 % 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 are not related in a simple way. whole: 0.56 (0.15), residues: 2924 helix: 1.64 (0.20), residues: 678 sheet: 0.65 (0.19), residues: 692 loop : -0.29 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.021 0.001 TYR A 904 PHE 0.013 0.001 PHE C 565 TRP 0.009 0.001 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00376 (24090) covalent geometry : angle 0.54298 (32783) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.25479 ( 76) hydrogen bonds : bond 0.04298 ( 1012) hydrogen bonds : angle 5.62445 ( 2838) link_NAG-ASN : bond 0.00332 ( 35) link_NAG-ASN : angle 2.20208 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.828 Fit side-chains REVERT: A 129 LYS cc_start: 0.7451 (ttmt) cc_final: 0.6578 (tptt) REVERT: A 190 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7353 (mtt180) REVERT: A 388 ASN cc_start: 0.8166 (m110) cc_final: 0.7688 (t0) REVERT: A 392 PHE cc_start: 0.7664 (m-80) cc_final: 0.7458 (m-80) REVERT: A 529 LYS cc_start: 0.7728 (mttt) cc_final: 0.7254 (mtmm) REVERT: A 567 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6832 (tpp80) REVERT: A 985 ASP cc_start: 0.7377 (t0) cc_final: 0.7085 (t0) REVERT: A 994 ASP cc_start: 0.8630 (t0) cc_final: 0.8294 (m-30) REVERT: A 1111 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: B 129 LYS cc_start: 0.6849 (tttt) cc_final: 0.6155 (tptp) REVERT: B 284 THR cc_start: 0.8411 (m) cc_final: 0.8052 (p) REVERT: B 501 TYR cc_start: 0.0893 (OUTLIER) cc_final: 0.0282 (m-10) REVERT: B 525 CYS cc_start: 0.3140 (OUTLIER) cc_final: 0.2712 (m) REVERT: B 544 ASN cc_start: 0.8084 (m-40) cc_final: 0.7793 (t0) REVERT: B 581 THR cc_start: 0.7993 (m) cc_final: 0.7788 (p) REVERT: B 804 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8165 (mp10) REVERT: B 950 ASP cc_start: 0.8893 (t0) cc_final: 0.8499 (m-30) REVERT: B 1002 GLN cc_start: 0.8715 (tt0) cc_final: 0.8464 (tt0) REVERT: C 54 LEU cc_start: 0.8925 (mt) cc_final: 0.8677 (mp) REVERT: C 227 VAL cc_start: 0.9000 (m) cc_final: 0.8778 (p) REVERT: C 237 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7662 (mtp-110) REVERT: C 269 TYR cc_start: 0.8081 (m-80) cc_final: 0.7823 (m-80) REVERT: C 360 ASN cc_start: 0.6842 (m110) cc_final: 0.6565 (t0) REVERT: C 365 TYR cc_start: 0.8514 (m-80) cc_final: 0.7871 (m-80) REVERT: C 619 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: C 869 MET cc_start: 0.9175 (mtt) cc_final: 0.8954 (mtt) REVERT: C 1010 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (mm110) outliers start: 55 outliers final: 37 residues processed: 211 average time/residue: 0.1387 time to fit residues: 48.6886 Evaluate side-chains 198 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 110 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN C 354 ASN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.184939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116674 restraints weight = 31376.011| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.38 r_work: 0.3271 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24163 Z= 0.150 Angle : 0.539 7.998 32964 Z= 0.278 Chirality : 0.045 0.226 3868 Planarity : 0.004 0.049 4178 Dihedral : 6.152 59.970 3917 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.97 % Allowed : 8.49 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 2924 helix: 1.67 (0.20), residues: 679 sheet: 0.59 (0.19), residues: 673 loop : -0.29 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.022 0.001 TYR A 904 PHE 0.014 0.001 PHE B 927 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00359 (24090) covalent geometry : angle 0.52429 (32783) SS BOND : bond 0.00345 ( 38) SS BOND : angle 1.16937 ( 76) hydrogen bonds : bond 0.04202 ( 1012) hydrogen bonds : angle 5.53044 ( 2838) link_NAG-ASN : bond 0.00324 ( 35) link_NAG-ASN : angle 2.12418 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.600 Fit side-chains REVERT: A 129 LYS cc_start: 0.7373 (ttmt) cc_final: 0.6519 (tptt) REVERT: A 190 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7589 (mtt-85) REVERT: A 388 ASN cc_start: 0.8214 (m110) cc_final: 0.7647 (t0) REVERT: A 529 LYS cc_start: 0.7775 (mttt) cc_final: 0.7225 (mtmm) REVERT: A 779 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8576 (tp40) REVERT: A 994 ASP cc_start: 0.8647 (t0) cc_final: 0.8301 (m-30) REVERT: A 1111 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: B 129 LYS cc_start: 0.6784 (tttt) cc_final: 0.6154 (tptp) REVERT: B 284 THR cc_start: 0.8426 (m) cc_final: 0.8068 (p) REVERT: B 501 TYR cc_start: 0.0824 (OUTLIER) cc_final: 0.0424 (m-10) REVERT: B 525 CYS cc_start: 0.2981 (OUTLIER) cc_final: 0.2625 (m) REVERT: B 544 ASN cc_start: 0.8111 (m-40) cc_final: 0.7804 (t0) REVERT: B 581 THR cc_start: 0.8031 (m) cc_final: 0.7818 (p) REVERT: B 804 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8162 (mp10) REVERT: B 950 ASP cc_start: 0.8875 (t0) cc_final: 0.8490 (m-30) REVERT: B 1002 GLN cc_start: 0.8725 (tt0) cc_final: 0.8467 (tt0) REVERT: C 54 LEU cc_start: 0.8911 (mt) cc_final: 0.8666 (mp) REVERT: C 133 PHE cc_start: 0.2586 (t80) cc_final: 0.1801 (t80) REVERT: C 237 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7803 (mtp-110) REVERT: C 360 ASN cc_start: 0.6854 (m110) cc_final: 0.6560 (t0) REVERT: C 619 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: C 869 MET cc_start: 0.9167 (mtt) cc_final: 0.8960 (mtt) REVERT: C 1010 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8191 (mm110) outliers start: 50 outliers final: 35 residues processed: 202 average time/residue: 0.1423 time to fit residues: 47.8997 Evaluate side-chains 194 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 43 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 134 optimal weight: 40.0000 chunk 171 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 354 ASN B 580 GLN C 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119283 restraints weight = 31578.422| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.33 r_work: 0.3278 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24163 Z= 0.148 Angle : 0.535 8.014 32964 Z= 0.276 Chirality : 0.045 0.224 3868 Planarity : 0.003 0.048 4178 Dihedral : 6.088 59.673 3917 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.56 % Allowed : 8.65 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 2924 helix: 1.83 (0.20), residues: 665 sheet: 0.61 (0.18), residues: 713 loop : -0.36 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.026 0.001 TYR A 904 PHE 0.015 0.001 PHE B 927 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00353 (24090) covalent geometry : angle 0.51985 (32783) SS BOND : bond 0.00330 ( 38) SS BOND : angle 1.29503 ( 76) hydrogen bonds : bond 0.04128 ( 1012) hydrogen bonds : angle 5.46081 ( 2838) link_NAG-ASN : bond 0.00318 ( 35) link_NAG-ASN : angle 2.08957 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6597 (tptt) REVERT: A 190 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: A 388 ASN cc_start: 0.8210 (m110) cc_final: 0.7674 (t0) REVERT: A 529 LYS cc_start: 0.7690 (mttt) cc_final: 0.7147 (mtmm) REVERT: A 994 ASP cc_start: 0.8626 (t0) cc_final: 0.8253 (m-30) REVERT: A 1111 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: B 129 LYS cc_start: 0.6742 (tttt) cc_final: 0.6060 (tptp) REVERT: B 284 THR cc_start: 0.8455 (m) cc_final: 0.8105 (p) REVERT: B 501 TYR cc_start: 0.0810 (OUTLIER) cc_final: 0.0373 (m-10) REVERT: B 525 CYS cc_start: 0.3433 (OUTLIER) cc_final: 0.3114 (m) REVERT: B 544 ASN cc_start: 0.8073 (m-40) cc_final: 0.7772 (t0) REVERT: B 804 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8148 (mp10) REVERT: B 950 ASP cc_start: 0.8825 (t0) cc_final: 0.8466 (m-30) REVERT: B 1002 GLN cc_start: 0.8648 (tt0) cc_final: 0.8383 (tt0) REVERT: C 237 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7750 (mtp-110) REVERT: C 360 ASN cc_start: 0.6887 (m110) cc_final: 0.6539 (t0) REVERT: C 619 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: C 869 MET cc_start: 0.9166 (mtt) cc_final: 0.8955 (mtt) REVERT: C 1010 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8159 (mm110) outliers start: 65 outliers final: 44 residues processed: 206 average time/residue: 0.1467 time to fit residues: 50.4414 Evaluate side-chains 197 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 226 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 109 optimal weight: 0.0570 chunk 173 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.186103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121813 restraints weight = 31554.566| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.55 r_work: 0.3220 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 24163 Z= 0.102 Angle : 0.511 11.304 32964 Z= 0.263 Chirality : 0.044 0.222 3868 Planarity : 0.003 0.047 4178 Dihedral : 5.935 57.782 3917 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.04 % Allowed : 9.20 % Favored : 88.76 % 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 are not related in a simple way. whole: 0.66 (0.15), residues: 2924 helix: 2.01 (0.21), residues: 666 sheet: 0.62 (0.19), residues: 673 loop : -0.29 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.024 0.001 TYR A 904 PHE 0.018 0.001 PHE B 927 TRP 0.007 0.001 TRP B 353 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00229 (24090) covalent geometry : angle 0.49343 (32783) SS BOND : bond 0.00284 ( 38) SS BOND : angle 1.65765 ( 76) hydrogen bonds : bond 0.03729 ( 1012) hydrogen bonds : angle 5.34477 ( 2838) link_NAG-ASN : bond 0.00304 ( 35) link_NAG-ASN : angle 1.97823 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7418 (ttmt) cc_final: 0.6711 (tttt) REVERT: A 190 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7480 (mtt180) REVERT: A 388 ASN cc_start: 0.8224 (m110) cc_final: 0.7758 (t0) REVERT: A 529 LYS cc_start: 0.7686 (mttt) cc_final: 0.6911 (mmtm) REVERT: A 994 ASP cc_start: 0.8564 (t0) cc_final: 0.8236 (m-30) REVERT: B 129 LYS cc_start: 0.6701 (tttt) cc_final: 0.6055 (tptp) REVERT: B 189 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 226 LEU cc_start: 0.7518 (mt) cc_final: 0.7302 (mt) REVERT: B 266 TYR cc_start: 0.7439 (m-80) cc_final: 0.7203 (m-80) REVERT: B 284 THR cc_start: 0.8428 (m) cc_final: 0.8091 (p) REVERT: B 501 TYR cc_start: 0.0834 (OUTLIER) cc_final: 0.0363 (m-10) REVERT: B 544 ASN cc_start: 0.8087 (m-40) cc_final: 0.7783 (t0) REVERT: B 804 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8188 (mp10) REVERT: B 950 ASP cc_start: 0.8788 (t0) cc_final: 0.8395 (m-30) REVERT: B 1002 GLN cc_start: 0.8677 (tt0) cc_final: 0.8401 (tt0) REVERT: C 237 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7717 (mtp-110) REVERT: C 360 ASN cc_start: 0.6842 (m110) cc_final: 0.6528 (t0) REVERT: C 869 MET cc_start: 0.9150 (mtt) cc_final: 0.8943 (mtt) REVERT: C 1010 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8229 (mm110) outliers start: 52 outliers final: 39 residues processed: 197 average time/residue: 0.1404 time to fit residues: 46.3633 Evaluate side-chains 194 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 149 optimal weight: 0.0770 chunk 31 optimal weight: 0.0370 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.188305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123020 restraints weight = 31442.905| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.48 r_work: 0.3311 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24163 Z= 0.096 Angle : 0.495 8.913 32964 Z= 0.255 Chirality : 0.044 0.228 3868 Planarity : 0.003 0.051 4178 Dihedral : 5.741 58.088 3916 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.81 % Allowed : 9.36 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 2924 helix: 2.10 (0.20), residues: 674 sheet: 0.73 (0.19), residues: 710 loop : -0.30 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.024 0.001 TYR A 904 PHE 0.019 0.001 PHE B 927 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00212 (24090) covalent geometry : angle 0.48091 (32783) SS BOND : bond 0.00317 ( 38) SS BOND : angle 1.31349 ( 76) hydrogen bonds : bond 0.03545 ( 1012) hydrogen bonds : angle 5.21963 ( 2838) link_NAG-ASN : bond 0.00290 ( 35) link_NAG-ASN : angle 1.87992 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7453 (ttmt) cc_final: 0.6753 (tttt) REVERT: A 190 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7567 (mtt180) REVERT: A 388 ASN cc_start: 0.8227 (m110) cc_final: 0.7834 (t0) REVERT: A 529 LYS cc_start: 0.7706 (mttt) cc_final: 0.7032 (mmtt) REVERT: A 994 ASP cc_start: 0.8503 (t0) cc_final: 0.8189 (m-30) REVERT: B 129 LYS cc_start: 0.6711 (tttt) cc_final: 0.6101 (tptp) REVERT: B 189 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 226 LEU cc_start: 0.7506 (mt) cc_final: 0.7299 (mt) REVERT: B 266 TYR cc_start: 0.7437 (m-80) cc_final: 0.7214 (m-80) REVERT: B 284 THR cc_start: 0.8441 (m) cc_final: 0.8138 (p) REVERT: B 501 TYR cc_start: 0.0637 (OUTLIER) cc_final: 0.0214 (m-10) REVERT: B 544 ASN cc_start: 0.8061 (m-40) cc_final: 0.7756 (t0) REVERT: B 804 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8174 (mp10) REVERT: B 1002 GLN cc_start: 0.8629 (tt0) cc_final: 0.8363 (tt0) REVERT: C 237 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7739 (mtp-110) REVERT: C 269 TYR cc_start: 0.7564 (m-80) cc_final: 0.7193 (m-80) REVERT: C 354 ASN cc_start: 0.7628 (m110) cc_final: 0.7085 (t0) REVERT: C 360 ASN cc_start: 0.6869 (m110) cc_final: 0.6546 (t0) REVERT: C 869 MET cc_start: 0.9131 (mtt) cc_final: 0.8908 (mtt) REVERT: C 1010 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8181 (mm110) outliers start: 46 outliers final: 36 residues processed: 195 average time/residue: 0.1470 time to fit residues: 47.7456 Evaluate side-chains 189 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 265 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 10 optimal weight: 0.0010 chunk 91 optimal weight: 0.0670 chunk 196 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN C 99 ASN C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.187894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119965 restraints weight = 31587.762| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.28 r_work: 0.3375 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24163 Z= 0.090 Angle : 0.482 8.776 32964 Z= 0.247 Chirality : 0.043 0.225 3868 Planarity : 0.003 0.048 4178 Dihedral : 5.594 58.140 3915 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 9.91 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 2924 helix: 2.27 (0.21), residues: 669 sheet: 0.77 (0.18), residues: 722 loop : -0.20 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 357 TYR 0.029 0.001 TYR A 904 PHE 0.020 0.001 PHE B 927 TRP 0.010 0.001 TRP A 64 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00195 (24090) covalent geometry : angle 0.47025 (32783) SS BOND : bond 0.00262 ( 38) SS BOND : angle 1.11224 ( 76) hydrogen bonds : bond 0.03355 ( 1012) hydrogen bonds : angle 5.10507 ( 2838) link_NAG-ASN : bond 0.00288 ( 35) link_NAG-ASN : angle 1.77209 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7507 (ttmt) cc_final: 0.6808 (tttt) REVERT: A 190 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7542 (mtt180) REVERT: A 388 ASN cc_start: 0.8270 (m110) cc_final: 0.7877 (t0) REVERT: A 529 LYS cc_start: 0.7702 (mttt) cc_final: 0.7030 (mmtt) REVERT: A 531 THR cc_start: 0.8974 (t) cc_final: 0.8725 (p) REVERT: A 734 THR cc_start: 0.9100 (m) cc_final: 0.8847 (p) REVERT: A 994 ASP cc_start: 0.8454 (t0) cc_final: 0.8154 (m-30) REVERT: B 129 LYS cc_start: 0.6915 (tttt) cc_final: 0.6233 (tptp) REVERT: B 189 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8284 (tt) REVERT: B 266 TYR cc_start: 0.7420 (m-80) cc_final: 0.7219 (m-80) REVERT: B 284 THR cc_start: 0.8401 (m) cc_final: 0.8136 (p) REVERT: B 544 ASN cc_start: 0.7987 (m-40) cc_final: 0.7664 (t0) REVERT: B 804 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8142 (mp10) REVERT: B 1002 GLN cc_start: 0.8561 (tt0) cc_final: 0.8291 (tt0) REVERT: C 237 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7809 (mtm110) REVERT: C 269 TYR cc_start: 0.7584 (m-80) cc_final: 0.7262 (m-80) REVERT: C 354 ASN cc_start: 0.7622 (m110) cc_final: 0.7118 (t0) REVERT: C 360 ASN cc_start: 0.6801 (m110) cc_final: 0.6413 (t0) REVERT: C 364 ASP cc_start: 0.7702 (t0) cc_final: 0.7454 (t0) REVERT: C 396 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: C 581 THR cc_start: 0.7678 (p) cc_final: 0.7462 (t) REVERT: C 869 MET cc_start: 0.9105 (mtt) cc_final: 0.8879 (mtt) REVERT: C 1010 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8124 (mm110) outliers start: 44 outliers final: 38 residues processed: 192 average time/residue: 0.1438 time to fit residues: 46.5683 Evaluate side-chains 196 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 193 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.191073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140264 restraints weight = 31398.890| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.66 r_work: 0.3326 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24163 Z= 0.109 Angle : 0.496 8.419 32964 Z= 0.252 Chirality : 0.043 0.227 3868 Planarity : 0.003 0.048 4178 Dihedral : 5.615 59.102 3915 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 9.75 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 2924 helix: 2.22 (0.20), residues: 670 sheet: 0.78 (0.18), residues: 720 loop : -0.21 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.017 0.001 TYR A 904 PHE 0.019 0.001 PHE B 927 TRP 0.009 0.001 TRP A 64 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00252 (24090) covalent geometry : angle 0.48278 (32783) SS BOND : bond 0.00272 ( 38) SS BOND : angle 1.12033 ( 76) hydrogen bonds : bond 0.03487 ( 1012) hydrogen bonds : angle 5.11727 ( 2838) link_NAG-ASN : bond 0.00346 ( 35) link_NAG-ASN : angle 1.86126 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6729 (tttt) REVERT: A 190 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7468 (mtt180) REVERT: A 388 ASN cc_start: 0.8296 (m110) cc_final: 0.7903 (t0) REVERT: A 529 LYS cc_start: 0.7714 (mttt) cc_final: 0.7000 (mmtt) REVERT: A 531 THR cc_start: 0.8963 (t) cc_final: 0.8701 (p) REVERT: A 734 THR cc_start: 0.9122 (m) cc_final: 0.8893 (p) REVERT: A 994 ASP cc_start: 0.8577 (t0) cc_final: 0.8258 (m-30) REVERT: B 129 LYS cc_start: 0.6872 (tttt) cc_final: 0.6193 (tptp) REVERT: B 189 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8284 (tt) REVERT: B 284 THR cc_start: 0.8454 (m) cc_final: 0.8165 (p) REVERT: B 501 TYR cc_start: 0.0671 (OUTLIER) cc_final: 0.0116 (m-10) REVERT: B 544 ASN cc_start: 0.8048 (m-40) cc_final: 0.7715 (t0) REVERT: B 804 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8165 (mp10) REVERT: B 1002 GLN cc_start: 0.8632 (tt0) cc_final: 0.8382 (tt0) REVERT: C 237 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7819 (mtm110) REVERT: C 269 TYR cc_start: 0.7639 (m-80) cc_final: 0.7362 (m-80) REVERT: C 354 ASN cc_start: 0.7668 (m110) cc_final: 0.7169 (t0) REVERT: C 360 ASN cc_start: 0.6750 (m110) cc_final: 0.6417 (t0) REVERT: C 364 ASP cc_start: 0.7793 (t0) cc_final: 0.7541 (t0) REVERT: C 396 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: C 869 MET cc_start: 0.9154 (mtt) cc_final: 0.8922 (mtt) REVERT: C 1010 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8251 (mm110) outliers start: 46 outliers final: 39 residues processed: 191 average time/residue: 0.1390 time to fit residues: 45.0661 Evaluate side-chains 194 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 193 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 133 optimal weight: 40.0000 chunk 188 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140031 restraints weight = 31319.941| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.53 r_work: 0.3308 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 24163 Z= 0.178 Angle : 0.706 59.153 32964 Z= 0.417 Chirality : 0.045 0.578 3868 Planarity : 0.004 0.179 4178 Dihedral : 5.639 59.113 3915 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 9.87 % Favored : 88.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 2924 helix: 2.21 (0.20), residues: 670 sheet: 0.79 (0.18), residues: 720 loop : -0.22 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.017 0.001 TYR B1067 PHE 0.019 0.001 PHE B 927 TRP 0.008 0.001 TRP A 64 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00357 (24090) covalent geometry : angle 0.69864 (32783) SS BOND : bond 0.00277 ( 38) SS BOND : angle 1.08186 ( 76) hydrogen bonds : bond 0.03616 ( 1012) hydrogen bonds : angle 5.11879 ( 2838) link_NAG-ASN : bond 0.00328 ( 35) link_NAG-ASN : angle 1.85874 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7669.62 seconds wall clock time: 131 minutes 26.57 seconds (7886.57 seconds total)