Starting phenix.real_space_refine on Sat Jul 4 19:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v20_31632/07_2026/7v20_31632.cif" } resolution = 2.86 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= 0.000 sd= 0.072 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 101 5.16 5 C 14625 2.51 5 N 3744 2.21 5 O 4483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22953 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7431 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 10 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 8, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7485 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 53, 'TRANS': 926} Chain breaks: 11 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'TYR:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7393 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 927} Chain breaks: 11 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 205 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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 chiralities: 12 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: F, G, H, I, J, L, M, N Time building chain proxies: 5.82, per 1000 atoms: 0.25 Number of scatterers: 22953 At special positions: 0 Unit cell: (133.92, 136.08, 168.48, 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 101 16.00 O 4483 8.00 N 3744 7.00 C 14625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM22321 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 43 sheets defined 27.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.602A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.541A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.562A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.843A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.320A 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 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.610A 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: 3.720A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.291A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.525A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.572A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.920A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 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: 3.818A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.551A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.932A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.286A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.701A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.422A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.509A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.559A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.680A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.640A 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: 4.308A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.629A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.126A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.629A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.412A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.801A 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: 7.804A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.888A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.771A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.815A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.528A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.486A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.526A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.010A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.625A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.877A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.512A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.212A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.864A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.784A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.568A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.637A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.399A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.485A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.323A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.323A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.568A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.502A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.734A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.327A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.986A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.569A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.984A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.573A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.872A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.559A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7308 1.35 - 1.48: 6219 1.48 - 1.61: 9794 1.61 - 1.74: 3 1.74 - 1.87: 122 Bond restraints: 23446 Sorted by residual: bond pdb=" CG ASN A 343 " pdb=" ND2 ASN A 343 " ideal model delta sigma weight residual 1.328 1.474 -0.146 2.10e-02 2.27e+03 4.84e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.533 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CA ASN C 616 " pdb=" C ASN C 616 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.23e-02 6.61e+03 2.73e+01 bond pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 1.328 1.233 0.095 2.10e-02 2.27e+03 2.03e+01 bond pdb=" CB ASN B1074 " pdb=" CG ASN B1074 " ideal model delta sigma weight residual 1.516 1.414 0.102 2.50e-02 1.60e+03 1.67e+01 ... (remaining 23441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 31324 2.58 - 5.16: 574 5.16 - 7.74: 55 7.74 - 10.32: 17 10.32 - 12.90: 5 Bond angle restraints: 31975 Sorted by residual: angle pdb=" N ASN C 616 " pdb=" CA ASN C 616 " pdb=" C ASN C 616 " ideal model delta sigma weight residual 110.24 122.41 -12.17 1.30e+00 5.92e-01 8.77e+01 angle pdb=" CA ASN C 616 " pdb=" C ASN C 616 " pdb=" N CYS C 617 " ideal model delta sigma weight residual 115.64 107.66 7.98 1.39e+00 5.18e-01 3.30e+01 angle pdb=" N THR C 761 " pdb=" CA THR C 761 " pdb=" C THR C 761 " ideal model delta sigma weight residual 113.41 106.49 6.92 1.22e+00 6.72e-01 3.22e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 127.30 -12.90 2.30e+00 1.89e-01 3.14e+01 angle pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 114.40 127.04 -12.64 2.30e+00 1.89e-01 3.02e+01 ... (remaining 31970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12560 17.95 - 35.90: 838 35.90 - 53.84: 127 53.84 - 71.79: 30 71.79 - 89.74: 28 Dihedral angle restraints: 13583 sinusoidal: 5047 harmonic: 8536 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -173.97 87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA VAL C 615 " pdb=" C VAL C 615 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual 180.00 135.04 44.96 0 5.00e+00 4.00e-02 8.09e+01 dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta harmonic sigma weight residual -180.00 -136.68 -43.32 0 5.00e+00 4.00e-02 7.51e+01 ... (remaining 13580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3820 0.166 - 0.333: 25 0.333 - 0.499: 3 0.499 - 0.665: 2 0.665 - 0.832: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CA ASN C 616 " pdb=" N ASN C 616 " pdb=" C ASN C 616 " pdb=" CB ASN C 616 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CG LEU C 229 " pdb=" CB LEU C 229 " pdb=" CD1 LEU C 229 " pdb=" CD2 LEU C 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.34e+00 ... (remaining 3849 not shown) Planarity restraints: 4112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.006 2.00e-02 2.50e+03 6.04e-02 4.56e+01 pdb=" CG ASN A 331 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.041 2.00e-02 2.50e+03 4.62e-02 2.67e+01 pdb=" CG ASN C 616 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 987 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.063 5.00e-02 4.00e+02 ... (remaining 4109 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 196 2.57 - 3.16: 18909 3.16 - 3.74: 33304 3.74 - 4.32: 47327 4.32 - 4.90: 79055 Nonbonded interactions: 178791 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 1.992 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.047 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.052 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.117 3.040 ... (remaining 178786 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 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 344 or (resid 345 through 346 and (name N or name CA or na \ me C or name O or name CB )) or resid 347 through 350 or (resid 351 through 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 through 36 \ 3 or (resid 364 and (name N or name CA or name C or name O or name CB )) or resi \ d 365 through 368 or (resid 369 and (name N or name CA or name C or name O or na \ me CB )) or resid 370 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 407 or (resid 408 and (name N or n \ ame CA or name C or name O or name CB )) or resid 409 through 441 or (resid 442 \ and (name N or name CA or name C or name O or name CB )) or resid 443 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 496 or (resid 497 through 498 and (name N or name CA or name C or name O or na \ me CB )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 620 or resid 641 t \ hrough 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 333 or (resid 334 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 348 or (resid 34 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 350 or (resi \ d 351 through 352 and (name N or name CA or name C or name O or name CB )) or re \ sid 353 through 363 or (resid 364 and (name N or name CA or name C or name O or \ name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name \ C or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 426 or (resid 42 \ 7 through 428 and (name N or name CA or name C or name O or name CB )) or resid \ 429 through 441 or (resid 442 and (name N or name CA or name C or name O or name \ CB )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name \ N or name CA or name C or name O or name CB )) or resid 494 through 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 508 or (resid 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 344 or (r \ esid 345 through 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 454 or resid 491 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.000 Find NCS groups from input model: 0.700 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.146 23528 Z= 0.289 Angle : 1.005 38.406 32185 Z= 0.506 Chirality : 0.058 0.832 3852 Planarity : 0.006 0.113 4075 Dihedral : 12.958 89.739 7955 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 0.04 % Allowed : 0.21 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.61 (0.15), residues: 2862 helix: 0.26 (0.20), residues: 704 sheet: 0.37 (0.20), residues: 633 loop : -1.06 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 319 TYR 0.046 0.002 TYR C 904 PHE 0.047 0.003 PHE B 275 TRP 0.015 0.002 TRP A 886 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (23446) covalent geometry : angle 0.86644 / 0.47 (31975) SS BOND : bond 0.00608 / 0.37 ( 36) SS BOND : angle 3.56840 / 2.17 ( 72) hydrogen bonds : bond 0.16729 / 10.57 ( 997) hydrogen bonds : angle 8.24499 / 5.74 ( 2805) link_BETA1-4 : bond 0.00976 / 0.61 ( 9) link_BETA1-4 : angle 1.69198 / 1.03 ( 27) link_NAG-ASN : bond 0.02100 / 1.61 ( 37) link_NAG-ASN : angle 8.21386 / 5.31 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 1081 ILE cc_start: 0.8113 (pt) cc_final: 0.7801 (pt) outliers start: 1 outliers final: 2 residues processed: 282 average time/residue: 0.4896 time to fit residues: 165.0193 Evaluate side-chains 199 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN A 580 GLN A 655 HIS A1058 HIS A1135 ASN B 196 ASN B 239 GLN B 271 GLN B 658 ASN B 755 GLN B 804 GLN B 919 ASN B 992 GLN B1005 GLN C 675 GLN C1083 HIS C1135 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.200636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137456 restraints weight = 30761.963| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.23 r_work: 0.3441 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23528 Z= 0.160 Angle : 0.701 13.239 32185 Z= 0.351 Chirality : 0.049 0.290 3852 Planarity : 0.005 0.067 4075 Dihedral : 5.210 80.382 3097 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 8.39 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 2862 helix: 0.79 (0.20), residues: 699 sheet: 0.63 (0.20), residues: 612 loop : -0.94 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.026 0.002 TYR B 170 PHE 0.023 0.002 PHE C 43 TRP 0.017 0.002 TRP A 104 HIS 0.008 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (23446) covalent geometry : angle 0.66439 / 0.34 (31975) SS BOND : bond 0.00885 / 0.67 ( 36) SS BOND : angle 2.64223 / 1.61 ( 72) hydrogen bonds : bond 0.04291 / 2.84 ( 997) hydrogen bonds : angle 6.40016 / 4.47 ( 2805) link_BETA1-4 : bond 0.00620 / 0.39 ( 9) link_BETA1-4 : angle 1.58728 / 1.15 ( 27) link_NAG-ASN : bond 0.00570 / 0.33 ( 37) link_NAG-ASN : angle 3.19695 / 2.42 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8175 (m-80) cc_final: 0.7644 (m-80) REVERT: A 318 PHE cc_start: 0.6215 (t80) cc_final: 0.6005 (t80) REVERT: A 1135 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7657 (m110) REVERT: B 92 PHE cc_start: 0.7061 (m-80) cc_final: 0.6779 (m-80) REVERT: B 697 MET cc_start: 0.9007 (ptm) cc_final: 0.8738 (ptp) REVERT: B 751 ASN cc_start: 0.8738 (m-40) cc_final: 0.8480 (m-40) REVERT: B 919 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8782 (p0) REVERT: C 1100 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7457 (m) REVERT: C 1118 ASP cc_start: 0.8553 (t70) cc_final: 0.8249 (t0) outliers start: 47 outliers final: 20 residues processed: 274 average time/residue: 0.4587 time to fit residues: 151.6974 Evaluate side-chains 220 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 264 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 286 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 787 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1101 HIS B 271 GLN B 658 ASN B 919 ASN B 992 GLN B1005 GLN B1010 GLN B1074 ASN C 360 ASN C 394 ASN C 641 ASN C 926 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.198038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140946 restraints weight = 31378.160| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.78 r_work: 0.3474 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23528 Z= 0.164 Angle : 0.653 12.642 32185 Z= 0.328 Chirality : 0.047 0.268 3852 Planarity : 0.005 0.057 4075 Dihedral : 4.593 30.091 3092 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 11.32 % Favored : 85.83 % 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: -0.10 (0.15), residues: 2862 helix: 1.12 (0.20), residues: 686 sheet: 0.54 (0.19), residues: 623 loop : -0.88 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 646 TYR 0.023 0.001 TYR B 265 PHE 0.020 0.001 PHE A 565 TRP 0.012 0.002 TRP A 104 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (23446) covalent geometry : angle 0.62166 / 0.32 (31975) SS BOND : bond 0.00493 / 0.34 ( 36) SS BOND : angle 2.33982 / 1.49 ( 72) hydrogen bonds : bond 0.04162 / 2.69 ( 997) hydrogen bonds : angle 6.08916 / 4.25 ( 2805) link_BETA1-4 : bond 0.00498 / 0.33 ( 9) link_BETA1-4 : angle 1.42369 / 0.97 ( 27) link_NAG-ASN : bond 0.00689 / 0.39 ( 37) link_NAG-ASN : angle 2.84644 / 2.18 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.6750 (pt) cc_final: 0.6538 (pp) REVERT: A 191 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 269 TYR cc_start: 0.8362 (m-80) cc_final: 0.7863 (m-80) REVERT: A 574 ASP cc_start: 0.7520 (t0) cc_final: 0.7268 (t0) REVERT: A 1132 ILE cc_start: 0.7199 (pt) cc_final: 0.6933 (pp) REVERT: B 196 ASN cc_start: 0.5723 (t0) cc_final: 0.5511 (m-40) REVERT: B 324 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6076 (pm20) REVERT: B 697 MET cc_start: 0.9087 (ptm) cc_final: 0.8844 (ptp) REVERT: B 814 LYS cc_start: 0.7492 (mmtm) cc_final: 0.7210 (mmtm) REVERT: B 904 TYR cc_start: 0.7438 (t80) cc_final: 0.7113 (t80) REVERT: C 354 ASN cc_start: 0.6307 (t0) cc_final: 0.5757 (p0) REVERT: C 754 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8061 (mm) REVERT: C 926 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 988 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 1100 THR cc_start: 0.8156 (p) cc_final: 0.7882 (m) REVERT: C 1118 ASP cc_start: 0.8600 (t70) cc_final: 0.8301 (t0) outliers start: 69 outliers final: 29 residues processed: 276 average time/residue: 0.4239 time to fit residues: 143.1915 Evaluate side-chains 233 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A1005 GLN A1135 ASN B 271 GLN B 544 ASN B 658 ASN B 992 GLN B1010 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 658 ASN C 926 GLN C1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.187233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127582 restraints weight = 30001.712| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.52 r_work: 0.3327 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 23528 Z= 0.300 Angle : 0.778 11.848 32185 Z= 0.394 Chirality : 0.053 0.336 3852 Planarity : 0.006 0.068 4075 Dihedral : 5.158 29.435 3092 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 4.09 % Allowed : 13.26 % Favored : 82.64 % 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: -0.53 (0.15), residues: 2862 helix: 0.75 (0.20), residues: 706 sheet: 0.06 (0.18), residues: 671 loop : -1.09 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1107 TYR 0.043 0.002 TYR A 904 PHE 0.027 0.002 PHE C 565 TRP 0.020 0.002 TRP A 886 HIS 0.006 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.30 (23446) covalent geometry : angle 0.75050 / 0.39 (31975) SS BOND : bond 0.00555 / 0.36 ( 36) SS BOND : angle 2.62597 / 1.60 ( 72) hydrogen bonds : bond 0.04886 / 3.17 ( 997) hydrogen bonds : angle 6.30286 / 4.38 ( 2805) link_BETA1-4 : bond 0.00504 / 0.32 ( 9) link_BETA1-4 : angle 1.44897 / 0.90 ( 27) link_NAG-ASN : bond 0.00537 / 0.33 ( 37) link_NAG-ASN : angle 2.85381 / 2.20 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 0.938 Fit side-chains REVERT: A 105 ILE cc_start: 0.8203 (pt) cc_final: 0.7952 (pp) REVERT: A 129 LYS cc_start: 0.6917 (mttt) cc_final: 0.6156 (mmtt) REVERT: A 237 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7057 (mtp85) REVERT: A 269 TYR cc_start: 0.8604 (m-80) cc_final: 0.8303 (m-10) REVERT: A 578 ASP cc_start: 0.7725 (t70) cc_final: 0.7497 (t0) REVERT: A 740 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8843 (tmm) REVERT: A 1132 ILE cc_start: 0.7806 (pt) cc_final: 0.7559 (tt) REVERT: B 32 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 194 PHE cc_start: 0.7857 (m-80) cc_final: 0.7435 (m-80) REVERT: B 814 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7420 (mmtm) REVERT: B 904 TYR cc_start: 0.7256 (t80) cc_final: 0.6710 (t80) REVERT: B 949 GLN cc_start: 0.8637 (tp40) cc_final: 0.8414 (tp40) REVERT: C 193 VAL cc_start: 0.6347 (t) cc_final: 0.6077 (t) REVERT: C 388 ASN cc_start: 0.7805 (m-40) cc_final: 0.7479 (t0) REVERT: C 521 PRO cc_start: 0.5456 (Cg_exo) cc_final: 0.5197 (Cg_endo) REVERT: C 645 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 738 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7822 (t) REVERT: C 787 GLN cc_start: 0.8973 (mt0) cc_final: 0.8729 (mt0) REVERT: C 988 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: C 1050 MET cc_start: 0.9264 (ptm) cc_final: 0.8975 (ptm) REVERT: C 1100 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8700 (m) REVERT: C 1118 ASP cc_start: 0.8627 (t70) cc_final: 0.8420 (t0) outliers start: 99 outliers final: 34 residues processed: 307 average time/residue: 0.4593 time to fit residues: 170.0208 Evaluate side-chains 211 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 42 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 532 ASN B 658 ASN B 919 ASN B 935 GLN B 992 GLN C 641 ASN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.188633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133638 restraints weight = 30105.602| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.34 r_work: 0.3377 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23528 Z= 0.150 Angle : 0.648 12.546 32185 Z= 0.321 Chirality : 0.047 0.396 3852 Planarity : 0.005 0.046 4075 Dihedral : 4.673 27.658 3092 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.18 % Allowed : 15.58 % Favored : 81.24 % 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: -0.25 (0.15), residues: 2862 helix: 1.09 (0.20), residues: 693 sheet: 0.23 (0.19), residues: 645 loop : -0.93 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.020 0.001 TYR A 904 PHE 0.017 0.001 PHE A 565 TRP 0.011 0.001 TRP C 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (23446) covalent geometry : angle 0.61852 / 0.31 (31975) SS BOND : bond 0.00560 / 0.38 ( 36) SS BOND : angle 2.30221 / 1.38 ( 72) hydrogen bonds : bond 0.03777 / 2.47 ( 997) hydrogen bonds : angle 6.00555 / 4.18 ( 2805) link_BETA1-4 : bond 0.00272 / 0.17 ( 9) link_BETA1-4 : angle 1.14426 / 0.74 ( 27) link_NAG-ASN : bond 0.00415 / 0.23 ( 37) link_NAG-ASN : angle 2.77646 / 2.20 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8638 (m-80) cc_final: 0.8206 (m-10) REVERT: A 585 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7926 (pp) REVERT: A 1132 ILE cc_start: 0.7882 (pt) cc_final: 0.7584 (tt) REVERT: A 1142 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6563 (mp-120) REVERT: B 194 PHE cc_start: 0.7740 (m-80) cc_final: 0.7371 (m-80) REVERT: B 814 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7466 (mmtm) REVERT: B 904 TYR cc_start: 0.7271 (t80) cc_final: 0.6896 (t80) REVERT: B 994 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: C 193 VAL cc_start: 0.6539 (t) cc_final: 0.6288 (t) REVERT: C 388 ASN cc_start: 0.7744 (m-40) cc_final: 0.7479 (t0) REVERT: C 389 ASP cc_start: 0.8403 (p0) cc_final: 0.8024 (p0) REVERT: C 521 PRO cc_start: 0.5437 (Cg_exo) cc_final: 0.5157 (Cg_endo) REVERT: C 564 GLN cc_start: 0.6776 (tm-30) cc_final: 0.6244 (tm-30) REVERT: C 787 GLN cc_start: 0.8948 (mt0) cc_final: 0.8640 (mt0) REVERT: C 988 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: C 1050 MET cc_start: 0.9196 (ptm) cc_final: 0.8924 (ptm) REVERT: C 1118 ASP cc_start: 0.8486 (t70) cc_final: 0.8281 (t0) outliers start: 77 outliers final: 28 residues processed: 243 average time/residue: 0.4449 time to fit residues: 131.1308 Evaluate side-chains 195 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 148 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 992 GLN C 658 ASN C 703 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131698 restraints weight = 30261.862| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.54 r_work: 0.3334 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23528 Z= 0.155 Angle : 0.626 12.292 32185 Z= 0.314 Chirality : 0.047 0.261 3852 Planarity : 0.005 0.045 4075 Dihedral : 4.478 25.266 3092 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.35 % Allowed : 16.24 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 2862 helix: 1.18 (0.21), residues: 700 sheet: 0.26 (0.19), residues: 646 loop : -0.91 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 237 TYR 0.022 0.001 TYR B1067 PHE 0.037 0.001 PHE C 565 TRP 0.012 0.001 TRP C 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (23446) covalent geometry : angle 0.60413 / 0.31 (31975) SS BOND : bond 0.00584 / 0.38 ( 36) SS BOND : angle 2.09607 / 1.24 ( 72) hydrogen bonds : bond 0.03643 / 2.39 ( 997) hydrogen bonds : angle 5.84546 / 4.06 ( 2805) link_BETA1-4 : bond 0.00284 / 0.18 ( 9) link_BETA1-4 : angle 0.97571 / 0.58 ( 27) link_NAG-ASN : bond 0.00548 / 0.34 ( 37) link_NAG-ASN : angle 2.35862 / 1.90 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 192 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 269 TYR cc_start: 0.8687 (m-80) cc_final: 0.8362 (m-10) REVERT: A 585 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7840 (pp) REVERT: A 646 ARG cc_start: 0.8607 (tpt170) cc_final: 0.8401 (tpt-90) REVERT: A 1132 ILE cc_start: 0.7924 (pt) cc_final: 0.7648 (tt) REVERT: B 53 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: B 88 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 194 PHE cc_start: 0.7758 (m-80) cc_final: 0.7336 (m-80) REVERT: B 304 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8436 (mptt) REVERT: B 314 GLN cc_start: 0.8574 (tp40) cc_final: 0.8364 (tp40) REVERT: B 814 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7445 (mmtm) REVERT: B 904 TYR cc_start: 0.7435 (t80) cc_final: 0.6949 (t80) REVERT: C 388 ASN cc_start: 0.7637 (m-40) cc_final: 0.7436 (t0) REVERT: C 521 PRO cc_start: 0.5859 (Cg_exo) cc_final: 0.5636 (Cg_endo) REVERT: C 564 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6621 (tm-30) REVERT: C 646 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7658 (tpt90) REVERT: C 787 GLN cc_start: 0.9018 (mt0) cc_final: 0.8734 (mt0) REVERT: C 988 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 1050 MET cc_start: 0.9256 (ptm) cc_final: 0.8951 (ptm) REVERT: C 1141 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7080 (tp) outliers start: 81 outliers final: 38 residues processed: 244 average time/residue: 0.4538 time to fit residues: 134.2558 Evaluate side-chains 217 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 272 optimal weight: 0.2980 chunk 209 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 388 ASN B 762 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.189094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132353 restraints weight = 30392.289| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.56 r_work: 0.3373 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23528 Z= 0.123 Angle : 0.596 11.932 32185 Z= 0.299 Chirality : 0.046 0.256 3852 Planarity : 0.004 0.046 4075 Dihedral : 4.265 23.891 3092 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.85 % Allowed : 17.15 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2862 helix: 1.25 (0.20), residues: 712 sheet: 0.40 (0.19), residues: 631 loop : -0.84 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.024 0.001 TYR A 170 PHE 0.030 0.001 PHE C 565 TRP 0.012 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (23446) covalent geometry : angle 0.57347 / 0.29 (31975) SS BOND : bond 0.00484 / 0.33 ( 36) SS BOND : angle 2.18617 / 1.27 ( 72) hydrogen bonds : bond 0.03412 / 2.23 ( 997) hydrogen bonds : angle 5.70707 / 3.95 ( 2805) link_BETA1-4 : bond 0.00304 / 0.20 ( 9) link_BETA1-4 : angle 0.95397 / 0.58 ( 27) link_NAG-ASN : bond 0.00409 / 0.23 ( 37) link_NAG-ASN : angle 2.23408 / 1.81 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8547 (mt) REVERT: A 269 TYR cc_start: 0.8712 (m-80) cc_final: 0.8380 (m-10) REVERT: A 585 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7495 (pp) REVERT: A 646 ARG cc_start: 0.8511 (tpt170) cc_final: 0.8281 (tpt-90) REVERT: B 53 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6745 (m-30) REVERT: B 88 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7594 (t0) REVERT: B 194 PHE cc_start: 0.7675 (m-80) cc_final: 0.7259 (m-80) REVERT: B 304 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8394 (mptt) REVERT: B 314 GLN cc_start: 0.8537 (tp40) cc_final: 0.8312 (tp40) REVERT: B 814 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7436 (mmtm) REVERT: B 904 TYR cc_start: 0.7304 (t80) cc_final: 0.6930 (t80) REVERT: B 994 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: C 388 ASN cc_start: 0.7642 (m-40) cc_final: 0.7385 (t0) REVERT: C 521 PRO cc_start: 0.6316 (Cg_exo) cc_final: 0.6098 (Cg_endo) REVERT: C 534 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (m) REVERT: C 564 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6601 (tm-30) REVERT: C 565 PHE cc_start: 0.8516 (p90) cc_final: 0.8185 (p90) REVERT: C 599 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8623 (p) REVERT: C 646 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7611 (tpt90) REVERT: C 787 GLN cc_start: 0.8977 (mt0) cc_final: 0.8675 (mt0) REVERT: C 988 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 1050 MET cc_start: 0.9212 (ptm) cc_final: 0.8940 (ptm) REVERT: C 1141 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7148 (tp) outliers start: 69 outliers final: 37 residues processed: 230 average time/residue: 0.4028 time to fit residues: 113.5903 Evaluate side-chains 216 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 69 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 140 optimal weight: 8.9990 chunk 4 optimal weight: 0.0270 chunk 103 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 216 optimal weight: 0.2980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 540 ASN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131304 restraints weight = 29813.786| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.53 r_work: 0.3369 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23528 Z= 0.125 Angle : 0.585 11.784 32185 Z= 0.294 Chirality : 0.045 0.253 3852 Planarity : 0.004 0.047 4075 Dihedral : 4.173 23.789 3092 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.60 % Allowed : 17.81 % Favored : 79.59 % 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: -0.03 (0.15), residues: 2862 helix: 1.31 (0.20), residues: 711 sheet: 0.36 (0.19), residues: 646 loop : -0.83 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.024 0.001 TYR A 170 PHE 0.029 0.001 PHE C 565 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (23446) covalent geometry : angle 0.56508 / 0.29 (31975) SS BOND : bond 0.00471 / 0.32 ( 36) SS BOND : angle 1.98061 / 1.15 ( 72) hydrogen bonds : bond 0.03327 / 2.18 ( 997) hydrogen bonds : angle 5.60241 / 3.87 ( 2805) link_BETA1-4 : bond 0.00290 / 0.19 ( 9) link_BETA1-4 : angle 0.94578 / 0.57 ( 27) link_NAG-ASN : bond 0.00403 / 0.23 ( 37) link_NAG-ASN : angle 2.13052 / 1.72 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.628 Fit side-chains REVERT: A 54 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8541 (mt) REVERT: A 129 LYS cc_start: 0.6879 (mttt) cc_final: 0.6106 (ttmm) REVERT: A 170 TYR cc_start: 0.7288 (t80) cc_final: 0.7020 (t80) REVERT: A 269 TYR cc_start: 0.8711 (m-80) cc_final: 0.8371 (m-10) REVERT: A 553 THR cc_start: 0.7730 (p) cc_final: 0.6882 (m) REVERT: A 646 ARG cc_start: 0.8513 (tpt170) cc_final: 0.8279 (tpt-90) REVERT: B 53 ASP cc_start: 0.7047 (m-30) cc_final: 0.6819 (m-30) REVERT: B 88 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7647 (t0) REVERT: B 192 PHE cc_start: 0.8193 (m-10) cc_final: 0.7876 (m-10) REVERT: B 194 PHE cc_start: 0.7753 (m-80) cc_final: 0.7363 (m-80) REVERT: B 238 PHE cc_start: 0.6989 (p90) cc_final: 0.6651 (p90) REVERT: B 304 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8392 (mptt) REVERT: B 314 GLN cc_start: 0.8561 (tp40) cc_final: 0.8308 (tp40) REVERT: B 904 TYR cc_start: 0.7313 (t80) cc_final: 0.6939 (t80) REVERT: C 388 ASN cc_start: 0.7669 (m-40) cc_final: 0.7361 (t0) REVERT: C 521 PRO cc_start: 0.6388 (Cg_exo) cc_final: 0.6186 (Cg_endo) REVERT: C 534 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8121 (m) REVERT: C 564 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6677 (tm-30) REVERT: C 565 PHE cc_start: 0.8490 (p90) cc_final: 0.8206 (p90) REVERT: C 646 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7587 (tpt90) REVERT: C 787 GLN cc_start: 0.8975 (mt0) cc_final: 0.8664 (mt0) REVERT: C 988 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 1050 MET cc_start: 0.9212 (ptm) cc_final: 0.8924 (ptm) REVERT: C 1141 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7329 (tp) REVERT: C 1144 GLU cc_start: 0.7165 (mp0) cc_final: 0.6816 (mp0) outliers start: 63 outliers final: 43 residues processed: 224 average time/residue: 0.3981 time to fit residues: 108.8811 Evaluate side-chains 218 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 31 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 388 ASN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126601 restraints weight = 29872.980| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.92 r_work: 0.3291 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23528 Z= 0.146 Angle : 0.597 11.779 32185 Z= 0.299 Chirality : 0.046 0.252 3852 Planarity : 0.004 0.047 4075 Dihedral : 4.214 23.384 3092 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.56 % Allowed : 18.18 % Favored : 79.26 % 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: -0.04 (0.15), residues: 2862 helix: 1.30 (0.20), residues: 706 sheet: 0.41 (0.19), residues: 638 loop : -0.87 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.023 0.001 TYR A 170 PHE 0.028 0.001 PHE C 565 TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (23446) covalent geometry : angle 0.57755 / 0.29 (31975) SS BOND : bond 0.00489 / 0.33 ( 36) SS BOND : angle 1.96321 / 1.14 ( 72) hydrogen bonds : bond 0.03453 / 2.25 ( 997) hydrogen bonds : angle 5.62232 / 3.89 ( 2805) link_BETA1-4 : bond 0.00278 / 0.19 ( 9) link_BETA1-4 : angle 0.96990 / 0.58 ( 27) link_NAG-ASN : bond 0.00390 / 0.23 ( 37) link_NAG-ASN : angle 2.12685 / 1.72 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 129 LYS cc_start: 0.6946 (mttt) cc_final: 0.6397 (mttm) REVERT: A 170 TYR cc_start: 0.7539 (t80) cc_final: 0.7264 (t80) REVERT: A 269 TYR cc_start: 0.8634 (m-80) cc_final: 0.8377 (m-10) REVERT: A 677 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: A 1142 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: B 88 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7572 (t0) REVERT: B 192 PHE cc_start: 0.8330 (m-10) cc_final: 0.8054 (m-10) REVERT: B 194 PHE cc_start: 0.7807 (m-80) cc_final: 0.7390 (m-80) REVERT: B 304 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8348 (mptt) REVERT: B 314 GLN cc_start: 0.8504 (tp40) cc_final: 0.8259 (tp40) REVERT: B 869 MET cc_start: 0.8933 (mtm) cc_final: 0.8694 (mtm) REVERT: B 904 TYR cc_start: 0.7047 (t80) cc_final: 0.6762 (t80) REVERT: B 994 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 388 ASN cc_start: 0.7659 (m-40) cc_final: 0.7423 (t0) REVERT: C 534 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8141 (m) REVERT: C 564 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 565 PHE cc_start: 0.8491 (p90) cc_final: 0.8191 (p90) REVERT: C 646 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7636 (tpt90) REVERT: C 787 GLN cc_start: 0.8819 (mt0) cc_final: 0.8513 (mt0) REVERT: C 1050 MET cc_start: 0.9099 (ptm) cc_final: 0.8814 (ptm) REVERT: C 1141 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7522 (tp) REVERT: C 1144 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6563 (mp0) outliers start: 62 outliers final: 42 residues processed: 214 average time/residue: 0.4077 time to fit residues: 106.6473 Evaluate side-chains 213 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 252 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 chunk 141 optimal weight: 0.1980 chunk 212 optimal weight: 8.9990 chunk 225 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 677 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120119 restraints weight = 30038.273| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.33 r_work: 0.3257 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23528 Z= 0.115 Angle : 0.586 11.679 32185 Z= 0.295 Chirality : 0.045 0.252 3852 Planarity : 0.004 0.053 4075 Dihedral : 4.110 23.868 3092 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 19.13 % Favored : 78.88 % 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: 0.02 (0.15), residues: 2862 helix: 1.41 (0.20), residues: 699 sheet: 0.47 (0.19), residues: 637 loop : -0.85 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.024 0.001 TYR A 170 PHE 0.030 0.001 PHE B 565 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (23446) covalent geometry : angle 0.56779 / 0.29 (31975) SS BOND : bond 0.00487 / 0.34 ( 36) SS BOND : angle 1.81295 / 1.06 ( 72) hydrogen bonds : bond 0.03234 / 2.11 ( 997) hydrogen bonds : angle 5.51237 / 3.80 ( 2805) link_BETA1-4 : bond 0.00295 / 0.19 ( 9) link_BETA1-4 : angle 0.93201 / 0.56 ( 27) link_NAG-ASN : bond 0.00375 / 0.21 ( 37) link_NAG-ASN : angle 2.04828 / 1.67 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.795 Fit side-chains REVERT: A 54 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 129 LYS cc_start: 0.6749 (mttt) cc_final: 0.6157 (mttm) REVERT: A 170 TYR cc_start: 0.7259 (t80) cc_final: 0.6951 (t80) REVERT: A 269 TYR cc_start: 0.8680 (m-80) cc_final: 0.8275 (m-10) REVERT: A 677 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: A 811 LYS cc_start: 0.7692 (mmmm) cc_final: 0.6094 (mttp) REVERT: B 88 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7497 (t0) REVERT: B 192 PHE cc_start: 0.8302 (m-10) cc_final: 0.7994 (m-10) REVERT: B 194 PHE cc_start: 0.7805 (m-80) cc_final: 0.7356 (m-80) REVERT: B 238 PHE cc_start: 0.7124 (p90) cc_final: 0.6790 (p90) REVERT: B 304 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: B 314 GLN cc_start: 0.8666 (tp40) cc_final: 0.8393 (tp40) REVERT: B 869 MET cc_start: 0.9117 (mtm) cc_final: 0.8914 (mtm) REVERT: B 904 TYR cc_start: 0.7207 (t80) cc_final: 0.6780 (t80) REVERT: B 994 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: C 388 ASN cc_start: 0.7486 (m-40) cc_final: 0.7172 (t0) REVERT: C 453 TYR cc_start: 0.5823 (p90) cc_final: 0.5417 (p90) REVERT: C 534 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8175 (m) REVERT: C 564 GLN cc_start: 0.7413 (tm-30) cc_final: 0.6676 (tm-30) REVERT: C 565 PHE cc_start: 0.8469 (p90) cc_final: 0.8147 (p90) REVERT: C 646 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7488 (tpt90) REVERT: C 787 GLN cc_start: 0.8927 (mt0) cc_final: 0.8608 (mt0) REVERT: C 794 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8682 (pp) REVERT: C 1050 MET cc_start: 0.9291 (ptm) cc_final: 0.8993 (ptm) REVERT: C 1141 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7219 (tp) REVERT: C 1144 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6627 (mp0) outliers start: 48 outliers final: 35 residues processed: 211 average time/residue: 0.4076 time to fit residues: 105.1135 Evaluate side-chains 210 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.0060 chunk 168 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 259 optimal weight: 0.0050 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 677 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 532 ASN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120541 restraints weight = 30128.294| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.24 r_work: 0.3261 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23528 Z= 0.117 Angle : 0.581 11.566 32185 Z= 0.291 Chirality : 0.045 0.253 3852 Planarity : 0.004 0.046 4075 Dihedral : 4.071 23.693 3092 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.02 % Allowed : 19.26 % Favored : 78.72 % 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: 0.05 (0.15), residues: 2862 helix: 1.44 (0.21), residues: 699 sheet: 0.48 (0.19), residues: 632 loop : -0.84 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.024 0.001 TYR A 170 PHE 0.027 0.001 PHE C 565 TRP 0.012 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (23446) covalent geometry : angle 0.56360 / 0.29 (31975) SS BOND : bond 0.00484 / 0.33 ( 36) SS BOND : angle 1.78164 / 1.04 ( 72) hydrogen bonds : bond 0.03214 / 2.10 ( 997) hydrogen bonds : angle 5.46385 / 3.76 ( 2805) link_BETA1-4 : bond 0.00326 / 0.22 ( 9) link_BETA1-4 : angle 0.94800 / 0.57 ( 27) link_NAG-ASN : bond 0.00364 / 0.21 ( 37) link_NAG-ASN : angle 2.01237 / 1.64 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8339.04 seconds wall clock time: 142 minutes 50.62 seconds (8570.62 seconds total)