Starting phenix.real_space_refine on Sat Mar 7 01:30:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpf_32685/03_2026/7wpf_32685_neut.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 151 5.16 5 C 23009 2.51 5 N 5977 2.21 5 O 7065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36202 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7676 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 5, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7672 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 52, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 191 Chain: "C" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7700 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 9, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 194 Chain: "R" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1659 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1648 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1656 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 8.27, per 1000 atoms: 0.23 Number of scatterers: 36202 At special positions: 0 Unit cell: (196.936, 199.408, 228.248, 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 151 16.00 O 7065 8.00 N 5977 7.00 C 23009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 150 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 105 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 150 " - pdb=" SG CYS U 206 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.04 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 194 " distance=2.03 Simple disulfide: pdb=" SG CYS W 31 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 150 " - pdb=" SG CYS X 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 31 " - pdb=" SG CYS Z 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 165 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8826 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 79 sheets defined 19.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 345 removed outlier: 4.737A pdb=" N THR A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.193A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.763A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.791A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.564A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.675A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.687A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.040A 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: 3.506A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.222A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.532A pdb=" N VAL B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.856A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.818A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.846A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.473A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.139A 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.355A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.635A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.633A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.528A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.479A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.771A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.540A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.957A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.941A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.565A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.631A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 137 through 141 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'S' and resid 121 through 127 removed outlier: 3.572A pdb=" N SER S 127 " --> pdb=" O GLU S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 153 Processing helix chain 'S' and resid 183 through 189 Processing helix chain 'T' and resid 96 through 100 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 137 through 141 Processing helix chain 'U' and resid 166 through 168 No H-bonds generated for 'chain 'U' and resid 166 through 168' Processing helix chain 'V' and resid 79 through 83 removed outlier: 4.509A pdb=" N ILE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 126 Processing helix chain 'V' and resid 150 through 153 Processing helix chain 'V' and resid 183 through 189 Processing helix chain 'W' and resid 71 through 75 removed outlier: 3.905A pdb=" N GLN W 74 " --> pdb=" O ASP W 71 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY W 75 " --> pdb=" O SER W 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 71 through 75' Processing helix chain 'W' and resid 83 through 85 No H-bonds generated for 'chain 'W' and resid 83 through 85' Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 167 through 171 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 121 through 127 removed outlier: 3.793A pdb=" N SER Y 127 " --> pdb=" O GLU Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 153 Processing helix chain 'Y' and resid 183 through 189 removed outlier: 3.766A pdb=" N HIS Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 100 removed outlier: 3.673A pdb=" N THR Z 100 " --> pdb=" O PRO Z 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.613A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.617A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.089A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.825A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.682A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.328A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.169A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.812A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.812A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.442A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.539A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.571A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.047A 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: 4.040A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.703A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.628A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.090A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.764A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.414A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.079A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.074A 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: 4.908A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.580A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.953A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.752A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.287A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.662A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.761A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.948A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.047A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.816A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.446A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.539A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'R' and resid 10 through 12 removed outlier: 4.027A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR R 57 " --> pdb=" O ILE R 52 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 130 through 133 removed outlier: 6.054A pdb=" N TYR R 186 " --> pdb=" O ASP R 154 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER R 187 " --> pdb=" O ALA R 178 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA R 178 " --> pdb=" O SER R 187 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER R 189 " --> pdb=" O PHE R 176 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 161 through 163 Processing sheet with id=AF4, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.864A pdb=" N THR S 22 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.571A pdb=" N GLN S 38 " --> pdb=" O THR S 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR S 87 " --> pdb=" O TYR S 36 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU S 47 " --> pdb=" O TRP S 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 10 through 13 Processing sheet with id=AF7, first strand: chain 'S' and resid 114 through 118 Processing sheet with id=AF8, first strand: chain 'S' and resid 147 through 148 Processing sheet with id=AF9, first strand: chain 'T' and resid 14 through 17 Processing sheet with id=AG1, first strand: chain 'T' and resid 19 through 21 removed outlier: 5.307A pdb=" N TRP T 120 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE T 107 " --> pdb=" O TRP T 120 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN T 122 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA T 42 " --> pdb=" O ASP T 108 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA T 58 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG T 47 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE T 56 " --> pdb=" O ARG T 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 3 through 6 removed outlier: 3.535A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP U 73 " --> pdb=" O THR U 78 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.024A pdb=" N THR U 120 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS U 12 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 130 through 133 removed outlier: 3.640A pdb=" N PHE U 132 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 130 through 133 removed outlier: 3.640A pdb=" N PHE U 132 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 160 through 164 Processing sheet with id=AG7, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.671A pdb=" N THR V 22 " --> pdb=" O SER V 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS V 23 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE V 71 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 10 through 13 removed outlier: 5.143A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP V 50 " --> pdb=" O ASN V 53 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.702A pdb=" N THR V 97 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 116 through 118 removed outlier: 5.194A pdb=" N TYR V 173 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 145 through 148 Processing sheet with id=AH3, first strand: chain 'W' and resid 14 through 17 removed outlier: 3.694A pdb=" N GLN W 14 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 19 through 21 removed outlier: 3.543A pdb=" N THR W 127 " --> pdb=" O GLY W 19 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 54 through 60 removed outlier: 7.028A pdb=" N TRP W 45 " --> pdb=" O VAL W 57 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL W 59 " --> pdb=" O MET W 43 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET W 43 " --> pdb=" O VAL W 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.567A pdb=" N THR X 78 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.594A pdb=" N GLU X 10 " --> pdb=" O MET X 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 120 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS X 12 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 130 through 133 removed outlier: 3.663A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU X 151 " --> pdb=" O PHE X 132 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER X 187 " --> pdb=" O ALA X 178 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA X 178 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AI1, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.732A pdb=" N THR Y 22 " --> pdb=" O SER Y 7 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.603A pdb=" N ILE Y 48 " --> pdb=" O TRP Y 35 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.617A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 114 through 118 removed outlier: 3.697A pdb=" N SER Y 176 " --> pdb=" O SER Y 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER Y 162 " --> pdb=" O SER Y 176 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 146 through 148 Processing sheet with id=AI6, first strand: chain 'Z' and resid 14 through 17 removed outlier: 3.887A pdb=" N THR Z 78 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 19 through 21 removed outlier: 6.098A pdb=" N GLY Z 19 " --> pdb=" O THR Z 127 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS Z 105 " --> pdb=" O GLY Z 121 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY Z 123 " --> pdb=" O TYR Z 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR Z 103 " --> pdb=" O GLY Z 123 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN Z 125 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA Z 101 " --> pdb=" O GLN Z 125 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA Z 42 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA Z 58 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG Z 47 " --> pdb=" O PHE Z 56 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE Z 56 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) 1471 hydrogen bonds defined for protein. 3921 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: 10.41 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11599 1.34 - 1.47: 9395 1.47 - 1.59: 15840 1.59 - 1.71: 0 1.71 - 1.84: 191 Bond restraints: 37025 Sorted by residual: bond pdb=" N LYS C 195 " pdb=" CA LYS C 195 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS B 195 " pdb=" CA LYS B 195 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.27e-02 6.20e+03 5.59e+00 bond pdb=" N GLN T 10 " pdb=" CA GLN T 10 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.76e+00 bond pdb=" N GLN Z 10 " pdb=" CA GLN Z 10 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.70e+00 bond pdb=" C PHE A 194 " pdb=" N LYS A 195 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.37e-02 5.33e+03 4.42e+00 ... (remaining 37020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 50336 3.70 - 7.39: 122 7.39 - 11.09: 22 11.09 - 14.78: 4 14.78 - 18.48: 4 Bond angle restraints: 50488 Sorted by residual: angle pdb=" C SER U 103 " pdb=" N SER U 104 " pdb=" CA SER U 104 " ideal model delta sigma weight residual 123.91 142.39 -18.48 1.66e+00 3.63e-01 1.24e+02 angle pdb=" N ALA Z 67 " pdb=" CA ALA Z 67 " pdb=" C ALA Z 67 " ideal model delta sigma weight residual 108.86 117.20 -8.34 1.41e+00 5.03e-01 3.50e+01 angle pdb=" OG1 THR R 126 " pdb=" CB THR R 126 " pdb=" CG2 THR R 126 " ideal model delta sigma weight residual 109.30 120.57 -11.27 2.00e+00 2.50e-01 3.17e+01 angle pdb=" OG1 THR X 28 " pdb=" CB THR X 28 " pdb=" CG2 THR X 28 " ideal model delta sigma weight residual 109.30 120.49 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" OG1 THR X 126 " pdb=" CB THR X 126 " pdb=" CG2 THR X 126 " ideal model delta sigma weight residual 109.30 120.48 -11.18 2.00e+00 2.50e-01 3.12e+01 ... (remaining 50483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 21035 17.85 - 35.71: 1136 35.71 - 53.56: 170 53.56 - 71.41: 44 71.41 - 89.27: 41 Dihedral angle restraints: 22426 sinusoidal: 8684 harmonic: 13742 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -163.44 77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.48 -75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 166.37 -73.37 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 22423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 5845 0.356 - 0.712: 34 0.712 - 1.068: 0 1.068 - 1.423: 4 1.423 - 1.779: 8 Chirality restraints: 5891 Sorted by residual: chirality pdb=" CB ILE Y 117 " pdb=" CA ILE Y 117 " pdb=" CG1 ILE Y 117 " pdb=" CG2 ILE Y 117 " both_signs ideal model delta sigma weight residual False 2.64 0.87 1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" CG LEU T 29 " pdb=" CB LEU T 29 " pdb=" CD1 LEU T 29 " pdb=" CD2 LEU T 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CB ILE R 112 " pdb=" CA ILE R 112 " pdb=" CG1 ILE R 112 " pdb=" CG2 ILE R 112 " both_signs ideal model delta sigma weight residual False 2.64 1.01 1.64 2.00e-01 2.50e+01 6.69e+01 ... (remaining 5888 not shown) Planarity restraints: 6515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 230 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 40 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO R 41 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1068 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A1069 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A1069 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1069 " 0.035 5.00e-02 4.00e+02 ... (remaining 6512 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 335 2.60 - 3.17: 32217 3.17 - 3.75: 53919 3.75 - 4.32: 75744 4.32 - 4.90: 127414 Nonbonded interactions: 289629 Sorted by model distance: nonbonded pdb=" O TYR S 49 " pdb=" OH TYR S 91 " model vdw 2.025 3.040 nonbonded pdb=" O HIS U 174 " pdb=" OG SER U 190 " model vdw 2.048 3.040 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.066 3.040 nonbonded pdb=" OH TYR A 351 " pdb=" OG SER X 103 " model vdw 2.087 3.040 nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.130 3.040 ... (remaining 289624 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 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 96 or (resid 97 through 98 and \ (name N or name CA or name C or name O or name CB )) or resid 99 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 6 through 133 or (resid 134 and (name N or name CA or name C or name O or name C \ B )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 160 or (resid 161 through 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 209 or (re \ sid 210 and (name N or name CA or name C or name O or name CB )) or resid 215 th \ rough 253 or (resid 254 and (name N or name CA or name C or name O or name CB )) \ or resid 255 through 318 or (resid 319 and (name N or name CA or name C or name \ O or name CB )) or resid 320 through 355 or (resid 356 through 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 throug \ h 404 or (resid 405 through 406 and (name N or name CA or name C or name O or na \ me CB )) or resid 407 through 453 or (resid 454 and (name N or name CA or name C \ or name O or name CB )) or resid 455 through 458 or (resid 459 and (name N or n \ ame CA or name C or name O or name CB )) or resid 460 through 553 or (resid 554 \ and (name N or name CA or name C or name O or name CB )) or resid 555 or (resid \ 556 through 558 and (name N or name CA or name C or name O or name CB )) or resi \ d 559 through 563 or (resid 564 and (name N or name CA or name C or name O or na \ me CB )) or resid 565 through 570 or (resid 571 through 572 and (name N or name \ CA or name C or name O or name CB )) or resid 573 through 620 or resid 641 throu \ gh 676 or (resid 690 and (name N or name CA or name C or name O or name CB )) or \ resid 691 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 827 or (resid 828 and (name N or name CA or n \ ame C or name O or name CB )) or resid 855 through 984 or (resid 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 987 or (resid \ 988 through 989 and (name N or name CA or name C or name O or name CB )) or res \ id 990 through 993 or (resid 994 and (name N or name CA or name C or name O or n \ ame CB )) or resid 995 through 1037 or (resid 1038 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name \ N or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (re \ sid 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 \ through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 96 or (resid 97 through 98 and (name N or name CA or \ name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 133 or (resid \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 160 or (resid 161 through 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 209 or (resid 210 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 253 or (resid 254 \ and (name N or name CA or name C or name O or name CB )) or resid 255 through 3 \ 18 or (resid 319 and (name N or name CA or name C or name O or name CB )) or res \ id 320 through 331 or (resid 332 and (name N or name CA or name C or name O or n \ ame CB )) or resid 333 through 355 or (resid 356 through 357 and (name N or name \ CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and \ (name N or name CA or name C or name O or name CB )) or resid 389 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 453 or (resid 454 and (name N or name CA or name C or nam \ e O or name CB )) or resid 455 through 458 or (resid 459 and (name N or name CA \ or name C or name O or name CB )) or resid 460 through 553 or (resid 554 and (na \ me N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thr \ ough 558 and (name N or name CA or name C or name O or name CB )) or resid 559 t \ hrough 563 or (resid 564 and (name N or name CA or name C or name O or name CB ) \ ) or resid 565 through 570 or (resid 571 through 572 and (name N or name CA or n \ ame C or name O or name CB )) or resid 573 through 620 or resid 641 through 676 \ or (resid 690 and (name N or name CA or name C or name O or name CB )) or resid \ 691 through 747 or (resid 748 and (name N or name CA or name C or name O or name \ CB )) or resid 749 through 827 or (resid 828 and (name N or name CA or name C o \ r name O or name CB )) or resid 855 through 984 or (resid 985 and (name N or nam \ e CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 th \ rough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1037 or (resid 1038 and (name N or name CA or name C or name O or name C \ B )) or resid 1039 through 1050 or (resid 1051 and (name N or name CA or name C \ or name O or name CB )) or resid 1052 through 1110 or (resid 1111 and (name N or \ name CA or name C or name O or name CB )) or resid 1112 through 1143 or (resid \ 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or re \ sid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 107 or (resid 108 thr \ ough 113 and (name N or name CA or name C or name O or name CB )) or resid 114 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 223 or (resid \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throu \ gh 248 or (resid 249 through 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 368 or (resid 369 \ and (name N or name CA or name C or name O or name CB )) or resid 370 through 4 \ 02 or (resid 403 and (name N or name CA or name C or name O or name CB )) or (re \ sid 404 through 406 and (name N or name CA or name C or name O or name CB )) or \ resid 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 423 or (resid 424 and (name N or name CA or name C or name \ O or name CB )) or resid 425 through 427 or (resid 428 and (name N or name CA o \ r name C or name O or name CB )) or resid 429 through 438 or (resid 439 and (nam \ e N or name CA or name C or name O or name CB )) or resid 440 through 441 or (re \ sid 442 and (name N or name CA or name C or name O or name CB )) or resid 443 or \ (resid 444 through 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 508 or (resid 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 through 556 or (resid 557 through \ 558 and (name N or name CA or name C or name O or name CB )) or resid 559 throug \ h 568 or (resid 569 through 572 and (name N or name CA or name C or name O or na \ me CB )) or resid 573 through 662 or (resid 663 and (name N or name CA or name C \ or name O or name CB )) or resid 664 through 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 739 or (resid 740 \ and (name N or name CA or name C or name O or name CB )) or resid 741 through 79 \ 4 or (resid 795 and (name N or name CA or name C or name O or name CB )) or resi \ d 796 through 807 or (resid 808 and (name N or name CA or name C or name O or na \ me CB )) or resid 809 through 818 or (resid 819 and (name N or name CA or name C \ or name O or name CB )) or resid 820 through 824 or (resid 825 and (name N or n \ ame CA or name C or name O or name CB )) or resid 826 through 917 or (resid 918 \ and (name N or name CA or name C or name O or name CB )) or resid 919 through 94 \ 6 or (resid 947 and (name N or name CA or name C or name O or name CB )) or resi \ d 948 through 963 or (resid 964 and (name N or name CA or name C or name O or na \ me CB )) or resid 965 through 993 or (resid 994 and (name N or name CA or name C \ or name O or name CB )) or resid 995 through 1072 or (resid 1073 and (name N or \ name CA or name C or name O or name CB )) or resid 1074 through 1137 or (resid \ 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 thro \ ugh 1140 or (resid 1141 through 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name CA o \ r name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 through 225)) selection = (chain 'U' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 225)) selection = (chain 'X' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) \ or resid 175 through 225)) } ncs_group { reference = (chain 'S' and (resid 1 through 32 or (resid 33 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 130 or (resid 131 and (name N or name CA or name C or name O or name CB \ )) or resid 132 through 213)) selection = (chain 'V' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 a \ nd (name N or name CA or name C or name O or name CB )) or resid 109 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 213)) selection = (chain 'Y' and (resid 1 through 32 or (resid 33 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (nam \ e N or name CA or name C or name O or name CB )) or resid 50 through 144 or (res \ id 145 and (name N or name CA or name C or name O or name CB )) or resid 146 thr \ ough 213)) } ncs_group { reference = (chain 'T' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = (chain 'W' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = chain 'Z' } 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: 7.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 35.980 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 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 : 0.003 0.057 37117 Z= 0.158 Angle : 0.689 18.475 50710 Z= 0.386 Chirality : 0.088 1.779 5891 Planarity : 0.004 0.080 6479 Dihedral : 11.676 89.268 13438 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.82 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 4.70 % 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: -0.16 (0.12), residues: 4677 helix: 1.39 (0.21), residues: 702 sheet: 0.25 (0.13), residues: 1479 loop : -0.75 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.024 0.001 TYR V 87 PHE 0.030 0.001 PHE Y 98 TRP 0.032 0.002 TRP W 45 HIS 0.010 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00304 (37025) covalent geometry : angle 0.68227 (50488) SS BOND : bond 0.00326 ( 54) SS BOND : angle 1.24672 ( 108) hydrogen bonds : bond 0.22741 ( 1433) hydrogen bonds : angle 8.78334 ( 3921) link_BETA1-4 : bond 0.00150 ( 2) link_BETA1-4 : angle 1.75064 ( 6) link_NAG-ASN : bond 0.00230 ( 36) link_NAG-ASN : angle 1.84334 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.5846 (p0) cc_final: 0.5513 (p0) REVERT: A 765 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7431 (ttm110) REVERT: A 773 GLU cc_start: 0.7073 (tp30) cc_final: 0.6720 (mm-30) REVERT: A 1002 GLN cc_start: 0.7384 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 99 ASN cc_start: 0.7873 (p0) cc_final: 0.7603 (p0) REVERT: B 317 ASN cc_start: 0.6900 (m110) cc_final: 0.6638 (m-40) REVERT: B 773 GLU cc_start: 0.6625 (tt0) cc_final: 0.6305 (tt0) REVERT: B 922 LEU cc_start: 0.7687 (tp) cc_final: 0.7484 (tt) REVERT: B 1017 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6478 (tm-30) REVERT: C 353 TRP cc_start: 0.7493 (p-90) cc_final: 0.7237 (p-90) REVERT: C 950 ASP cc_start: 0.6807 (m-30) cc_final: 0.6529 (m-30) REVERT: C 1084 ASP cc_start: 0.6758 (m-30) cc_final: 0.6531 (m-30) REVERT: R 48 MET cc_start: 0.0548 (ttp) cc_final: -0.0036 (tpp) REVERT: W 92 MET cc_start: 0.1444 (mpp) cc_final: 0.1238 (mmt) outliers start: 1 outliers final: 2 residues processed: 495 average time/residue: 0.5490 time to fit residues: 339.4448 Evaluate side-chains 422 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 592 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.0010 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 470 optimal weight: 6.9990 overall best weight: 0.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 955 ASN A1135 ASN B 196 ASN B 317 ASN B 422 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN B 992 GLN B1134 ASN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C1135 ASN S 198 HIS ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.248959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.184430 restraints weight = 61792.629| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.67 r_work: 0.3939 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37117 Z= 0.132 Angle : 0.659 20.979 50710 Z= 0.341 Chirality : 0.053 1.777 5891 Planarity : 0.005 0.058 6479 Dihedral : 5.723 58.097 5876 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 1.21 % Allowed : 7.21 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % 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: -0.13 (0.12), residues: 4677 helix: 1.38 (0.20), residues: 711 sheet: 0.30 (0.13), residues: 1511 loop : -0.75 (0.13), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 81 TYR 0.025 0.002 TYR A 265 PHE 0.028 0.002 PHE B 970 TRP 0.024 0.001 TRP R 106 HIS 0.006 0.001 HIS X 210 Details of bonding type rmsd covalent geometry : bond 0.00282 (37025) covalent geometry : angle 0.63720 (50488) SS BOND : bond 0.00388 ( 54) SS BOND : angle 1.66569 ( 108) hydrogen bonds : bond 0.04239 ( 1433) hydrogen bonds : angle 6.50608 ( 3921) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.25669 ( 6) link_NAG-ASN : bond 0.00652 ( 36) link_NAG-ASN : angle 3.32101 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 448 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8039 (tppt) cc_final: 0.7726 (tppt) REVERT: A 138 ASP cc_start: 0.7176 (t0) cc_final: 0.6797 (m-30) REVERT: A 269 TYR cc_start: 0.7932 (m-80) cc_final: 0.7648 (m-80) REVERT: A 334 ASN cc_start: 0.6935 (p0) cc_final: 0.6449 (p0) REVERT: A 979 ASP cc_start: 0.7817 (m-30) cc_final: 0.7601 (m-30) REVERT: A 1002 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 1008 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8624 (t) REVERT: B 99 ASN cc_start: 0.8270 (p0) cc_final: 0.7878 (p0) REVERT: B 205 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8737 (t) REVERT: B 969 LYS cc_start: 0.8247 (mppt) cc_final: 0.7994 (mppt) REVERT: B 1017 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 390 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8416 (mp) REVERT: C 574 ASP cc_start: 0.7278 (t0) cc_final: 0.7020 (t0) REVERT: C 814 LYS cc_start: 0.8122 (mttp) cc_final: 0.7666 (mmtm) REVERT: C 825 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8624 (mmtt) REVERT: C 950 ASP cc_start: 0.7549 (m-30) cc_final: 0.6994 (m-30) REVERT: C 969 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8471 (mtmm) REVERT: R 48 MET cc_start: 0.1699 (ttp) cc_final: 0.1259 (tmt) REVERT: W 92 MET cc_start: 0.0550 (mpp) cc_final: 0.0171 (mmt) REVERT: X 48 MET cc_start: -0.0631 (mmm) cc_final: -0.1008 (mmm) REVERT: X 81 MET cc_start: 0.3581 (tmm) cc_final: 0.2582 (mmp) REVERT: Y 4 MET cc_start: 0.3314 (ptt) cc_final: 0.2954 (ptt) outliers start: 46 outliers final: 21 residues processed: 474 average time/residue: 0.5494 time to fit residues: 325.9238 Evaluate side-chains 451 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 427 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain V residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 64 optimal weight: 0.0870 chunk 364 optimal weight: 30.0000 chunk 368 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 330 optimal weight: 8.9990 chunk 284 optimal weight: 0.9980 chunk 390 optimal weight: 10.0000 chunk 422 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 901 GLN A 957 GLN A 992 GLN A1135 ASN B 66 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 949 GLN B 978 ASN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 703 ASN C 804 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.244765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181572 restraints weight = 61656.546| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.35 r_work: 0.3891 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37117 Z= 0.173 Angle : 0.632 16.381 50710 Z= 0.328 Chirality : 0.049 0.903 5891 Planarity : 0.005 0.062 6479 Dihedral : 5.657 59.546 5874 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 9.61 % Favored : 88.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % 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: -0.20 (0.12), residues: 4677 helix: 1.31 (0.20), residues: 697 sheet: 0.29 (0.13), residues: 1529 loop : -0.82 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.023 0.002 TYR A 279 PHE 0.025 0.002 PHE A1089 TRP 0.020 0.001 TRP R 106 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00395 (37025) covalent geometry : angle 0.60970 (50488) SS BOND : bond 0.00309 ( 54) SS BOND : angle 1.63376 ( 108) hydrogen bonds : bond 0.04328 ( 1433) hydrogen bonds : angle 6.20997 ( 3921) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 1.45353 ( 6) link_NAG-ASN : bond 0.00448 ( 36) link_NAG-ASN : angle 3.35091 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 447 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8099 (tppt) cc_final: 0.7698 (tppt) REVERT: A 334 ASN cc_start: 0.6898 (p0) cc_final: 0.6368 (p0) REVERT: A 650 LEU cc_start: 0.7179 (tp) cc_final: 0.6723 (tt) REVERT: A 811 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7871 (ttpp) REVERT: A 1002 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 1008 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8796 (t) REVERT: B 99 ASN cc_start: 0.8287 (p0) cc_final: 0.7864 (p0) REVERT: B 717 ASN cc_start: 0.7121 (t0) cc_final: 0.6679 (t0) REVERT: B 752 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (tt) REVERT: B 868 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 969 LYS cc_start: 0.8391 (mppt) cc_final: 0.8122 (mppt) REVERT: B 1017 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 1050 MET cc_start: 0.8060 (ptp) cc_final: 0.7836 (ptp) REVERT: C 353 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.7042 (p-90) REVERT: C 539 VAL cc_start: 0.8311 (m) cc_final: 0.8088 (p) REVERT: C 574 ASP cc_start: 0.7322 (t0) cc_final: 0.6837 (t0) REVERT: C 724 THR cc_start: 0.7641 (p) cc_final: 0.7364 (m) REVERT: C 777 ASN cc_start: 0.8740 (m110) cc_final: 0.8333 (m-40) REVERT: C 825 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8635 (mmtt) REVERT: C 949 GLN cc_start: 0.8581 (mm110) cc_final: 0.8364 (mm-40) REVERT: C 950 ASP cc_start: 0.7568 (m-30) cc_final: 0.7061 (m-30) REVERT: R 48 MET cc_start: 0.1676 (ttp) cc_final: 0.1284 (tmt) REVERT: X 81 MET cc_start: 0.3492 (tmm) cc_final: 0.2615 (mmp) REVERT: Y 4 MET cc_start: 0.1828 (ptt) cc_final: 0.1614 (ptt) outliers start: 71 outliers final: 40 residues processed: 486 average time/residue: 0.5500 time to fit residues: 333.9190 Evaluate side-chains 463 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 419 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 253 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 367 optimal weight: 9.9990 chunk 323 optimal weight: 0.0770 chunk 315 optimal weight: 50.0000 chunk 274 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 364 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 777 ASN A 949 GLN A 957 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 317 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN C 66 HIS C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 703 ASN C 935 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.244859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.182306 restraints weight = 61488.189| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.31 r_work: 0.3881 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 37117 Z= 0.172 Angle : 0.631 15.698 50710 Z= 0.325 Chirality : 0.048 0.752 5891 Planarity : 0.005 0.062 6479 Dihedral : 5.537 56.239 5872 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.55 % Allowed : 10.66 % Favored : 86.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % 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: -0.21 (0.12), residues: 4677 helix: 1.16 (0.19), residues: 711 sheet: 0.34 (0.13), residues: 1540 loop : -0.83 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.023 0.002 TYR B1067 PHE 0.027 0.002 PHE B 592 TRP 0.017 0.001 TRP R 106 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00398 (37025) covalent geometry : angle 0.60577 (50488) SS BOND : bond 0.00347 ( 54) SS BOND : angle 2.01319 ( 108) hydrogen bonds : bond 0.03964 ( 1433) hydrogen bonds : angle 6.02350 ( 3921) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.28405 ( 6) link_NAG-ASN : bond 0.00587 ( 36) link_NAG-ASN : angle 3.33411 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 447 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8076 (tppt) cc_final: 0.7559 (tppt) REVERT: A 334 ASN cc_start: 0.6910 (p0) cc_final: 0.6376 (p0) REVERT: A 655 TYR cc_start: 0.7512 (t80) cc_final: 0.7019 (t80) REVERT: A 811 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7828 (ttpp) REVERT: A 1002 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 99 ASN cc_start: 0.8295 (p0) cc_final: 0.7869 (p0) REVERT: B 317 ASN cc_start: 0.7783 (m-40) cc_final: 0.7427 (m110) REVERT: B 717 ASN cc_start: 0.7090 (t0) cc_final: 0.6585 (t0) REVERT: B 752 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8632 (tt) REVERT: B 1017 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 189 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 282 ASN cc_start: 0.7651 (m-40) cc_final: 0.7380 (m-40) REVERT: C 353 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.7263 (p-90) REVERT: C 539 VAL cc_start: 0.8287 (m) cc_final: 0.8068 (p) REVERT: C 574 ASP cc_start: 0.7326 (t0) cc_final: 0.6773 (t0) REVERT: C 586 ASP cc_start: 0.7505 (m-30) cc_final: 0.7182 (t0) REVERT: C 737 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7556 (t70) REVERT: C 814 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7913 (mttp) REVERT: C 825 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8658 (mmtt) REVERT: C 950 ASP cc_start: 0.7494 (m-30) cc_final: 0.6978 (m-30) REVERT: C 1094 VAL cc_start: 0.4620 (OUTLIER) cc_final: 0.4202 (m) REVERT: R 48 MET cc_start: 0.1693 (ttp) cc_final: 0.1355 (tmt) REVERT: X 48 MET cc_start: -0.0364 (mmm) cc_final: -0.0936 (mmm) REVERT: X 81 MET cc_start: 0.3464 (tmm) cc_final: 0.2595 (mmp) outliers start: 97 outliers final: 44 residues processed: 500 average time/residue: 0.5619 time to fit residues: 350.9777 Evaluate side-chains 471 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 420 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain Z residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 334 optimal weight: 50.0000 chunk 251 optimal weight: 0.4980 chunk 322 optimal weight: 50.0000 chunk 352 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 307 optimal weight: 50.0000 chunk 428 optimal weight: 50.0000 chunk 232 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 762 GLN A 957 GLN A1088 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 66 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN C 66 HIS C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 703 ASN C 777 ASN C1088 HIS ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.243869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181075 restraints weight = 60816.222| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.79 r_work: 0.3781 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 37117 Z= 0.326 Angle : 0.720 17.365 50710 Z= 0.374 Chirality : 0.052 0.645 5891 Planarity : 0.005 0.063 6479 Dihedral : 5.925 57.464 5872 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.18 % Allowed : 11.50 % Favored : 85.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.51 (0.12), residues: 4677 helix: 0.52 (0.19), residues: 712 sheet: 0.22 (0.13), residues: 1497 loop : -0.93 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 355 TYR 0.038 0.002 TYR B 170 PHE 0.046 0.003 PHE A 855 TRP 0.023 0.002 TRP C1102 HIS 0.015 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00761 (37025) covalent geometry : angle 0.69338 (50488) SS BOND : bond 0.00461 ( 54) SS BOND : angle 2.27412 ( 108) hydrogen bonds : bond 0.04802 ( 1433) hydrogen bonds : angle 6.19379 ( 3921) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 1.34114 ( 6) link_NAG-ASN : bond 0.00714 ( 36) link_NAG-ASN : angle 3.64048 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 455 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8139 (tppt) cc_final: 0.7503 (tppt) REVERT: A 269 TYR cc_start: 0.8126 (m-80) cc_final: 0.7728 (m-80) REVERT: A 326 ILE cc_start: 0.7759 (pt) cc_final: 0.7487 (mt) REVERT: A 334 ASN cc_start: 0.7079 (p0) cc_final: 0.6539 (p0) REVERT: A 650 LEU cc_start: 0.7373 (tp) cc_final: 0.7072 (tt) REVERT: A 811 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7974 (ttpp) REVERT: A 867 ASP cc_start: 0.7466 (m-30) cc_final: 0.7186 (m-30) REVERT: A 1002 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 1047 TYR cc_start: 0.7052 (m-10) cc_final: 0.6810 (m-10) REVERT: A 1113 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: B 99 ASN cc_start: 0.8315 (p0) cc_final: 0.7862 (p0) REVERT: B 274 THR cc_start: 0.8289 (m) cc_final: 0.8061 (t) REVERT: B 317 ASN cc_start: 0.7966 (m-40) cc_final: 0.7682 (m110) REVERT: B 574 ASP cc_start: 0.7956 (t0) cc_final: 0.7695 (t0) REVERT: B 577 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7176 (ttm110) REVERT: B 717 ASN cc_start: 0.7150 (t0) cc_final: 0.6714 (t0) REVERT: B 720 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 753 LEU cc_start: 0.8452 (tp) cc_final: 0.8149 (tm) REVERT: B 804 GLN cc_start: 0.7779 (mt0) cc_final: 0.7345 (mt0) REVERT: B 969 LYS cc_start: 0.8446 (mppt) cc_final: 0.8188 (mppt) REVERT: C 66 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6741 (m-70) REVERT: C 188 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7523 (p0) REVERT: C 189 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7978 (tp) REVERT: C 282 ASN cc_start: 0.7812 (m-40) cc_final: 0.7533 (m-40) REVERT: C 353 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7501 (p-90) REVERT: C 433 VAL cc_start: 0.8579 (t) cc_final: 0.8311 (m) REVERT: C 539 VAL cc_start: 0.8404 (m) cc_final: 0.8177 (p) REVERT: C 574 ASP cc_start: 0.7595 (t0) cc_final: 0.7123 (t0) REVERT: C 586 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7390 (t0) REVERT: C 737 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7853 (t0) REVERT: C 780 GLU cc_start: 0.7967 (tt0) cc_final: 0.7708 (tt0) REVERT: C 825 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8733 (mmtt) REVERT: C 950 ASP cc_start: 0.7683 (m-30) cc_final: 0.7192 (m-30) REVERT: C 969 LYS cc_start: 0.8860 (mtmm) cc_final: 0.8467 (mtpp) REVERT: C 998 THR cc_start: 0.8911 (t) cc_final: 0.8639 (p) REVERT: C 1021 SER cc_start: 0.8296 (t) cc_final: 0.8005 (p) REVERT: C 1094 VAL cc_start: 0.5153 (OUTLIER) cc_final: 0.4690 (m) REVERT: R 48 MET cc_start: 0.1756 (ttp) cc_final: 0.1488 (tmt) REVERT: R 81 MET cc_start: -0.1399 (ttt) cc_final: -0.1618 (ttt) REVERT: U 48 MET cc_start: 0.6798 (mpp) cc_final: 0.6572 (mpp) REVERT: V 176 SER cc_start: 0.0089 (t) cc_final: -0.1033 (m) REVERT: X 48 MET cc_start: -0.0393 (mmm) cc_final: -0.0999 (mmm) REVERT: Y 4 MET cc_start: 0.2396 (ptt) cc_final: 0.1264 (ptt) outliers start: 121 outliers final: 73 residues processed: 521 average time/residue: 0.5245 time to fit residues: 346.0131 Evaluate side-chains 526 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 443 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 453 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 418 optimal weight: 0.0970 chunk 354 optimal weight: 50.0000 chunk 401 optimal weight: 50.0000 chunk 162 optimal weight: 0.7980 chunk 141 optimal weight: 50.0000 chunk 294 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 384 optimal weight: 40.0000 overall best weight: 2.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 762 GLN A 957 GLN B 30 ASN B 66 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN C 99 ASN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN C 787 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 174 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.243077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178825 restraints weight = 60542.581| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.99 r_work: 0.3836 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.118 37117 Z= 0.426 Angle : 0.788 16.607 50710 Z= 0.412 Chirality : 0.056 0.501 5891 Planarity : 0.006 0.065 6479 Dihedral : 6.241 58.915 5872 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.92 % Allowed : 12.26 % Favored : 83.82 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.12), residues: 4677 helix: 0.04 (0.18), residues: 708 sheet: 0.13 (0.13), residues: 1495 loop : -1.11 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.042 0.003 TYR B 170 PHE 0.056 0.003 PHE A 855 TRP 0.034 0.002 TRP X 36 HIS 0.024 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00992 (37025) covalent geometry : angle 0.76186 (50488) SS BOND : bond 0.00460 ( 54) SS BOND : angle 2.45664 ( 108) hydrogen bonds : bond 0.05280 ( 1433) hydrogen bonds : angle 6.35616 ( 3921) link_BETA1-4 : bond 0.00220 ( 2) link_BETA1-4 : angle 1.36061 ( 6) link_NAG-ASN : bond 0.00761 ( 36) link_NAG-ASN : angle 3.79689 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 454 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8304 (m-80) cc_final: 0.7950 (m-80) REVERT: A 334 ASN cc_start: 0.7255 (p0) cc_final: 0.6688 (p0) REVERT: A 581 THR cc_start: 0.8041 (p) cc_final: 0.7813 (t) REVERT: A 598 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 650 LEU cc_start: 0.7675 (tp) cc_final: 0.7311 (tt) REVERT: A 1002 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 99 ASN cc_start: 0.8370 (p0) cc_final: 0.7932 (p0) REVERT: B 577 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7086 (ttm110) REVERT: B 717 ASN cc_start: 0.7341 (t0) cc_final: 0.6955 (t0) REVERT: B 753 LEU cc_start: 0.8604 (tp) cc_final: 0.8314 (tm) REVERT: B 804 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: B 916 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6474 (tp) REVERT: B 957 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: B 969 LYS cc_start: 0.8491 (mppt) cc_final: 0.8240 (mppt) REVERT: C 129 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7068 (tmmt) REVERT: C 282 ASN cc_start: 0.7924 (m-40) cc_final: 0.7632 (m-40) REVERT: C 289 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8694 (p) REVERT: C 353 TRP cc_start: 0.8057 (OUTLIER) cc_final: 0.7762 (p-90) REVERT: C 433 VAL cc_start: 0.8757 (t) cc_final: 0.8507 (m) REVERT: C 451 TYR cc_start: 0.7318 (m-80) cc_final: 0.6908 (m-80) REVERT: C 574 ASP cc_start: 0.8027 (t0) cc_final: 0.7502 (t0) REVERT: C 586 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (t0) REVERT: C 780 GLU cc_start: 0.8158 (tt0) cc_final: 0.7932 (tt0) REVERT: C 900 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.4149 (mmt) REVERT: C 969 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8510 (mtpp) REVERT: C 998 THR cc_start: 0.9033 (t) cc_final: 0.8782 (p) REVERT: C 1021 SER cc_start: 0.8421 (t) cc_final: 0.8148 (p) REVERT: C 1055 SER cc_start: 0.8711 (t) cc_final: 0.8375 (p) REVERT: C 1072 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: C 1091 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7705 (mtt180) REVERT: C 1094 VAL cc_start: 0.5652 (OUTLIER) cc_final: 0.5042 (m) REVERT: S 4 MET cc_start: -0.0119 (ptt) cc_final: -0.0936 (ptt) REVERT: V 176 SER cc_start: -0.0027 (t) cc_final: -0.1271 (m) REVERT: X 48 MET cc_start: 0.0117 (mmm) cc_final: -0.0654 (mmm) REVERT: Y 4 MET cc_start: 0.1921 (ptt) cc_final: 0.0749 (ptt) outliers start: 149 outliers final: 79 residues processed: 536 average time/residue: 0.5086 time to fit residues: 347.9829 Evaluate side-chains 526 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 435 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 89 optimal weight: 0.9980 chunk 303 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 292 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 460 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN B 66 HIS B 81 ASN B 317 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 66 HIS C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 321 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.244428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.179040 restraints weight = 61062.030| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.23 r_work: 0.3857 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37117 Z= 0.179 Angle : 0.647 15.660 50710 Z= 0.334 Chirality : 0.047 0.427 5891 Planarity : 0.005 0.063 6479 Dihedral : 5.775 58.648 5872 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.89 % Allowed : 14.26 % Favored : 82.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % 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: -0.51 (0.12), residues: 4677 helix: 0.65 (0.19), residues: 709 sheet: 0.29 (0.13), residues: 1509 loop : -1.03 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1091 TYR 0.026 0.002 TYR C 265 PHE 0.032 0.002 PHE B 592 TRP 0.018 0.001 TRP X 36 HIS 0.007 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00414 (37025) covalent geometry : angle 0.62338 (50488) SS BOND : bond 0.00339 ( 54) SS BOND : angle 1.90972 ( 108) hydrogen bonds : bond 0.03974 ( 1433) hydrogen bonds : angle 5.98022 ( 3921) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 1.50898 ( 6) link_NAG-ASN : bond 0.00493 ( 36) link_NAG-ASN : angle 3.36903 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 454 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8103 (tppt) cc_final: 0.7449 (tppt) REVERT: A 269 TYR cc_start: 0.8000 (m-80) cc_final: 0.7611 (m-80) REVERT: A 334 ASN cc_start: 0.7154 (p0) cc_final: 0.6563 (p0) REVERT: A 581 THR cc_start: 0.7746 (p) cc_final: 0.7498 (t) REVERT: A 650 LEU cc_start: 0.7228 (tp) cc_final: 0.6909 (tt) REVERT: A 712 ILE cc_start: 0.8418 (tt) cc_final: 0.8183 (tp) REVERT: A 1002 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 99 ASN cc_start: 0.8213 (p0) cc_final: 0.7798 (p0) REVERT: B 577 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.6814 (mtp-110) REVERT: B 717 ASN cc_start: 0.7072 (t0) cc_final: 0.6551 (t0) REVERT: B 753 LEU cc_start: 0.8447 (tp) cc_final: 0.8171 (tm) REVERT: B 820 ASP cc_start: 0.7326 (p0) cc_final: 0.7016 (p0) REVERT: C 189 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 336 CYS cc_start: 0.5621 (OUTLIER) cc_final: 0.3527 (t) REVERT: C 353 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.7519 (p-90) REVERT: C 395 VAL cc_start: 0.7493 (p) cc_final: 0.7257 (m) REVERT: C 433 VAL cc_start: 0.8577 (t) cc_final: 0.8303 (m) REVERT: C 451 TYR cc_start: 0.7220 (m-80) cc_final: 0.6775 (m-80) REVERT: C 574 ASP cc_start: 0.7432 (t0) cc_final: 0.6921 (t0) REVERT: C 586 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7175 (t0) REVERT: C 780 GLU cc_start: 0.7995 (tt0) cc_final: 0.7740 (tt0) REVERT: C 969 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8443 (mtpp) REVERT: C 998 THR cc_start: 0.8758 (t) cc_final: 0.8491 (p) REVERT: C 1094 VAL cc_start: 0.4852 (OUTLIER) cc_final: 0.4429 (m) REVERT: S 4 MET cc_start: 0.0641 (ptt) cc_final: -0.0308 (ptt) REVERT: V 176 SER cc_start: -0.0218 (t) cc_final: -0.1325 (m) REVERT: X 48 MET cc_start: -0.0293 (mmm) cc_final: -0.0960 (mmm) REVERT: Y 4 MET cc_start: 0.2373 (ptt) cc_final: 0.1174 (ptt) outliers start: 110 outliers final: 73 residues processed: 516 average time/residue: 0.5324 time to fit residues: 345.6438 Evaluate side-chains 506 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 428 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 87 TYR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 15 optimal weight: 8.9990 chunk 229 optimal weight: 0.0980 chunk 439 optimal weight: 7.9990 chunk 454 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 200 optimal weight: 0.0040 chunk 285 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 0.0770 chunk 429 optimal weight: 8.9990 chunk 442 optimal weight: 5.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 777 ASN A 957 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN C 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.246536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.181222 restraints weight = 60719.384| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.61 r_work: 0.3864 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37117 Z= 0.134 Angle : 0.625 14.997 50710 Z= 0.319 Chirality : 0.046 0.381 5891 Planarity : 0.005 0.063 6479 Dihedral : 5.507 56.601 5872 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.47 % Allowed : 14.47 % Favored : 83.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % 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: -0.34 (0.12), residues: 4677 helix: 0.99 (0.19), residues: 711 sheet: 0.35 (0.13), residues: 1506 loop : -0.96 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1091 TYR 0.021 0.001 TYR C 265 PHE 0.033 0.002 PHE B 592 TRP 0.019 0.001 TRP U 106 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00305 (37025) covalent geometry : angle 0.60144 (50488) SS BOND : bond 0.00358 ( 54) SS BOND : angle 1.64603 ( 108) hydrogen bonds : bond 0.03638 ( 1433) hydrogen bonds : angle 5.80398 ( 3921) link_BETA1-4 : bond 0.00184 ( 2) link_BETA1-4 : angle 1.30009 ( 6) link_NAG-ASN : bond 0.00533 ( 36) link_NAG-ASN : angle 3.36792 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 428 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8146 (tppt) cc_final: 0.7505 (tppt) REVERT: A 269 TYR cc_start: 0.8044 (m-80) cc_final: 0.7679 (m-80) REVERT: A 334 ASN cc_start: 0.7151 (p0) cc_final: 0.6527 (p0) REVERT: A 581 THR cc_start: 0.7726 (p) cc_final: 0.7458 (t) REVERT: A 650 LEU cc_start: 0.7248 (tp) cc_final: 0.6905 (tt) REVERT: A 1002 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 99 ASN cc_start: 0.8232 (p0) cc_final: 0.7814 (p0) REVERT: B 717 ASN cc_start: 0.7071 (t0) cc_final: 0.6510 (t0) REVERT: B 753 LEU cc_start: 0.8504 (tp) cc_final: 0.8236 (tm) REVERT: B 820 ASP cc_start: 0.7291 (p0) cc_final: 0.7015 (p0) REVERT: B 977 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7260 (mt) REVERT: C 129 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6750 (tmmt) REVERT: C 189 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (tp) REVERT: C 336 CYS cc_start: 0.4817 (OUTLIER) cc_final: 0.2208 (t) REVERT: C 353 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.7498 (p-90) REVERT: C 395 VAL cc_start: 0.7421 (p) cc_final: 0.7214 (m) REVERT: C 433 VAL cc_start: 0.8572 (t) cc_final: 0.8312 (m) REVERT: C 451 TYR cc_start: 0.7215 (m-80) cc_final: 0.6794 (m-80) REVERT: C 796 TYR cc_start: 0.7914 (t80) cc_final: 0.7708 (t80) REVERT: C 825 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8579 (mttp) REVERT: C 931 ILE cc_start: 0.7975 (mm) cc_final: 0.7673 (pp) REVERT: C 969 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8397 (mtpp) REVERT: C 998 THR cc_start: 0.8740 (t) cc_final: 0.8490 (p) REVERT: C 1094 VAL cc_start: 0.4758 (OUTLIER) cc_final: 0.4296 (m) REVERT: S 4 MET cc_start: 0.0526 (ptt) cc_final: -0.0435 (ptt) REVERT: V 176 SER cc_start: -0.0106 (t) cc_final: -0.1212 (m) REVERT: X 48 MET cc_start: 0.0050 (mmm) cc_final: -0.0697 (mmm) REVERT: Y 4 MET cc_start: 0.1837 (ptt) cc_final: 0.0698 (ptt) outliers start: 94 outliers final: 67 residues processed: 494 average time/residue: 0.5115 time to fit residues: 320.4704 Evaluate side-chains 495 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 422 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 87 TYR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 100 optimal weight: 1.9990 chunk 392 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 375 optimal weight: 50.0000 chunk 176 optimal weight: 0.7980 chunk 425 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 208 optimal weight: 0.0050 chunk 58 optimal weight: 0.5980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 613 GLN A 957 GLN B 81 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.244640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182345 restraints weight = 61120.373| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.54 r_work: 0.3839 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 37117 Z= 0.210 Angle : 0.660 14.946 50710 Z= 0.338 Chirality : 0.048 0.352 5891 Planarity : 0.005 0.063 6479 Dihedral : 5.579 54.688 5872 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.55 % Allowed : 14.82 % Favored : 82.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.70 % 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: -0.43 (0.12), residues: 4677 helix: 0.84 (0.19), residues: 705 sheet: 0.31 (0.13), residues: 1504 loop : -1.00 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1019 TYR 0.028 0.002 TYR C 265 PHE 0.034 0.002 PHE B 592 TRP 0.019 0.001 TRP U 106 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00487 (37025) covalent geometry : angle 0.63656 (50488) SS BOND : bond 0.00325 ( 54) SS BOND : angle 1.83117 ( 108) hydrogen bonds : bond 0.04020 ( 1433) hydrogen bonds : angle 5.86715 ( 3921) link_BETA1-4 : bond 0.00318 ( 2) link_BETA1-4 : angle 1.27810 ( 6) link_NAG-ASN : bond 0.00537 ( 36) link_NAG-ASN : angle 3.40924 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 424 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8108 (tppt) cc_final: 0.7432 (tppt) REVERT: A 269 TYR cc_start: 0.8052 (m-80) cc_final: 0.7674 (m-80) REVERT: A 334 ASN cc_start: 0.6960 (p0) cc_final: 0.6317 (p0) REVERT: A 581 THR cc_start: 0.7767 (p) cc_final: 0.7521 (t) REVERT: A 650 LEU cc_start: 0.7309 (tp) cc_final: 0.6999 (tt) REVERT: A 712 ILE cc_start: 0.8391 (tt) cc_final: 0.8189 (tp) REVERT: A 1002 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 99 ASN cc_start: 0.8251 (p0) cc_final: 0.7815 (p0) REVERT: B 577 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7054 (ttm110) REVERT: B 717 ASN cc_start: 0.7137 (t0) cc_final: 0.6644 (t0) REVERT: B 820 ASP cc_start: 0.7295 (p0) cc_final: 0.6983 (p0) REVERT: B 919 ASN cc_start: 0.6570 (t0) cc_final: 0.6266 (m-40) REVERT: B 957 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: B 969 LYS cc_start: 0.8340 (mppt) cc_final: 0.8049 (mppt) REVERT: B 977 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7287 (mt) REVERT: C 129 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6757 (tmmt) REVERT: C 189 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7978 (tp) REVERT: C 336 CYS cc_start: 0.4733 (OUTLIER) cc_final: 0.2119 (t) REVERT: C 433 VAL cc_start: 0.8559 (t) cc_final: 0.8301 (m) REVERT: C 434 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7719 (mp) REVERT: C 451 TYR cc_start: 0.7183 (m-80) cc_final: 0.6770 (m-80) REVERT: C 780 GLU cc_start: 0.7856 (tt0) cc_final: 0.7601 (tt0) REVERT: C 823 PHE cc_start: 0.7582 (m-80) cc_final: 0.7295 (m-80) REVERT: C 825 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8605 (mttp) REVERT: C 931 ILE cc_start: 0.8018 (mm) cc_final: 0.7716 (pp) REVERT: C 969 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8416 (mtpp) REVERT: C 998 THR cc_start: 0.8786 (t) cc_final: 0.8508 (p) REVERT: C 1072 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: C 1089 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: C 1091 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (mtt180) REVERT: C 1094 VAL cc_start: 0.5002 (OUTLIER) cc_final: 0.4533 (m) REVERT: S 4 MET cc_start: 0.0321 (ptt) cc_final: -0.0592 (ptt) REVERT: V 176 SER cc_start: -0.0101 (t) cc_final: -0.1182 (m) REVERT: X 48 MET cc_start: -0.0088 (mmm) cc_final: -0.0829 (mmm) REVERT: Y 4 MET cc_start: 0.1884 (ptt) cc_final: 0.0801 (ptt) outliers start: 97 outliers final: 73 residues processed: 486 average time/residue: 0.5250 time to fit residues: 322.6823 Evaluate side-chains 508 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 425 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 87 TYR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 344 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 467 optimal weight: 4.9990 chunk 294 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 262 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 30 ASN C 81 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 14 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.245378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183862 restraints weight = 61425.633| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.30 r_work: 0.3892 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37117 Z= 0.153 Angle : 0.625 14.421 50710 Z= 0.320 Chirality : 0.046 0.344 5891 Planarity : 0.005 0.063 6479 Dihedral : 5.416 53.770 5872 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.29 % Allowed : 15.29 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % 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: -0.32 (0.12), residues: 4677 helix: 1.04 (0.20), residues: 703 sheet: 0.37 (0.13), residues: 1527 loop : -0.97 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1019 TYR 0.024 0.001 TYR C 265 PHE 0.035 0.002 PHE B 592 TRP 0.021 0.001 TRP U 106 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00353 (37025) covalent geometry : angle 0.60410 (50488) SS BOND : bond 0.00312 ( 54) SS BOND : angle 1.60727 ( 108) hydrogen bonds : bond 0.03667 ( 1433) hydrogen bonds : angle 5.73288 ( 3921) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.27086 ( 6) link_NAG-ASN : bond 0.00504 ( 36) link_NAG-ASN : angle 3.22590 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 424 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8080 (tppt) cc_final: 0.7399 (tppt) REVERT: A 334 ASN cc_start: 0.6868 (p0) cc_final: 0.6289 (p0) REVERT: A 581 THR cc_start: 0.7726 (p) cc_final: 0.7490 (t) REVERT: A 712 ILE cc_start: 0.8326 (tt) cc_final: 0.8126 (tp) REVERT: A 970 PHE cc_start: 0.8597 (m-80) cc_final: 0.8109 (m-80) REVERT: A 983 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8501 (mtm110) REVERT: A 1002 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 99 ASN cc_start: 0.8223 (p0) cc_final: 0.7808 (p0) REVERT: B 717 ASN cc_start: 0.7012 (t0) cc_final: 0.6457 (t0) REVERT: B 820 ASP cc_start: 0.7212 (p0) cc_final: 0.6978 (p0) REVERT: B 957 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: B 977 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7284 (mt) REVERT: C 129 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6680 (tmmt) REVERT: C 189 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7965 (tp) REVERT: C 336 CYS cc_start: 0.4509 (OUTLIER) cc_final: 0.1667 (t) REVERT: C 451 TYR cc_start: 0.7147 (m-80) cc_final: 0.6730 (m-80) REVERT: C 574 ASP cc_start: 0.7350 (t0) cc_final: 0.6965 (t0) REVERT: C 780 GLU cc_start: 0.7784 (tt0) cc_final: 0.7526 (tt0) REVERT: C 823 PHE cc_start: 0.7510 (m-80) cc_final: 0.7284 (m-80) REVERT: C 825 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8589 (mttp) REVERT: C 931 ILE cc_start: 0.8002 (mm) cc_final: 0.7685 (pp) REVERT: C 969 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8350 (mtpp) REVERT: C 998 THR cc_start: 0.8766 (t) cc_final: 0.8507 (p) REVERT: C 1072 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 1094 VAL cc_start: 0.4814 (OUTLIER) cc_final: 0.4349 (m) REVERT: S 4 MET cc_start: -0.0101 (ptt) cc_final: -0.0989 (ptt) REVERT: Y 4 MET cc_start: 0.1526 (ptt) cc_final: 0.0511 (ptt) outliers start: 87 outliers final: 68 residues processed: 482 average time/residue: 0.5424 time to fit residues: 327.6961 Evaluate side-chains 492 residues out of total 4092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 417 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 87 TYR Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 14 GLN Chi-restraints excluded: chain Z residue 118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 146 optimal weight: 50.0000 chunk 441 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 322 optimal weight: 30.0000 chunk 468 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 30 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 14 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.245434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.183688 restraints weight = 60948.725| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.32 r_work: 0.3872 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 37117 Z= 0.207 Angle : 0.827 59.199 50710 Z= 0.455 Chirality : 0.049 0.637 5891 Planarity : 0.005 0.114 6479 Dihedral : 5.473 53.763 5872 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.32 % Allowed : 15.34 % Favored : 82.34 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.32 (0.12), residues: 4677 helix: 1.04 (0.20), residues: 704 sheet: 0.37 (0.13), residues: 1527 loop : -0.97 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.224 0.002 TYR A 707 PHE 0.033 0.002 PHE B 592 TRP 0.055 0.002 TRP U 36 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00446 (37025) covalent geometry : angle 0.79847 (50488) SS BOND : bond 0.00316 ( 54) SS BOND : angle 1.57825 ( 108) hydrogen bonds : bond 0.03696 ( 1433) hydrogen bonds : angle 5.73495 ( 3921) link_BETA1-4 : bond 0.01391 ( 2) link_BETA1-4 : angle 1.45198 ( 6) link_NAG-ASN : bond 0.02259 ( 36) link_NAG-ASN : angle 4.50149 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15921.44 seconds wall clock time: 270 minutes 28.51 seconds (16228.51 seconds total)