Starting phenix.real_space_refine on Thu Mar 5 23:10:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.map" model { file = "/net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bnn_12230/03_2026/7bnn_12230.cif" } resolution = 3.5 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= 0.004 sd= 0.060 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 114 5.16 5 C 16402 2.51 5 N 4236 2.21 5 O 5023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 25775 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8340 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8375 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 54, 'TRANS': 1016} Chain breaks: 6 Chain: "C" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8364 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.31, per 1000 atoms: 0.21 Number of scatterers: 25775 At special positions: 0 Unit cell: (160.65, 150.45, 196.35, 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 114 16.00 O 5023 8.00 N 4236 7.00 C 16402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 57 sheets defined 21.1% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.677A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 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 759 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.523A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.267A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.049A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.588A 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: 3.577A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.589A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.698A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.860A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.678A 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 761 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 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 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.023A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.502A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 956 removed outlier: 4.062A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B1012 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.985A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.753A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.300A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.756A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.931A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1006 removed outlier: 5.947A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1033 removed outlier: 3.565A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.748A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.753A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.706A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.429A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.540A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.502A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.693A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.693A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 664 through 667 removed outlier: 3.587A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.635A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.620A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.673A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.711A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.663A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.931A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AC8, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.029A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.149A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.515A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.768A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.720A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.255A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.997A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.621A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 6.552A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE7, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.647A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 47 through 49 removed outlier: 4.165A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.824A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.128A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.743A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.641A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.945A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.646A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 725 through 728 removed outlier: 4.023A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 765 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8220 1.35 - 1.47: 6659 1.47 - 1.59: 11333 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26356 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 9.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 26351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 35047 1.82 - 3.63: 737 3.63 - 5.45: 63 5.45 - 7.27: 12 7.27 - 9.08: 3 Bond angle restraints: 35862 Sorted by residual: angle pdb=" N LEU B1012 " pdb=" CA LEU B1012 " pdb=" C LEU B1012 " ideal model delta sigma weight residual 113.18 107.15 6.03 1.33e+00 5.65e-01 2.06e+01 angle pdb=" N GLU C 619 " pdb=" CA GLU C 619 " pdb=" C GLU C 619 " ideal model delta sigma weight residual 113.43 108.83 4.60 1.26e+00 6.30e-01 1.33e+01 angle pdb=" C ASN C 616 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ILE A 233 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 120.82 125.25 -4.43 1.47e+00 4.63e-01 9.06e+00 ... (remaining 35857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 15392 23.40 - 46.80: 800 46.80 - 70.19: 102 70.19 - 93.59: 32 93.59 - 116.99: 24 Dihedral angle restraints: 16350 sinusoidal: 7023 harmonic: 9327 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -148.77 62.77 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -26.06 -59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -137.46 51.46 1 1.00e+01 1.00e-02 3.62e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4005 0.100 - 0.201: 189 0.201 - 0.301: 2 0.301 - 0.401: 5 0.401 - 0.502: 2 Chirality restraints: 4203 Sorted by residual: chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 4200 not shown) Planarity restraints: 4625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 617 " 0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C CYS A 617 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS A 617 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 618 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 209 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 330 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.032 5.00e-02 4.00e+02 ... (remaining 4622 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 698 2.68 - 3.24: 24670 3.24 - 3.79: 37564 3.79 - 4.35: 48309 4.35 - 4.90: 81361 Nonbonded interactions: 192602 Sorted by model distance: nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.129 3.120 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.168 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.197 3.120 nonbonded pdb=" OD2 ASP B 578 " pdb=" OG1 THR B 581 " model vdw 2.205 3.040 nonbonded pdb=" OG SER B 591 " pdb=" OE1 GLU B 619 " model vdw 2.218 3.040 ... (remaining 192597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 616 or (resid 617 and (name N or name CA or nam \ e C or name CB or name SG )) or resid 618 through 956 or resid 958 through 1006 \ or resid 1008 through 1309)) selection = (chain 'B' and (resid 14 through 616 or (resid 617 and (name N or name CA or nam \ e C or name CB or name SG )) or resid 618 through 620 or resid 641 through 827 o \ r resid 855 through 1006 or resid 1008 through 1309)) selection = (chain 'C' and (resid 14 through 620 or resid 641 through 827 or resid 855 throu \ gh 956 or resid 958 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.300 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.004 0.059 26447 Z= 0.173 Angle : 0.647 22.037 36094 Z= 0.322 Chirality : 0.047 0.502 4203 Planarity : 0.004 0.064 4584 Dihedral : 14.573 116.988 10227 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 3167 helix: 1.63 (0.23), residues: 606 sheet: -2.24 (0.19), residues: 673 loop : -2.62 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.012 0.001 TYR A 508 PHE 0.015 0.001 PHE B 906 TRP 0.022 0.001 TRP B 886 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00360 (26356) covalent geometry : angle 0.60371 (35862) SS BOND : bond 0.00393 ( 41) SS BOND : angle 1.40479 ( 82) hydrogen bonds : bond 0.22839 ( 757) hydrogen bonds : angle 7.97378 ( 2052) link_BETA1-4 : bond 0.00893 ( 8) link_BETA1-4 : angle 2.51616 ( 24) link_BETA1-6 : bond 0.00493 ( 1) link_BETA1-6 : angle 1.54791 ( 3) link_NAG-ASN : bond 0.00512 ( 41) link_NAG-ASN : angle 3.72604 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7839 (t70) cc_final: 0.7610 (t70) REVERT: A 490 PHE cc_start: 0.8755 (t80) cc_final: 0.8236 (t80) REVERT: B 33 THR cc_start: 0.8157 (p) cc_final: 0.7923 (p) REVERT: B 396 TYR cc_start: 0.7831 (m-80) cc_final: 0.7323 (m-80) REVERT: C 140 PHE cc_start: 0.8527 (p90) cc_final: 0.8086 (p90) REVERT: C 505 TYR cc_start: 0.6653 (t80) cc_final: 0.6354 (t80) REVERT: C 740 MET cc_start: 0.7535 (ttt) cc_final: 0.7200 (ttt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1422 time to fit residues: 51.1940 Evaluate side-chains 146 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A1106 GLN B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B1106 GLN C 146 HIS C 207 HIS C1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095308 restraints weight = 49062.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097630 restraints weight = 33096.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097477 restraints weight = 22068.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098157 restraints weight = 22619.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098307 restraints weight = 20326.906| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26447 Z= 0.127 Angle : 0.632 21.149 36094 Z= 0.312 Chirality : 0.047 0.472 4203 Planarity : 0.004 0.051 4584 Dihedral : 9.188 99.597 4481 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.54 % Allowed : 5.89 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.15), residues: 3167 helix: 1.85 (0.23), residues: 615 sheet: -1.80 (0.20), residues: 652 loop : -2.53 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.021 0.001 TYR A1067 PHE 0.033 0.001 PHE C 133 TRP 0.020 0.002 TRP C 353 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00280 (26356) covalent geometry : angle 0.59272 (35862) SS BOND : bond 0.00854 ( 41) SS BOND : angle 1.74530 ( 82) hydrogen bonds : bond 0.05475 ( 757) hydrogen bonds : angle 5.78761 ( 2052) link_BETA1-4 : bond 0.00815 ( 8) link_BETA1-4 : angle 2.28022 ( 24) link_BETA1-6 : bond 0.00752 ( 1) link_BETA1-6 : angle 1.92456 ( 3) link_NAG-ASN : bond 0.00521 ( 41) link_NAG-ASN : angle 3.42116 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7357 (mm) cc_final: 0.6448 (tp) REVERT: A 177 MET cc_start: 0.6291 (pmm) cc_final: 0.6027 (pmm) REVERT: A 189 LEU cc_start: 0.8311 (tp) cc_final: 0.7933 (mt) REVERT: A 380 TYR cc_start: 0.7249 (m-80) cc_final: 0.6956 (m-10) REVERT: A 392 PHE cc_start: 0.8054 (m-80) cc_final: 0.7795 (m-80) REVERT: A 490 PHE cc_start: 0.8620 (t80) cc_final: 0.8176 (t80) REVERT: B 396 TYR cc_start: 0.7760 (m-80) cc_final: 0.7307 (m-80) REVERT: C 140 PHE cc_start: 0.8446 (p90) cc_final: 0.7802 (p90) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.1371 time to fit residues: 43.9338 Evaluate side-chains 156 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 42 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 140 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.141220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095320 restraints weight = 49330.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096688 restraints weight = 30740.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095965 restraints weight = 23567.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096332 restraints weight = 25066.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096431 restraints weight = 22659.403| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26447 Z= 0.141 Angle : 0.614 21.417 36094 Z= 0.301 Chirality : 0.046 0.454 4203 Planarity : 0.004 0.049 4584 Dihedral : 8.494 93.442 4481 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.71 % Allowed : 8.67 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3167 helix: 1.84 (0.23), residues: 615 sheet: -1.73 (0.20), residues: 671 loop : -2.44 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.020 0.001 TYR A1067 PHE 0.025 0.001 PHE C 133 TRP 0.014 0.001 TRP A 886 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00333 (26356) covalent geometry : angle 0.57608 (35862) SS BOND : bond 0.00404 ( 41) SS BOND : angle 1.51474 ( 82) hydrogen bonds : bond 0.05467 ( 757) hydrogen bonds : angle 5.43201 ( 2052) link_BETA1-4 : bond 0.00842 ( 8) link_BETA1-4 : angle 2.21096 ( 24) link_BETA1-6 : bond 0.01161 ( 1) link_BETA1-6 : angle 2.46428 ( 3) link_NAG-ASN : bond 0.00506 ( 41) link_NAG-ASN : angle 3.36209 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7415 (mm) cc_final: 0.6530 (tp) REVERT: A 189 LEU cc_start: 0.8319 (tp) cc_final: 0.7917 (mt) REVERT: A 274 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8529 (t) REVERT: A 380 TYR cc_start: 0.7322 (m-80) cc_final: 0.7113 (m-10) REVERT: A 392 PHE cc_start: 0.8143 (m-80) cc_final: 0.7856 (m-80) REVERT: A 490 PHE cc_start: 0.8607 (t80) cc_final: 0.8167 (t80) REVERT: B 374 PHE cc_start: 0.8405 (m-80) cc_final: 0.8153 (m-80) REVERT: B 396 TYR cc_start: 0.7762 (m-80) cc_final: 0.7246 (m-80) REVERT: C 140 PHE cc_start: 0.8372 (p90) cc_final: 0.7882 (p90) REVERT: C 354 ASN cc_start: 0.8450 (t0) cc_final: 0.8235 (t0) REVERT: C 1002 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8034 (mm-40) outliers start: 20 outliers final: 11 residues processed: 177 average time/residue: 0.1358 time to fit residues: 41.7474 Evaluate side-chains 156 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 259 optimal weight: 20.0000 chunk 308 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 135 optimal weight: 1.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.089947 restraints weight = 49263.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092807 restraints weight = 30314.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094657 restraints weight = 22270.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095900 restraints weight = 18300.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096652 restraints weight = 16219.225| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26447 Z= 0.177 Angle : 0.630 21.220 36094 Z= 0.309 Chirality : 0.047 0.457 4203 Planarity : 0.004 0.048 4584 Dihedral : 7.856 90.796 4481 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.18 % Allowed : 10.56 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 3167 helix: 1.64 (0.22), residues: 619 sheet: -1.71 (0.20), residues: 694 loop : -2.44 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.041 0.001 TYR C 505 PHE 0.023 0.001 PHE C 133 TRP 0.019 0.001 TRP B 886 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00427 (26356) covalent geometry : angle 0.59365 (35862) SS BOND : bond 0.00409 ( 41) SS BOND : angle 1.60151 ( 82) hydrogen bonds : bond 0.06074 ( 757) hydrogen bonds : angle 5.24956 ( 2052) link_BETA1-4 : bond 0.00790 ( 8) link_BETA1-4 : angle 2.17356 ( 24) link_BETA1-6 : bond 0.01581 ( 1) link_BETA1-6 : angle 2.05590 ( 3) link_NAG-ASN : bond 0.00499 ( 41) link_NAG-ASN : angle 3.31388 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.820 Fit side-chains REVERT: A 189 LEU cc_start: 0.8340 (tp) cc_final: 0.8015 (mt) REVERT: A 274 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8489 (t) REVERT: A 394 ASN cc_start: 0.5948 (t0) cc_final: 0.5562 (t0) REVERT: A 490 PHE cc_start: 0.8620 (t80) cc_final: 0.8157 (t80) REVERT: B 374 PHE cc_start: 0.8720 (m-80) cc_final: 0.8367 (m-80) REVERT: B 396 TYR cc_start: 0.7901 (m-80) cc_final: 0.7273 (m-80) REVERT: C 140 PHE cc_start: 0.8250 (p90) cc_final: 0.7777 (p90) REVERT: C 354 ASN cc_start: 0.8457 (t0) cc_final: 0.8153 (t0) REVERT: C 394 ASN cc_start: 0.8423 (m110) cc_final: 0.8130 (m110) REVERT: C 524 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6752 (p) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.1400 time to fit residues: 43.9769 Evaluate side-chains 155 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 263 optimal weight: 0.0470 chunk 173 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 281 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 291 optimal weight: 0.0980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093337 restraints weight = 48937.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095540 restraints weight = 33829.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096276 restraints weight = 23809.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096476 restraints weight = 22089.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096742 restraints weight = 20827.361| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26447 Z= 0.115 Angle : 0.591 21.019 36094 Z= 0.287 Chirality : 0.046 0.437 4203 Planarity : 0.003 0.050 4584 Dihedral : 7.323 90.658 4481 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 3167 helix: 1.85 (0.22), residues: 619 sheet: -1.47 (0.20), residues: 671 loop : -2.36 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.027 0.001 TYR C 473 PHE 0.018 0.001 PHE C 133 TRP 0.015 0.001 TRP B 886 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00262 (26356) covalent geometry : angle 0.55526 (35862) SS BOND : bond 0.00412 ( 41) SS BOND : angle 1.37307 ( 82) hydrogen bonds : bond 0.05027 ( 757) hydrogen bonds : angle 4.98534 ( 2052) link_BETA1-4 : bond 0.00840 ( 8) link_BETA1-4 : angle 2.26219 ( 24) link_BETA1-6 : bond 0.01112 ( 1) link_BETA1-6 : angle 1.35425 ( 3) link_NAG-ASN : bond 0.00507 ( 41) link_NAG-ASN : angle 3.22224 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7279 (mm) cc_final: 0.6304 (tp) REVERT: A 177 MET cc_start: 0.6289 (pmm) cc_final: 0.5880 (pmm) REVERT: A 189 LEU cc_start: 0.8396 (tp) cc_final: 0.8035 (mt) REVERT: A 394 ASN cc_start: 0.5962 (t0) cc_final: 0.5554 (t0) REVERT: A 490 PHE cc_start: 0.8633 (t80) cc_final: 0.8132 (t80) REVERT: B 374 PHE cc_start: 0.8464 (m-80) cc_final: 0.8197 (m-80) REVERT: B 396 TYR cc_start: 0.7594 (m-80) cc_final: 0.7074 (m-80) REVERT: C 140 PHE cc_start: 0.8362 (p90) cc_final: 0.7823 (p90) REVERT: C 354 ASN cc_start: 0.8442 (t0) cc_final: 0.8064 (t0) REVERT: C 394 ASN cc_start: 0.8490 (m110) cc_final: 0.8199 (m110) outliers start: 34 outliers final: 17 residues processed: 176 average time/residue: 0.1347 time to fit residues: 41.1811 Evaluate side-chains 161 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 159 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 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 66 HIS A 613 GLN A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092878 restraints weight = 49009.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095038 restraints weight = 32591.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095115 restraints weight = 22336.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095310 restraints weight = 22847.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095613 restraints weight = 21583.371| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26447 Z= 0.136 Angle : 0.597 20.912 36094 Z= 0.290 Chirality : 0.046 0.431 4203 Planarity : 0.003 0.046 4584 Dihedral : 6.837 87.076 4481 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.25 % Allowed : 13.16 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.15), residues: 3167 helix: 1.89 (0.22), residues: 613 sheet: -1.37 (0.20), residues: 674 loop : -2.35 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 408 TYR 0.031 0.001 TYR C 505 PHE 0.021 0.001 PHE C 347 TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00322 (26356) covalent geometry : angle 0.56236 (35862) SS BOND : bond 0.00410 ( 41) SS BOND : angle 1.34107 ( 82) hydrogen bonds : bond 0.05323 ( 757) hydrogen bonds : angle 4.90973 ( 2052) link_BETA1-4 : bond 0.00805 ( 8) link_BETA1-4 : angle 2.32803 ( 24) link_BETA1-6 : bond 0.00945 ( 1) link_BETA1-6 : angle 0.97815 ( 3) link_NAG-ASN : bond 0.00491 ( 41) link_NAG-ASN : angle 3.16699 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.699 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. REVERT: A 177 MET cc_start: 0.6219 (pmm) cc_final: 0.5909 (pmm) REVERT: A 189 LEU cc_start: 0.8435 (tp) cc_final: 0.8064 (mt) REVERT: A 394 ASN cc_start: 0.5982 (t0) cc_final: 0.5585 (t0) REVERT: A 490 PHE cc_start: 0.8720 (t80) cc_final: 0.8174 (t80) REVERT: B 117 LEU cc_start: 0.9117 (tp) cc_final: 0.8853 (tt) REVERT: B 374 PHE cc_start: 0.8478 (m-80) cc_final: 0.8198 (m-80) REVERT: B 396 TYR cc_start: 0.7615 (m-80) cc_final: 0.7088 (m-80) REVERT: C 140 PHE cc_start: 0.8401 (p90) cc_final: 0.7874 (p90) REVERT: C 354 ASN cc_start: 0.8448 (t0) cc_final: 0.8058 (t0) outliers start: 35 outliers final: 23 residues processed: 181 average time/residue: 0.1315 time to fit residues: 40.9528 Evaluate side-chains 167 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 308 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 208 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093098 restraints weight = 49295.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095208 restraints weight = 33276.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096117 restraints weight = 23806.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096035 restraints weight = 22576.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096378 restraints weight = 21132.940| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26447 Z= 0.116 Angle : 0.586 20.901 36094 Z= 0.282 Chirality : 0.045 0.419 4203 Planarity : 0.003 0.045 4584 Dihedral : 6.406 84.970 4481 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.32 % Allowed : 13.52 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 3167 helix: 1.93 (0.22), residues: 620 sheet: -1.21 (0.20), residues: 669 loop : -2.29 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.022 0.001 TYR A 453 PHE 0.020 0.001 PHE C 347 TRP 0.015 0.001 TRP C 258 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00270 (26356) covalent geometry : angle 0.55177 (35862) SS BOND : bond 0.00321 ( 41) SS BOND : angle 1.19956 ( 82) hydrogen bonds : bond 0.04884 ( 757) hydrogen bonds : angle 4.78409 ( 2052) link_BETA1-4 : bond 0.00832 ( 8) link_BETA1-4 : angle 2.44373 ( 24) link_BETA1-6 : bond 0.00833 ( 1) link_BETA1-6 : angle 0.94525 ( 3) link_NAG-ASN : bond 0.00492 ( 41) link_NAG-ASN : angle 3.11829 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.856 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. REVERT: A 189 LEU cc_start: 0.8411 (tp) cc_final: 0.8046 (mt) REVERT: A 394 ASN cc_start: 0.5909 (t0) cc_final: 0.5550 (t0) REVERT: A 490 PHE cc_start: 0.8713 (t80) cc_final: 0.8143 (t80) REVERT: B 117 LEU cc_start: 0.9002 (tp) cc_final: 0.8722 (tt) REVERT: B 374 PHE cc_start: 0.8559 (m-80) cc_final: 0.8332 (m-80) REVERT: B 396 TYR cc_start: 0.7579 (m-80) cc_final: 0.7076 (m-80) REVERT: C 140 PHE cc_start: 0.8379 (p90) cc_final: 0.7904 (p90) REVERT: C 354 ASN cc_start: 0.8476 (t0) cc_final: 0.8073 (t0) REVERT: C 394 ASN cc_start: 0.8541 (m110) cc_final: 0.8206 (m110) outliers start: 37 outliers final: 29 residues processed: 180 average time/residue: 0.1369 time to fit residues: 42.8575 Evaluate side-chains 176 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 228 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 319 optimal weight: 0.4980 chunk 315 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.139743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090771 restraints weight = 49547.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092876 restraints weight = 36404.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093522 restraints weight = 24665.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093647 restraints weight = 22182.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093912 restraints weight = 22310.620| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26447 Z= 0.174 Angle : 0.620 20.693 36094 Z= 0.303 Chirality : 0.046 0.427 4203 Planarity : 0.004 0.045 4584 Dihedral : 6.245 82.018 4481 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.50 % Allowed : 13.77 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.15), residues: 3167 helix: 1.76 (0.22), residues: 619 sheet: -1.30 (0.20), residues: 680 loop : -2.32 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.041 0.001 TYR C 505 PHE 0.022 0.001 PHE C 347 TRP 0.020 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00421 (26356) covalent geometry : angle 0.58753 (35862) SS BOND : bond 0.00444 ( 41) SS BOND : angle 1.39522 ( 82) hydrogen bonds : bond 0.05876 ( 757) hydrogen bonds : angle 4.91586 ( 2052) link_BETA1-4 : bond 0.00789 ( 8) link_BETA1-4 : angle 2.44059 ( 24) link_BETA1-6 : bond 0.00792 ( 1) link_BETA1-6 : angle 0.98739 ( 3) link_NAG-ASN : bond 0.00469 ( 41) link_NAG-ASN : angle 3.12128 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.818 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. REVERT: A 189 LEU cc_start: 0.8466 (tp) cc_final: 0.8098 (mt) REVERT: A 394 ASN cc_start: 0.5989 (t0) cc_final: 0.5575 (t0) REVERT: A 490 PHE cc_start: 0.8707 (t80) cc_final: 0.8121 (t80) REVERT: B 117 LEU cc_start: 0.8986 (tp) cc_final: 0.8771 (tt) REVERT: B 374 PHE cc_start: 0.8525 (m-80) cc_final: 0.8078 (m-80) REVERT: B 396 TYR cc_start: 0.7554 (m-80) cc_final: 0.7057 (m-80) REVERT: C 140 PHE cc_start: 0.8350 (p90) cc_final: 0.7914 (p90) REVERT: C 354 ASN cc_start: 0.8466 (t0) cc_final: 0.8057 (t0) REVERT: C 394 ASN cc_start: 0.8533 (m110) cc_final: 0.8192 (m110) outliers start: 42 outliers final: 34 residues processed: 181 average time/residue: 0.1362 time to fit residues: 42.7183 Evaluate side-chains 184 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 79 optimal weight: 0.6980 chunk 191 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 257 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092409 restraints weight = 49095.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096053 restraints weight = 32098.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096621 restraints weight = 22535.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097801 restraints weight = 18627.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097876 restraints weight = 18235.034| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26447 Z= 0.115 Angle : 0.587 20.501 36094 Z= 0.284 Chirality : 0.045 0.412 4203 Planarity : 0.003 0.045 4584 Dihedral : 6.074 81.686 4481 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.36 % Allowed : 14.23 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 3167 helix: 1.92 (0.22), residues: 620 sheet: -1.12 (0.20), residues: 656 loop : -2.23 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.029 0.001 TYR C 473 PHE 0.024 0.001 PHE C 347 TRP 0.018 0.001 TRP C 258 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00263 (26356) covalent geometry : angle 0.55459 (35862) SS BOND : bond 0.00361 ( 41) SS BOND : angle 1.19394 ( 82) hydrogen bonds : bond 0.04954 ( 757) hydrogen bonds : angle 4.74148 ( 2052) link_BETA1-4 : bond 0.00831 ( 8) link_BETA1-4 : angle 2.30121 ( 24) link_BETA1-6 : bond 0.00766 ( 1) link_BETA1-6 : angle 0.96512 ( 3) link_NAG-ASN : bond 0.00491 ( 41) link_NAG-ASN : angle 3.07335 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. REVERT: A 189 LEU cc_start: 0.8407 (tp) cc_final: 0.8109 (mt) REVERT: A 394 ASN cc_start: 0.5864 (t0) cc_final: 0.5511 (t0) REVERT: A 490 PHE cc_start: 0.8701 (t80) cc_final: 0.8096 (t80) REVERT: B 374 PHE cc_start: 0.8581 (m-80) cc_final: 0.8094 (m-80) REVERT: B 396 TYR cc_start: 0.7611 (m-80) cc_final: 0.7082 (m-80) REVERT: C 140 PHE cc_start: 0.8355 (p90) cc_final: 0.7920 (p90) REVERT: C 354 ASN cc_start: 0.8493 (t0) cc_final: 0.8094 (t0) REVERT: C 394 ASN cc_start: 0.8466 (m110) cc_final: 0.8148 (m110) outliers start: 38 outliers final: 32 residues processed: 184 average time/residue: 0.1316 time to fit residues: 42.3777 Evaluate side-chains 180 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 313 optimal weight: 0.0040 chunk 206 optimal weight: 0.0670 chunk 260 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 overall best weight: 0.6734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094083 restraints weight = 49090.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096205 restraints weight = 31518.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095820 restraints weight = 21751.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096186 restraints weight = 24572.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096392 restraints weight = 21959.551| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26447 Z= 0.124 Angle : 0.585 20.372 36094 Z= 0.285 Chirality : 0.045 0.406 4203 Planarity : 0.003 0.047 4584 Dihedral : 6.019 81.921 4481 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.25 % Allowed : 14.27 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 3167 helix: 1.96 (0.22), residues: 620 sheet: -1.07 (0.20), residues: 667 loop : -2.23 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 983 TYR 0.023 0.001 TYR C 473 PHE 0.015 0.001 PHE C 392 TRP 0.016 0.001 TRP C 258 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00290 (26356) covalent geometry : angle 0.55341 (35862) SS BOND : bond 0.00330 ( 41) SS BOND : angle 1.17696 ( 82) hydrogen bonds : bond 0.04984 ( 757) hydrogen bonds : angle 4.72132 ( 2052) link_BETA1-4 : bond 0.00828 ( 8) link_BETA1-4 : angle 2.19431 ( 24) link_BETA1-6 : bond 0.00672 ( 1) link_BETA1-6 : angle 1.16298 ( 3) link_NAG-ASN : bond 0.00486 ( 41) link_NAG-ASN : angle 3.03422 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. REVERT: A 189 LEU cc_start: 0.8433 (tp) cc_final: 0.8109 (mt) REVERT: A 394 ASN cc_start: 0.5841 (t0) cc_final: 0.5543 (t0) REVERT: A 490 PHE cc_start: 0.8682 (t80) cc_final: 0.8056 (t80) REVERT: B 374 PHE cc_start: 0.8444 (m-80) cc_final: 0.8009 (m-80) REVERT: B 396 TYR cc_start: 0.7510 (m-80) cc_final: 0.7037 (m-80) REVERT: C 140 PHE cc_start: 0.8278 (p90) cc_final: 0.7899 (p90) REVERT: C 354 ASN cc_start: 0.8440 (t0) cc_final: 0.8065 (t0) REVERT: C 394 ASN cc_start: 0.8492 (m110) cc_final: 0.8165 (m110) outliers start: 35 outliers final: 31 residues processed: 179 average time/residue: 0.1422 time to fit residues: 43.5550 Evaluate side-chains 179 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 134 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 207 optimal weight: 0.2980 chunk 244 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 343 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.139064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090081 restraints weight = 48764.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092587 restraints weight = 33338.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093403 restraints weight = 23205.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093786 restraints weight = 21503.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093988 restraints weight = 20648.373| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26447 Z= 0.204 Angle : 0.645 20.061 36094 Z= 0.317 Chirality : 0.046 0.415 4203 Planarity : 0.004 0.045 4584 Dihedral : 6.227 83.223 4481 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.53 % Allowed : 14.38 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3167 helix: 1.69 (0.22), residues: 619 sheet: -1.25 (0.20), residues: 695 loop : -2.28 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.044 0.001 TYR C 505 PHE 0.019 0.001 PHE A 86 TRP 0.020 0.002 TRP A 886 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00493 (26356) covalent geometry : angle 0.61565 (35862) SS BOND : bond 0.00386 ( 41) SS BOND : angle 1.52208 ( 82) hydrogen bonds : bond 0.06300 ( 757) hydrogen bonds : angle 4.97526 ( 2052) link_BETA1-4 : bond 0.00796 ( 8) link_BETA1-4 : angle 2.12528 ( 24) link_BETA1-6 : bond 0.00600 ( 1) link_BETA1-6 : angle 1.31521 ( 3) link_NAG-ASN : bond 0.00460 ( 41) link_NAG-ASN : angle 3.04253 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4335.45 seconds wall clock time: 75 minutes 36.67 seconds (4536.67 seconds total)