Starting phenix.real_space_refine on Sat May 24 02:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0p_42864/05_2025/8v0p_42864.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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 15898 2.51 5 N 4082 2.21 5 O 4831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24925 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8089 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8089 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8089 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 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: 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: "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: "L" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.31, per 1000 atoms: 0.53 Number of scatterers: 24925 At special positions: 0 Unit cell: (138.24, 132.84, 180.36, 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 4831 8.00 N 4082 7.00 C 15898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2, 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 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN C 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.8 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 44 sheets defined 24.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 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 383 through 387 removed outlier: 3.536A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.641A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.592A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.627A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.004A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.646A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.706A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.610A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.614A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.540A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1149 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.046A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.500A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.702A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.106A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.838A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.744A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.502A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.620A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.777A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.828A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.987A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.682A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.563A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.170A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.652A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.644A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.732A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.729A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 4.084A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.187A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.245A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.039A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.632A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.114A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.068A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 31 removed outlier: 7.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.022A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.046A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.509A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.507A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.612A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.616A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.440A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.995A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.819A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.117A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.643A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.613A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.943A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.037A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.748A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.898A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.189A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.496A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 902 hydrogen bonds defined for protein. 2502 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: 9.29 Time building geometry restraints manager: 6.40 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: 7906 1.35 - 1.47: 6599 1.47 - 1.60: 10830 1.60 - 1.73: 1 1.73 - 1.85: 141 Bond restraints: 25477 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CB PRO C 337 " pdb=" CG PRO C 337 " ideal model delta sigma weight residual 1.492 1.674 -0.182 5.00e-02 4.00e+02 1.33e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 25472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 34251 2.91 - 5.83: 344 5.83 - 8.74: 38 8.74 - 11.65: 9 11.65 - 14.57: 4 Bond angle restraints: 34646 Sorted by residual: angle pdb=" CA PRO C 337 " pdb=" N PRO C 337 " pdb=" CD PRO C 337 " ideal model delta sigma weight residual 112.00 97.82 14.18 1.40e+00 5.10e-01 1.03e+02 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 122.82 131.12 -8.30 1.42e+00 4.96e-01 3.42e+01 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C ASN A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 122.82 129.47 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" N PRO C 337 " pdb=" CD PRO C 337 " pdb=" CG PRO C 337 " ideal model delta sigma weight residual 103.20 96.25 6.95 1.50e+00 4.44e-01 2.14e+01 ... (remaining 34641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 14748 23.39 - 46.77: 891 46.77 - 70.15: 131 70.15 - 93.54: 25 93.54 - 116.92: 3 Dihedral angle restraints: 15798 sinusoidal: 6747 harmonic: 9051 Sorted by residual: 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 93.00 7.13 85.87 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -6.18 -79.82 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -15.79 -70.21 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 15795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3503 0.081 - 0.162: 539 0.162 - 0.243: 25 0.243 - 0.325: 4 0.325 - 0.406: 7 Chirality restraints: 4078 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 4075 not shown) Planarity restraints: 4450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 808 " 0.065 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 809 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 809 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 809 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.069 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO C 337 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 193 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C VAL B 193 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 193 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE B 194 " 0.021 2.00e-02 2.50e+03 ... (remaining 4447 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6862 2.82 - 3.34: 20059 3.34 - 3.86: 39596 3.86 - 4.38: 43452 4.38 - 4.90: 79043 Nonbonded interactions: 189012 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.294 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.298 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.304 3.040 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.323 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.323 3.040 ... (remaining 189007 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' selection = (chain 'B' and (resid 24 through 1149 or resid 1301 through 1308)) selection = (chain 'C' and (resid 24 through 1149 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.880 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.005 0.182 25565 Z= 0.227 Angle : 0.815 14.568 34865 Z= 0.421 Chirality : 0.055 0.406 4078 Planarity : 0.006 0.100 4412 Dihedral : 14.494 116.925 9855 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3063 helix: -0.41 (0.18), residues: 670 sheet: 0.14 (0.20), residues: 613 loop : -1.80 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 104 HIS 0.003 0.001 HIS C 519 PHE 0.039 0.002 PHE B 106 TYR 0.047 0.002 TYR B 453 ARG 0.009 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 38) link_NAG-ASN : angle 3.15321 ( 114) link_BETA1-4 : bond 0.00702 ( 9) link_BETA1-4 : angle 1.80165 ( 27) hydrogen bonds : bond 0.15604 ( 898) hydrogen bonds : angle 7.08871 ( 2502) SS BOND : bond 0.00526 ( 39) SS BOND : angle 1.72477 ( 78) covalent geometry : bond 0.00477 (25477) covalent geometry : angle 0.79144 (34646) Misc. bond : bond 0.00224 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 2.542 Fit side-chains revert: symmetry clash REVERT: B 884 SER cc_start: 0.8863 (m) cc_final: 0.8598 (m) REVERT: C 403 ARG cc_start: 0.6857 (mtp-110) cc_final: 0.6174 (ttm170) REVERT: C 507 PRO cc_start: 0.3865 (Cg_exo) cc_final: 0.3567 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3190 time to fit residues: 123.8438 Evaluate side-chains 174 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.7980 chunk 234 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 280 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: A 422 ASN A 564 GLN B 173 GLN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141498 restraints weight = 31890.793| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.16 r_work: 0.3181 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25565 Z= 0.117 Angle : 0.551 10.272 34865 Z= 0.276 Chirality : 0.045 0.389 4078 Planarity : 0.004 0.062 4412 Dihedral : 8.139 102.102 4311 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.52 % Allowed : 6.00 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3063 helix: 1.22 (0.20), residues: 677 sheet: 0.27 (0.21), residues: 583 loop : -1.57 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.004 0.001 HIS C 519 PHE 0.019 0.001 PHE B 92 TYR 0.019 0.001 TYR B 170 ARG 0.006 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 38) link_NAG-ASN : angle 2.37277 ( 114) link_BETA1-4 : bond 0.00225 ( 9) link_BETA1-4 : angle 1.16903 ( 27) hydrogen bonds : bond 0.04730 ( 898) hydrogen bonds : angle 5.30584 ( 2502) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.49712 ( 78) covalent geometry : bond 0.00275 (25477) covalent geometry : angle 0.52973 (34646) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 2.611 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.7987 (pt) cc_final: 0.7744 (pt) REVERT: A 423 TYR cc_start: 0.6028 (t80) cc_final: 0.5811 (t80) REVERT: B 740 MET cc_start: 0.8202 (mtp) cc_final: 0.7976 (ttt) REVERT: C 461 LEU cc_start: 0.7834 (tp) cc_final: 0.7590 (tp) REVERT: C 507 PRO cc_start: 0.4402 (Cg_exo) cc_final: 0.4071 (Cg_endo) outliers start: 14 outliers final: 11 residues processed: 211 average time/residue: 0.3242 time to fit residues: 113.3703 Evaluate side-chains 193 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 50.0000 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 275 optimal weight: 0.5980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 926 GLN B 314 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 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 = 0.4098 r_free = 0.4098 target = 0.183468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140587 restraints weight = 31632.144| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.31 r_work: 0.3184 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25565 Z= 0.108 Angle : 0.519 9.689 34865 Z= 0.258 Chirality : 0.044 0.375 4078 Planarity : 0.004 0.043 4412 Dihedral : 7.449 91.716 4311 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.56 % Allowed : 8.70 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3063 helix: 1.84 (0.21), residues: 680 sheet: 0.27 (0.21), residues: 593 loop : -1.47 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.006 0.001 HIS C 519 PHE 0.023 0.001 PHE C 429 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 38) link_NAG-ASN : angle 2.29527 ( 114) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 1.08227 ( 27) hydrogen bonds : bond 0.04343 ( 898) hydrogen bonds : angle 4.94550 ( 2502) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.38855 ( 78) covalent geometry : bond 0.00251 (25477) covalent geometry : angle 0.49863 (34646) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 2.416 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.7845 (pt) cc_final: 0.7624 (pt) REVERT: B 740 MET cc_start: 0.8259 (mtp) cc_final: 0.8007 (ttt) REVERT: B 870 ILE cc_start: 0.8976 (mm) cc_final: 0.8699 (mt) REVERT: C 220 PHE cc_start: 0.7086 (m-80) cc_final: 0.6611 (m-80) outliers start: 15 outliers final: 14 residues processed: 216 average time/residue: 0.3445 time to fit residues: 124.2024 Evaluate side-chains 202 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 257 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 142 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 564 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.182705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140482 restraints weight = 32000.697| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 4.24 r_work: 0.3163 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25565 Z= 0.108 Angle : 0.513 9.677 34865 Z= 0.254 Chirality : 0.044 0.365 4078 Planarity : 0.003 0.037 4412 Dihedral : 7.030 80.037 4311 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.15 % Allowed : 10.48 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3063 helix: 2.06 (0.21), residues: 682 sheet: 0.28 (0.21), residues: 583 loop : -1.39 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.022 0.001 PHE C1148 TYR 0.022 0.001 TYR B 170 ARG 0.002 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 38) link_NAG-ASN : angle 2.25744 ( 114) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 1.01733 ( 27) hydrogen bonds : bond 0.04227 ( 898) hydrogen bonds : angle 4.80210 ( 2502) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.34389 ( 78) covalent geometry : bond 0.00253 (25477) covalent geometry : angle 0.49266 (34646) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8458 (m-10) cc_final: 0.8110 (m-80) REVERT: A 402 ILE cc_start: 0.7920 (pt) cc_final: 0.7700 (pt) REVERT: A 403 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7378 (ttm-80) REVERT: B 740 MET cc_start: 0.8367 (mtp) cc_final: 0.8098 (ttt) REVERT: B 780 GLU cc_start: 0.8409 (tt0) cc_final: 0.8149 (tt0) REVERT: C 190 ARG cc_start: 0.7290 (ttt180) cc_final: 0.7064 (ttt180) REVERT: C 220 PHE cc_start: 0.7140 (m-80) cc_final: 0.6679 (m-80) REVERT: C 434 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6801 (mp) REVERT: C 517 LEU cc_start: 0.7716 (mm) cc_final: 0.7490 (mt) outliers start: 31 outliers final: 23 residues processed: 228 average time/residue: 0.3160 time to fit residues: 118.4569 Evaluate side-chains 216 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 216 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126172 restraints weight = 31850.950| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.22 r_work: 0.3231 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25565 Z= 0.130 Angle : 0.528 9.660 34865 Z= 0.262 Chirality : 0.044 0.358 4078 Planarity : 0.003 0.037 4412 Dihedral : 6.849 64.693 4311 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.11 % Allowed : 11.22 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3063 helix: 2.05 (0.21), residues: 687 sheet: 0.31 (0.21), residues: 553 loop : -1.35 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.019 0.001 PHE C 201 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 38) link_NAG-ASN : angle 2.34211 ( 114) link_BETA1-4 : bond 0.00330 ( 9) link_BETA1-4 : angle 1.03973 ( 27) hydrogen bonds : bond 0.04565 ( 898) hydrogen bonds : angle 4.81403 ( 2502) SS BOND : bond 0.00373 ( 39) SS BOND : angle 1.62663 ( 78) covalent geometry : bond 0.00316 (25477) covalent geometry : angle 0.50518 (34646) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7852 (t80) cc_final: 0.7602 (t80) REVERT: A 237 ARG cc_start: 0.6014 (ttp-170) cc_final: 0.5678 (ttp-170) REVERT: A 269 TYR cc_start: 0.8523 (m-10) cc_final: 0.8279 (m-80) REVERT: A 402 ILE cc_start: 0.7866 (pt) cc_final: 0.7625 (pt) REVERT: A 403 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7459 (ttm-80) REVERT: B 429 PHE cc_start: 0.7623 (t80) cc_final: 0.7303 (t80) REVERT: B 740 MET cc_start: 0.8473 (mtp) cc_final: 0.8154 (ttt) REVERT: C 220 PHE cc_start: 0.7174 (m-80) cc_final: 0.6732 (m-80) REVERT: C 507 PRO cc_start: 0.4541 (Cg_exo) cc_final: 0.3972 (Cg_endo) REVERT: C 816 SER cc_start: 0.8770 (m) cc_final: 0.8542 (m) outliers start: 30 outliers final: 24 residues processed: 214 average time/residue: 0.3109 time to fit residues: 111.1424 Evaluate side-chains 205 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 168 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 278 optimal weight: 0.1980 chunk 180 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 207 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 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 = 0.4061 r_free = 0.4061 target = 0.179782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132114 restraints weight = 31968.996| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.19 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25565 Z= 0.146 Angle : 0.540 9.796 34865 Z= 0.269 Chirality : 0.045 0.350 4078 Planarity : 0.003 0.037 4412 Dihedral : 6.694 59.932 4311 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.48 % Allowed : 11.93 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3063 helix: 2.11 (0.21), residues: 677 sheet: 0.23 (0.20), residues: 644 loop : -1.39 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.015 0.001 PHE B 377 TYR 0.025 0.001 TYR B 170 ARG 0.003 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 38) link_NAG-ASN : angle 2.42070 ( 114) link_BETA1-4 : bond 0.00291 ( 9) link_BETA1-4 : angle 1.00596 ( 27) hydrogen bonds : bond 0.04777 ( 898) hydrogen bonds : angle 4.81908 ( 2502) SS BOND : bond 0.00394 ( 39) SS BOND : angle 1.75511 ( 78) covalent geometry : bond 0.00358 (25477) covalent geometry : angle 0.51651 (34646) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6287 (ttp-170) cc_final: 0.5931 (ttp-170) REVERT: A 269 TYR cc_start: 0.8608 (m-10) cc_final: 0.8402 (m-80) REVERT: A 403 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7698 (ttm-80) REVERT: A 539 VAL cc_start: 0.8249 (m) cc_final: 0.7989 (m) REVERT: B 429 PHE cc_start: 0.7770 (t80) cc_final: 0.7411 (t80) REVERT: B 740 MET cc_start: 0.8416 (mtp) cc_final: 0.8119 (ttt) REVERT: C 220 PHE cc_start: 0.7251 (m-80) cc_final: 0.6868 (m-80) REVERT: C 507 PRO cc_start: 0.4417 (Cg_exo) cc_final: 0.4104 (Cg_endo) outliers start: 40 outliers final: 30 residues processed: 226 average time/residue: 0.3059 time to fit residues: 115.8979 Evaluate side-chains 215 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 48 optimal weight: 4.9990 chunk 176 optimal weight: 0.0040 chunk 82 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 564 GLN B 207 HIS B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.181970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139036 restraints weight = 31981.893| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 4.31 r_work: 0.3166 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25565 Z= 0.095 Angle : 0.507 9.565 34865 Z= 0.251 Chirality : 0.044 0.350 4078 Planarity : 0.003 0.036 4412 Dihedral : 6.480 58.079 4311 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.37 % Allowed : 12.52 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3063 helix: 2.28 (0.21), residues: 681 sheet: 0.33 (0.21), residues: 588 loop : -1.33 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.010 0.001 HIS A 519 PHE 0.032 0.001 PHE A 168 TYR 0.017 0.001 TYR A1067 ARG 0.001 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 38) link_NAG-ASN : angle 2.35340 ( 114) link_BETA1-4 : bond 0.00346 ( 9) link_BETA1-4 : angle 1.00037 ( 27) hydrogen bonds : bond 0.04128 ( 898) hydrogen bonds : angle 4.67852 ( 2502) SS BOND : bond 0.00316 ( 39) SS BOND : angle 1.42069 ( 78) covalent geometry : bond 0.00216 (25477) covalent geometry : angle 0.48449 (34646) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6154 (ttp-170) cc_final: 0.5838 (ttp-170) REVERT: A 317 ASN cc_start: 0.7903 (m-40) cc_final: 0.7428 (m-40) REVERT: A 403 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7676 (ttm-80) REVERT: A 539 VAL cc_start: 0.8145 (m) cc_final: 0.7887 (m) REVERT: A 584 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 429 PHE cc_start: 0.7672 (t80) cc_final: 0.7347 (t80) REVERT: B 870 ILE cc_start: 0.8991 (mm) cc_final: 0.8736 (mt) REVERT: C 220 PHE cc_start: 0.7179 (m-80) cc_final: 0.6796 (m-80) REVERT: C 403 ARG cc_start: 0.6491 (mtp-110) cc_final: 0.6092 (ttp80) REVERT: C 434 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6775 (mp) REVERT: C 507 PRO cc_start: 0.4255 (Cg_exo) cc_final: 0.3951 (Cg_endo) outliers start: 37 outliers final: 22 residues processed: 221 average time/residue: 0.3254 time to fit residues: 120.5892 Evaluate side-chains 204 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 564 GLN B 207 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 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 = 0.4075 r_free = 0.4075 target = 0.181002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138412 restraints weight = 31793.857| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.35 r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25565 Z= 0.113 Angle : 0.516 9.409 34865 Z= 0.255 Chirality : 0.044 0.350 4078 Planarity : 0.003 0.037 4412 Dihedral : 6.427 58.921 4311 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.33 % Allowed : 13.00 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3063 helix: 2.26 (0.21), residues: 681 sheet: 0.23 (0.20), residues: 602 loop : -1.26 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.009 0.001 HIS C 519 PHE 0.017 0.001 PHE B 106 TYR 0.021 0.001 TYR A 453 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 38) link_NAG-ASN : angle 2.34978 ( 114) link_BETA1-4 : bond 0.00338 ( 9) link_BETA1-4 : angle 1.00911 ( 27) hydrogen bonds : bond 0.04269 ( 898) hydrogen bonds : angle 4.67091 ( 2502) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.49414 ( 78) covalent geometry : bond 0.00270 (25477) covalent geometry : angle 0.49378 (34646) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6183 (ttp-170) cc_final: 0.5870 (ttp-170) REVERT: A 317 ASN cc_start: 0.7920 (m-40) cc_final: 0.7475 (m-40) REVERT: A 539 VAL cc_start: 0.8145 (m) cc_final: 0.7887 (m) REVERT: A 739 THR cc_start: 0.8706 (m) cc_final: 0.8482 (p) REVERT: B 429 PHE cc_start: 0.7653 (t80) cc_final: 0.7291 (t80) REVERT: B 870 ILE cc_start: 0.8993 (mm) cc_final: 0.8727 (mt) REVERT: C 220 PHE cc_start: 0.7166 (m-80) cc_final: 0.6787 (m-80) REVERT: C 434 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6716 (mp) REVERT: C 507 PRO cc_start: 0.4224 (Cg_exo) cc_final: 0.3901 (Cg_endo) outliers start: 36 outliers final: 25 residues processed: 213 average time/residue: 0.3142 time to fit residues: 111.6205 Evaluate side-chains 208 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 294 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 289 optimal weight: 0.0980 chunk 124 optimal weight: 0.0980 chunk 163 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 564 GLN A 901 GLN B 207 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133043 restraints weight = 31967.052| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.10 r_work: 0.3317 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25565 Z= 0.111 Angle : 0.519 10.686 34865 Z= 0.256 Chirality : 0.044 0.348 4078 Planarity : 0.003 0.036 4412 Dihedral : 6.395 58.649 4311 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.44 % Allowed : 12.96 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3063 helix: 2.29 (0.21), residues: 681 sheet: 0.31 (0.21), residues: 592 loop : -1.27 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.017 0.001 HIS B 207 PHE 0.024 0.001 PHE C 201 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 38) link_NAG-ASN : angle 2.34588 ( 114) link_BETA1-4 : bond 0.00332 ( 9) link_BETA1-4 : angle 1.00667 ( 27) hydrogen bonds : bond 0.04223 ( 898) hydrogen bonds : angle 4.65786 ( 2502) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.48867 ( 78) covalent geometry : bond 0.00264 (25477) covalent geometry : angle 0.49762 (34646) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6259 (ttp-170) cc_final: 0.5971 (ttp-170) REVERT: A 317 ASN cc_start: 0.7866 (m-40) cc_final: 0.7434 (m-40) REVERT: A 403 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7611 (ttm-80) REVERT: A 539 VAL cc_start: 0.8172 (m) cc_final: 0.7905 (m) REVERT: A 584 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 390 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6932 (pt) REVERT: B 429 PHE cc_start: 0.7785 (t80) cc_final: 0.7431 (t80) REVERT: B 870 ILE cc_start: 0.9002 (mm) cc_final: 0.8741 (mt) REVERT: C 220 PHE cc_start: 0.7198 (m-80) cc_final: 0.6862 (m-80) REVERT: C 434 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6869 (mp) REVERT: C 507 PRO cc_start: 0.4336 (Cg_exo) cc_final: 0.4021 (Cg_endo) outliers start: 39 outliers final: 30 residues processed: 214 average time/residue: 0.3169 time to fit residues: 113.8802 Evaluate side-chains 209 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN B 493 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 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 = 0.4064 r_free = 0.4064 target = 0.179934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137425 restraints weight = 31841.496| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.50 r_work: 0.3131 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25565 Z= 0.132 Angle : 0.532 11.709 34865 Z= 0.263 Chirality : 0.044 0.346 4078 Planarity : 0.003 0.039 4412 Dihedral : 6.416 59.149 4311 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.33 % Allowed : 13.11 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3063 helix: 2.26 (0.21), residues: 677 sheet: 0.25 (0.20), residues: 644 loop : -1.27 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.010 0.001 HIS A 207 PHE 0.018 0.001 PHE B 106 TYR 0.020 0.001 TYR A 453 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 38) link_NAG-ASN : angle 2.37294 ( 114) link_BETA1-4 : bond 0.00307 ( 9) link_BETA1-4 : angle 0.99448 ( 27) hydrogen bonds : bond 0.04454 ( 898) hydrogen bonds : angle 4.68834 ( 2502) SS BOND : bond 0.00368 ( 39) SS BOND : angle 1.57504 ( 78) covalent geometry : bond 0.00320 (25477) covalent geometry : angle 0.51014 (34646) Misc. bond : bond 0.00059 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6238 (ttp-170) cc_final: 0.5924 (ttp-170) REVERT: A 317 ASN cc_start: 0.7931 (m-40) cc_final: 0.7487 (m-40) REVERT: A 403 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7489 (ttm-80) REVERT: A 539 VAL cc_start: 0.8163 (m) cc_final: 0.7905 (m) REVERT: A 584 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 390 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6790 (pt) REVERT: B 429 PHE cc_start: 0.7748 (t80) cc_final: 0.7361 (t80) REVERT: B 870 ILE cc_start: 0.9018 (mm) cc_final: 0.8736 (mt) REVERT: C 220 PHE cc_start: 0.7211 (m-80) cc_final: 0.6875 (m-80) REVERT: C 507 PRO cc_start: 0.4196 (Cg_exo) cc_final: 0.3793 (Cg_endo) REVERT: C 508 TYR cc_start: 0.7719 (m-80) cc_final: 0.7151 (m-80) outliers start: 36 outliers final: 28 residues processed: 210 average time/residue: 0.3151 time to fit residues: 110.9795 Evaluate side-chains 207 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 171 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 245 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 493 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139740 restraints weight = 31828.278| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.50 r_work: 0.3149 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25565 Z= 0.104 Angle : 0.515 11.808 34865 Z= 0.253 Chirality : 0.044 0.346 4078 Planarity : 0.003 0.038 4412 Dihedral : 6.313 58.216 4311 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.11 % Allowed : 13.63 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3063 helix: 2.36 (0.21), residues: 682 sheet: 0.35 (0.21), residues: 592 loop : -1.24 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 PHE 0.020 0.001 PHE C 201 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 38) link_NAG-ASN : angle 2.33347 ( 114) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 0.94678 ( 27) hydrogen bonds : bond 0.04094 ( 898) hydrogen bonds : angle 4.60917 ( 2502) SS BOND : bond 0.00329 ( 39) SS BOND : angle 1.41810 ( 78) covalent geometry : bond 0.00242 (25477) covalent geometry : angle 0.49354 (34646) Misc. bond : bond 0.00051 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11979.19 seconds wall clock time: 208 minutes 22.10 seconds (12502.10 seconds total)