Starting phenix.real_space_refine on Sun May 25 02:30:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578.map" model { file = "/net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p9y_17578/05_2025/8p9y_17578_neut.cif" } resolution = 4.3 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= 0.022 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: 5 Type Number sf(0) Gaussians S 117 5.16 5 Na 3 4.78 5 C 16518 2.51 5 N 4256 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25937 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8425 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 1025} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8426 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 54, 'TRANS': 1026} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8374 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 54, 'TRANS': 1021} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 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: "M" 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 128 Unusual residues: {' NA': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 178 Unusual residues: {' NA': 1, 'NAG': 6, 'XIO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA A1310 " occ=0.00 residue: pdb="NA NA A1311 " occ=0.00 residue: pdb=" C02 XIO C1307 " occ=0.00 ... (91 atoms not shown) pdb=" S76 XIO C1307 " occ=0.00 residue: pdb="NA NA C1308 " occ=0.00 Time building chain proxies: 17.29, per 1000 atoms: 0.67 Number of scatterers: 25937 At special positions: 0 Unit cell: (149.625, 161.595, 174.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 Na 3 11.00 O 5043 8.00 N 4256 7.00 C 16518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.78 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.97 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.08 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.05 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.95 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.97 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.07 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.00 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.91 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.82 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.79 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.82 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.88 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.93 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 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=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.97 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25659 O5 NAG B1302 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, 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 M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 164 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 616 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 343 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 282 " " NAG M 1 " - " ASN C 343 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 3.3 seconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.9% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.738A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.514A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.589A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.460A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.960A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 829 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.562A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.026A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.505A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.039A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1031 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.919A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.522A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.876A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.544A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.590A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.017A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 830 removed outlier: 3.596A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.723A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.905A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.503A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.860A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.620A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.781A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.153A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.673A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.615A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 4.001A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.823A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.927A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.596A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.222A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.996A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.634A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.215A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.504A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.960A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.530A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 121 removed outlier: 12.312A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 12.803A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.751A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.655A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.684A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.404A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.565A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.587A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.052A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.570A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.153A 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: 3.775A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.487A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.535A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.415A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.193A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 554 removed outlier: 3.702A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.538A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.805A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.929A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.147A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 6.460A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.773A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.568A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.121A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.702A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.095A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.894A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.894A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.671A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2436 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: 12.21 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.08: 3 1.08 - 1.29: 4207 1.29 - 1.49: 11614 1.49 - 1.70: 10562 1.70 - 1.90: 150 Bond restraints: 26536 Sorted by residual: bond pdb=" C SER B 940 " pdb=" O SER B 940 " ideal model delta sigma weight residual 1.237 0.880 0.356 1.19e-02 7.06e+03 8.97e+02 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.236 0.943 0.293 1.31e-02 5.83e+03 5.00e+02 bond pdb=" C CYS B 617 " pdb=" O CYS B 617 " ideal model delta sigma weight residual 1.236 1.089 0.147 1.25e-02 6.40e+03 1.38e+02 bond pdb=" C CYS A 617 " pdb=" O CYS A 617 " ideal model delta sigma weight residual 1.236 1.376 -0.140 1.25e-02 6.40e+03 1.25e+02 bond pdb=" C THR C 676 " pdb=" O THR C 676 " ideal model delta sigma weight residual 1.231 1.007 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 26531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 35333 4.16 - 8.32: 721 8.32 - 12.48: 61 12.48 - 16.63: 20 16.63 - 20.79: 4 Bond angle restraints: 36139 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.56 140.35 -20.79 1.02e+00 9.61e-01 4.16e+02 angle pdb=" O PHE B 515 " pdb=" C PHE B 515 " pdb=" N GLU B 516 " ideal model delta sigma weight residual 122.59 104.84 17.75 1.33e+00 5.65e-01 1.78e+02 angle pdb=" CA ASP A1146 " pdb=" C ASP A1146 " pdb=" O ASP A1146 " ideal model delta sigma weight residual 120.80 101.37 19.43 1.70e+00 3.46e-01 1.31e+02 angle pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" O CYS B 617 " ideal model delta sigma weight residual 120.10 107.69 12.41 1.13e+00 7.83e-01 1.21e+02 angle pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" O CYS A 617 " ideal model delta sigma weight residual 120.10 107.90 12.20 1.13e+00 7.83e-01 1.17e+02 ... (remaining 36134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 15332 24.14 - 48.27: 875 48.27 - 72.41: 129 72.41 - 96.55: 24 96.55 - 120.68: 2 Dihedral angle restraints: 16362 sinusoidal: 6941 harmonic: 9421 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.13 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 13.00 80.00 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C VAL C 826 " pdb=" N VAL C 826 " pdb=" CA VAL C 826 " pdb=" CB VAL C 826 " ideal model delta harmonic sigma weight residual -122.00 -142.56 20.56 0 2.50e+00 1.60e-01 6.77e+01 ... (remaining 16359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.633: 4201 0.633 - 1.266: 3 1.266 - 1.899: 0 1.899 - 2.532: 2 2.532 - 3.165: 2 Chirality restraints: 4208 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 164 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 0.77 -3.17 2.00e-01 2.50e+01 2.50e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 0.50 -2.90 2.00e-01 2.50e+01 2.10e+02 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.40 -2.00 2.00e-01 2.50e+01 1.00e+02 ... (remaining 4205 not shown) Planarity restraints: 4661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C73 XIO C1307 " -0.031 2.00e-02 2.50e+03 1.39e-01 5.35e+02 pdb=" C74 XIO C1307 " -0.072 2.00e-02 2.50e+03 pdb=" C75 XIO C1307 " -0.040 2.00e-02 2.50e+03 pdb=" C87 XIO C1307 " -0.183 2.00e-02 2.50e+03 pdb=" C88 XIO C1307 " -0.162 2.00e-02 2.50e+03 pdb=" C89 XIO C1307 " 0.013 2.00e-02 2.50e+03 pdb=" C90 XIO C1307 " 0.168 2.00e-02 2.50e+03 pdb=" C91 XIO C1307 " 0.149 2.00e-02 2.50e+03 pdb=" C92 XIO C1307 " -0.024 2.00e-02 2.50e+03 pdb=" N86 XIO C1307 " -0.108 2.00e-02 2.50e+03 pdb=" S76 XIO C1307 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 XIO C1307 " -0.046 2.00e-02 2.50e+03 1.69e-01 3.57e+02 pdb=" C03 XIO C1307 " 0.145 2.00e-02 2.50e+03 pdb=" C72 XIO C1307 " 0.211 2.00e-02 2.50e+03 pdb=" N71 XIO C1307 " -0.270 2.00e-02 2.50e+03 pdb=" O01 XIO C1307 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 XIO C1307 " 0.131 2.00e-02 2.50e+03 1.56e-01 3.05e+02 pdb=" C43 XIO C1307 " -0.029 2.00e-02 2.50e+03 pdb=" C45 XIO C1307 " 0.195 2.00e-02 2.50e+03 pdb=" N44 XIO C1307 " -0.253 2.00e-02 2.50e+03 pdb=" O70 XIO C1307 " -0.044 2.00e-02 2.50e+03 ... (remaining 4658 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 20 1.87 - 2.63: 727 2.63 - 3.38: 36018 3.38 - 4.14: 61197 4.14 - 4.90: 105027 Nonbonded interactions: 202989 Sorted by model distance: nonbonded pdb=" CG ARG B 328 " pdb=" CB ASP B 578 " model vdw 1.112 3.840 nonbonded pdb=" NH2 ARG C 328 " pdb=" OG1 THR C 581 " model vdw 1.374 3.120 nonbonded pdb=" CZ3 TRP C 353 " pdb=" CD1 TYR C 423 " model vdw 1.521 3.640 nonbonded pdb=" NE ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 1.549 3.120 nonbonded pdb=" O ASP C 420 " pdb=" OD1 ASN C 460 " model vdw 1.616 3.040 ... (remaining 202984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 579 or (resid 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name CB or name SG )) or resid 618 throug \ h 621 or resid 641 through 939 or (resid 940 through 944 and (name N or name CA \ or name C or name O or name CB )) or resid 945 through 1146 or resid 1301 throug \ h 1306)) selection = (chain 'B' and (resid 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 616 or (resid 617 and (name N o \ r name CA or name C or name CB or name SG )) or resid 618 through 621 or resid 6 \ 41 through 829 or resid 854 through 939 or (resid 940 through 944 and (name N or \ name CA or name C or name O or name CB )) or resid 945 through 1146 or resid 13 \ 01 through 1306)) selection = (chain 'C' and (resid 15 through 579 or (resid 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 829 or resid 854 through 1146 o \ r resid 1301 through 1306)) } 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' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.220 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 62.590 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 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 : 0.018 0.943 26624 Z= 1.042 Angle : 1.738 43.734 36353 Z= 1.009 Chirality : 0.122 3.165 4208 Planarity : 0.009 0.169 4627 Dihedral : 14.416 120.683 10183 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 59.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.99 % Favored : 95.48 % Rotamer: Outliers : 7.52 % Allowed : 10.77 % Favored : 81.70 % Cbeta Deviations : 0.26 % 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: -0.03 (0.14), residues: 3207 helix: 2.50 (0.20), residues: 647 sheet: 0.26 (0.21), residues: 616 loop : -1.05 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP A 64 HIS 0.023 0.003 HIS B 245 PHE 0.049 0.006 PHE B 464 TYR 0.050 0.005 TYR A 266 ARG 0.036 0.003 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.04276 ( 34) link_NAG-ASN : angle 12.20058 ( 102) link_BETA1-4 : bond 0.00175 ( 10) link_BETA1-4 : angle 2.07411 ( 30) hydrogen bonds : bond 0.27868 ( 873) hydrogen bonds : angle 9.59373 ( 2436) SS BOND : bond 0.34551 ( 41) SS BOND : angle 11.05693 ( 82) covalent geometry : bond 0.01192 (26536) covalent geometry : angle 1.52864 (36139) Misc. bond : bond 0.20283 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 836 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 56 LEU cc_start: 0.8376 (tp) cc_final: 0.8147 (mt) REVERT: A 57 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.7842 (Cg_endo) REVERT: A 80 ASP cc_start: 0.8130 (t0) cc_final: 0.7835 (t70) REVERT: A 224 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8375 (pm20) REVERT: A 266 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: A 287 ASP cc_start: 0.7376 (t0) cc_final: 0.6892 (t0) REVERT: A 358 ILE cc_start: 0.7708 (mt) cc_final: 0.7053 (tp) REVERT: A 544 ASN cc_start: 0.7902 (m-40) cc_final: 0.7426 (p0) REVERT: A 732 THR cc_start: 0.8109 (p) cc_final: 0.7493 (t) REVERT: A 733 LYS cc_start: 0.8600 (mttt) cc_final: 0.7989 (mttm) REVERT: A 778 THR cc_start: 0.8196 (m) cc_final: 0.7939 (p) REVERT: A 788 ILE cc_start: 0.8117 (mm) cc_final: 0.7856 (mm) REVERT: A 866 THR cc_start: 0.5962 (p) cc_final: 0.5260 (m) REVERT: A 877 LEU cc_start: 0.8666 (mt) cc_final: 0.8291 (mm) REVERT: A 878 LEU cc_start: 0.8403 (tt) cc_final: 0.8145 (tt) REVERT: A 905 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7853 (mmm-85) REVERT: A 921 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7597 (tptp) REVERT: A 926 GLN cc_start: 0.8414 (mt0) cc_final: 0.7744 (mt0) REVERT: A 954 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6959 (tp-100) REVERT: A 957 GLN cc_start: 0.8503 (tt0) cc_final: 0.8105 (tm-30) REVERT: A 964 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8177 (tptm) REVERT: A 965 GLN cc_start: 0.8548 (mm110) cc_final: 0.8250 (mm-40) REVERT: A 991 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7031 (t) REVERT: A 995 ARG cc_start: 0.8480 (ttm170) cc_final: 0.8043 (tpp80) REVERT: A 997 ILE cc_start: 0.8761 (mt) cc_final: 0.8493 (mt) REVERT: A 1014 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7735 (mmm-85) REVERT: A 1019 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6366 (tpp80) REVERT: A 1023 ASN cc_start: 0.7704 (t0) cc_final: 0.7457 (t0) REVERT: A 1038 LYS cc_start: 0.8281 (mttt) cc_final: 0.7734 (ttmm) REVERT: A 1045 LYS cc_start: 0.7576 (tttp) cc_final: 0.7178 (tttp) REVERT: A 1106 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: A 1128 VAL cc_start: 0.7931 (p) cc_final: 0.7512 (m) REVERT: B 65 PHE cc_start: 0.8460 (m-80) cc_final: 0.8006 (m-80) REVERT: B 141 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4525 (tt) REVERT: B 187 LYS cc_start: 0.8195 (tptp) cc_final: 0.7822 (ptmt) REVERT: B 220 PHE cc_start: 0.3216 (OUTLIER) cc_final: 0.1398 (t80) REVERT: B 233 ILE cc_start: 0.5802 (pt) cc_final: 0.3982 (mt) REVERT: B 266 TYR cc_start: 0.6351 (m-10) cc_final: 0.5724 (m-10) REVERT: B 289 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 293 LEU cc_start: 0.8513 (tp) cc_final: 0.8193 (tt) REVERT: B 378 LYS cc_start: 0.6964 (ptmm) cc_final: 0.6738 (ttpp) REVERT: B 398 ASP cc_start: 0.6972 (m-30) cc_final: 0.6393 (m-30) REVERT: B 454 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: B 471 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: B 533 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 613 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5413 (tp40) REVERT: B 714 ILE cc_start: 0.8592 (mt) cc_final: 0.8359 (mp) REVERT: B 752 LEU cc_start: 0.8771 (mm) cc_final: 0.8492 (mm) REVERT: B 776 LYS cc_start: 0.8689 (tptp) cc_final: 0.8304 (tptp) REVERT: B 779 GLN cc_start: 0.7953 (tp40) cc_final: 0.7610 (tm-30) REVERT: B 814 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6900 (mmtt) REVERT: B 858 LEU cc_start: 0.7823 (mt) cc_final: 0.7588 (pp) REVERT: B 870 ILE cc_start: 0.8219 (mt) cc_final: 0.7979 (tt) REVERT: B 902 MET cc_start: 0.6910 (mmm) cc_final: 0.6600 (mmm) REVERT: B 905 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7757 (mmt-90) REVERT: B 926 GLN cc_start: 0.8312 (mt0) cc_final: 0.7864 (tp40) REVERT: B 949 GLN cc_start: 0.7841 (tp40) cc_final: 0.7634 (tp-100) REVERT: B 957 GLN cc_start: 0.8368 (mt0) cc_final: 0.8127 (tt0) REVERT: B 964 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8154 (ttmm) REVERT: B 966 LEU cc_start: 0.8460 (tp) cc_final: 0.8251 (pp) REVERT: B 970 PHE cc_start: 0.7114 (m-80) cc_final: 0.6641 (m-80) REVERT: B 1118 ASP cc_start: 0.8215 (p0) cc_final: 0.7922 (p0) REVERT: B 1133 VAL cc_start: 0.7628 (m) cc_final: 0.7369 (p) REVERT: C 34 ARG cc_start: 0.5779 (tpp-160) cc_final: 0.5479 (mmm160) REVERT: C 55 PHE cc_start: 0.3913 (OUTLIER) cc_final: 0.3542 (m-10) REVERT: C 66 HIS cc_start: 0.6937 (m170) cc_final: 0.5588 (m170) REVERT: C 96 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6017 (mm-30) REVERT: C 206 LYS cc_start: 0.7266 (tptm) cc_final: 0.6909 (tptm) REVERT: C 212 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7122 (mp) REVERT: C 235 ILE cc_start: 0.8503 (mt) cc_final: 0.7989 (mt) REVERT: C 276 LEU cc_start: 0.5838 (tp) cc_final: 0.5039 (tp) REVERT: C 277 LEU cc_start: 0.7204 (mt) cc_final: 0.6730 (mt) REVERT: C 308 VAL cc_start: 0.7258 (t) cc_final: 0.6989 (p) REVERT: C 370 ASN cc_start: 0.8169 (t0) cc_final: 0.7833 (t0) REVERT: C 377 PHE cc_start: 0.7694 (t80) cc_final: 0.7493 (t80) REVERT: C 406 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: C 436 TRP cc_start: 0.7329 (p-90) cc_final: 0.6927 (p-90) REVERT: C 440 ASN cc_start: 0.8834 (m-40) cc_final: 0.8243 (p0) REVERT: C 463 PRO cc_start: 0.6203 (Cg_endo) cc_final: 0.6001 (Cg_exo) REVERT: C 559 PHE cc_start: 0.7908 (m-10) cc_final: 0.7374 (m-80) REVERT: C 563 GLN cc_start: 0.7940 (mt0) cc_final: 0.7655 (mt0) REVERT: C 581 THR cc_start: 0.7540 (m) cc_final: 0.7182 (m) REVERT: C 588 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6071 (t) REVERT: C 611 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4730 (tt) REVERT: C 618 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 642 VAL cc_start: 0.8824 (m) cc_final: 0.8590 (p) REVERT: C 655 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8263 (p90) REVERT: C 657 ASN cc_start: 0.7928 (m-40) cc_final: 0.7555 (t0) REVERT: C 727 LEU cc_start: 0.8013 (mt) cc_final: 0.7766 (mt) REVERT: C 752 LEU cc_start: 0.8861 (mp) cc_final: 0.7905 (mm) REVERT: C 773 GLU cc_start: 0.8000 (tt0) cc_final: 0.7033 (tt0) REVERT: C 776 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8580 (ttpt) REVERT: C 824 ASN cc_start: 0.9195 (m110) cc_final: 0.8833 (p0) REVERT: C 877 LEU cc_start: 0.8683 (mt) cc_final: 0.8258 (mt) REVERT: C 878 LEU cc_start: 0.8525 (mt) cc_final: 0.8142 (mt) REVERT: C 901 GLN cc_start: 0.8015 (tt0) cc_final: 0.7562 (tt0) REVERT: C 905 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7248 (tpp80) REVERT: C 918 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 920 GLN cc_start: 0.8221 (tt0) cc_final: 0.7982 (tt0) REVERT: C 921 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: C 925 ASN cc_start: 0.8366 (m-40) cc_final: 0.8150 (m-40) REVERT: C 926 GLN cc_start: 0.8790 (mt0) cc_final: 0.8167 (mt0) REVERT: C 1013 ILE cc_start: 0.8644 (mt) cc_final: 0.8102 (mm) REVERT: C 1017 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 1021 SER cc_start: 0.8867 (t) cc_final: 0.8560 (p) REVERT: C 1083 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.4453 (t-90) REVERT: C 1092 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3718 (pp20) outliers start: 211 outliers final: 75 residues processed: 981 average time/residue: 0.3919 time to fit residues: 595.5108 Evaluate side-chains 790 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 691 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 245 HIS A 317 ASN A 394 ASN A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 690 GLN A 755 GLN A 764 ASN A 774 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 953 ASN A 978 ASN A1002 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 122 ASN B 165 ASN B 207 HIS B 211 ASN B 245 HIS B 334 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 641 ASN B 764 ASN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN B1119 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 207 HIS C 245 HIS C 317 ASN C 321 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 824 ASN C 856 ASN C 928 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.174778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133811 restraints weight = 54572.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138970 restraints weight = 33978.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.142765 restraints weight = 23640.322| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26624 Z= 0.213 Angle : 0.916 18.429 36353 Z= 0.445 Chirality : 0.059 1.199 4208 Planarity : 0.006 0.117 4627 Dihedral : 9.817 104.783 4458 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 0.46 % Allowed : 5.21 % Favored : 94.33 % 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 (0.14), residues: 3207 helix: 1.61 (0.19), residues: 676 sheet: 0.15 (0.20), residues: 659 loop : -1.06 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.013 0.002 HIS C 655 PHE 0.035 0.003 PHE B 275 TYR 0.025 0.002 TYR C 453 ARG 0.023 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01254 ( 34) link_NAG-ASN : angle 5.58149 ( 102) link_BETA1-4 : bond 0.01055 ( 10) link_BETA1-4 : angle 2.28191 ( 30) hydrogen bonds : bond 0.06307 ( 873) hydrogen bonds : angle 7.08698 ( 2436) SS BOND : bond 0.00690 ( 41) SS BOND : angle 3.34315 ( 82) covalent geometry : bond 0.00442 (26536) covalent geometry : angle 0.85207 (36139) Misc. bond : bond 0.00574 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 772 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7863 (ttpt) REVERT: A 49 HIS cc_start: 0.7704 (t-90) cc_final: 0.7379 (t-90) REVERT: A 80 ASP cc_start: 0.8058 (t0) cc_final: 0.7740 (t70) REVERT: A 224 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8254 (pm20) REVERT: A 271 GLN cc_start: 0.8210 (mp10) cc_final: 0.7935 (mp10) REVERT: A 287 ASP cc_start: 0.8392 (t0) cc_final: 0.8163 (t0) REVERT: A 298 GLU cc_start: 0.8279 (tt0) cc_final: 0.7874 (tt0) REVERT: A 318 PHE cc_start: 0.7547 (t80) cc_final: 0.7239 (t80) REVERT: A 342 PHE cc_start: 0.9059 (m-10) cc_final: 0.8763 (m-10) REVERT: A 532 ASN cc_start: 0.7924 (t0) cc_final: 0.7586 (t0) REVERT: A 567 ARG cc_start: 0.6266 (ptp-110) cc_final: 0.5617 (ttp-110) REVERT: A 571 ASP cc_start: 0.6708 (t0) cc_final: 0.6347 (t0) REVERT: A 656 VAL cc_start: 0.8638 (m) cc_final: 0.8375 (p) REVERT: A 658 ASN cc_start: 0.7461 (t0) cc_final: 0.7054 (t0) REVERT: A 740 MET cc_start: 0.8174 (tpp) cc_final: 0.7866 (tpp) REVERT: A 751 ASN cc_start: 0.8446 (m110) cc_final: 0.8150 (m110) REVERT: A 758 SER cc_start: 0.8304 (p) cc_final: 0.7821 (p) REVERT: A 762 GLN cc_start: 0.8728 (mm-40) cc_final: 0.7811 (mm-40) REVERT: A 765 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.7818 (ttp-170) REVERT: A 787 GLN cc_start: 0.7665 (pm20) cc_final: 0.7086 (pp30) REVERT: A 796 ASP cc_start: 0.8023 (m-30) cc_final: 0.7667 (m-30) REVERT: A 823 PHE cc_start: 0.8568 (t80) cc_final: 0.8238 (t80) REVERT: A 869 MET cc_start: 0.8936 (mtm) cc_final: 0.8207 (ptp) REVERT: A 912 THR cc_start: 0.7360 (p) cc_final: 0.7141 (p) REVERT: A 919 ASN cc_start: 0.8693 (m110) cc_final: 0.8373 (m110) REVERT: A 921 LYS cc_start: 0.8704 (mmtt) cc_final: 0.7972 (tptp) REVERT: A 926 GLN cc_start: 0.8945 (mt0) cc_final: 0.8383 (mt0) REVERT: A 928 ASN cc_start: 0.8343 (m-40) cc_final: 0.8066 (m-40) REVERT: A 933 LYS cc_start: 0.9039 (mttm) cc_final: 0.8389 (mmmm) REVERT: A 952 VAL cc_start: 0.9045 (t) cc_final: 0.8778 (p) REVERT: A 957 GLN cc_start: 0.8855 (tt0) cc_final: 0.8161 (tm-30) REVERT: A 964 LYS cc_start: 0.8882 (mttt) cc_final: 0.8397 (tptp) REVERT: A 965 GLN cc_start: 0.8854 (mm110) cc_final: 0.8650 (mm-40) REVERT: A 991 VAL cc_start: 0.7679 (p) cc_final: 0.7025 (t) REVERT: A 995 ARG cc_start: 0.8727 (ttm170) cc_final: 0.8364 (tpp80) REVERT: A 1005 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 1009 THR cc_start: 0.8842 (m) cc_final: 0.8538 (p) REVERT: A 1014 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8143 (mmm-85) REVERT: A 1023 ASN cc_start: 0.8437 (t0) cc_final: 0.8191 (t0) REVERT: A 1038 LYS cc_start: 0.8653 (mttt) cc_final: 0.8051 (mttm) REVERT: A 1064 HIS cc_start: 0.7571 (m170) cc_final: 0.6969 (m170) REVERT: A 1088 HIS cc_start: 0.7723 (m-70) cc_final: 0.7149 (m-70) REVERT: A 1105 THR cc_start: 0.6838 (t) cc_final: 0.6593 (m) REVERT: A 1114 ILE cc_start: 0.8923 (mp) cc_final: 0.8701 (tp) REVERT: B 65 PHE cc_start: 0.8081 (m-80) cc_final: 0.7260 (m-80) REVERT: B 92 PHE cc_start: 0.7761 (t80) cc_final: 0.7551 (t80) REVERT: B 224 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7646 (pm20) REVERT: B 277 LEU cc_start: 0.7751 (mm) cc_final: 0.7418 (mm) REVERT: B 287 ASP cc_start: 0.7486 (t0) cc_final: 0.6536 (p0) REVERT: B 300 LYS cc_start: 0.8703 (mttt) cc_final: 0.8253 (mttm) REVERT: B 309 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 329 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5436 (m-10) REVERT: B 331 ASN cc_start: 0.6990 (t0) cc_final: 0.6585 (m-40) REVERT: B 356 LYS cc_start: 0.7588 (mptt) cc_final: 0.6716 (mptt) REVERT: B 357 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6427 (tpp-160) REVERT: B 378 LYS cc_start: 0.7889 (ptmm) cc_final: 0.6981 (ttpp) REVERT: B 398 ASP cc_start: 0.6618 (m-30) cc_final: 0.5875 (m-30) REVERT: B 409 GLN cc_start: 0.8774 (mt0) cc_final: 0.8197 (mt0) REVERT: B 418 ILE cc_start: 0.8533 (mp) cc_final: 0.8278 (mp) REVERT: B 509 ARG cc_start: 0.7295 (tmm160) cc_final: 0.6772 (mmt180) REVERT: B 529 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7355 (tptp) REVERT: B 535 LYS cc_start: 0.8065 (tppp) cc_final: 0.7832 (tppt) REVERT: B 557 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7325 (mtmm) REVERT: B 578 ASP cc_start: 0.7839 (p0) cc_final: 0.7621 (p0) REVERT: B 583 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7844 (tp30) REVERT: B 702 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 714 ILE cc_start: 0.8696 (mt) cc_final: 0.8427 (mp) REVERT: B 725 GLU cc_start: 0.7714 (tt0) cc_final: 0.7248 (tm-30) REVERT: B 727 LEU cc_start: 0.7595 (mt) cc_final: 0.6794 (mt) REVERT: B 740 MET cc_start: 0.9081 (tpt) cc_final: 0.8395 (tpt) REVERT: B 756 TYR cc_start: 0.8087 (m-80) cc_final: 0.7538 (m-80) REVERT: B 758 SER cc_start: 0.8780 (t) cc_final: 0.8549 (m) REVERT: B 776 LYS cc_start: 0.9046 (tptp) cc_final: 0.8423 (tptp) REVERT: B 779 GLN cc_start: 0.8441 (tp40) cc_final: 0.7866 (tp-100) REVERT: B 780 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7458 (tp30) REVERT: B 823 PHE cc_start: 0.7632 (m-80) cc_final: 0.7398 (m-80) REVERT: B 860 VAL cc_start: 0.8649 (t) cc_final: 0.8439 (p) REVERT: B 869 MET cc_start: 0.8386 (mpp) cc_final: 0.7964 (ptp) REVERT: B 909 ILE cc_start: 0.8071 (pt) cc_final: 0.7855 (mm) REVERT: B 917 TYR cc_start: 0.7873 (m-80) cc_final: 0.7059 (m-10) REVERT: B 921 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8461 (mtpp) REVERT: B 926 GLN cc_start: 0.8688 (mt0) cc_final: 0.8380 (tp40) REVERT: B 928 ASN cc_start: 0.8441 (m-40) cc_final: 0.8232 (m-40) REVERT: B 934 ILE cc_start: 0.8478 (mm) cc_final: 0.8274 (mm) REVERT: B 954 GLN cc_start: 0.8057 (pp30) cc_final: 0.7853 (pp30) REVERT: B 955 ASN cc_start: 0.8598 (m110) cc_final: 0.7957 (m110) REVERT: B 957 GLN cc_start: 0.8853 (mt0) cc_final: 0.8527 (tt0) REVERT: B 964 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8478 (ttmm) REVERT: B 991 VAL cc_start: 0.9101 (m) cc_final: 0.8788 (t) REVERT: B 994 ASP cc_start: 0.8374 (t0) cc_final: 0.8061 (t0) REVERT: B 1001 LEU cc_start: 0.9075 (mt) cc_final: 0.8834 (mt) REVERT: B 1005 GLN cc_start: 0.8516 (pt0) cc_final: 0.8290 (pp30) REVERT: B 1024 LEU cc_start: 0.8827 (tt) cc_final: 0.8605 (tt) REVERT: B 1028 LYS cc_start: 0.8235 (tppt) cc_final: 0.7657 (tppt) REVERT: B 1034 LEU cc_start: 0.7954 (mt) cc_final: 0.7733 (mt) REVERT: B 1045 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7501 (tmmt) REVERT: B 1054 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7374 (tp40) REVERT: C 34 ARG cc_start: 0.6745 (tpp-160) cc_final: 0.6514 (tpp-160) REVERT: C 37 TYR cc_start: 0.6226 (p90) cc_final: 0.6004 (p90) REVERT: C 43 PHE cc_start: 0.7432 (t80) cc_final: 0.6578 (t80) REVERT: C 65 PHE cc_start: 0.8628 (m-80) cc_final: 0.8044 (m-80) REVERT: C 99 ASN cc_start: 0.8686 (m110) cc_final: 0.8318 (m-40) REVERT: C 203 ILE cc_start: 0.8151 (tt) cc_final: 0.7878 (tp) REVERT: C 229 LEU cc_start: 0.8457 (mp) cc_final: 0.8238 (mm) REVERT: C 237 ARG cc_start: 0.8479 (ptm-80) cc_final: 0.8087 (mtm110) REVERT: C 240 THR cc_start: 0.7701 (m) cc_final: 0.7305 (t) REVERT: C 277 LEU cc_start: 0.7856 (mt) cc_final: 0.7600 (mt) REVERT: C 356 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6195 (ttpp) REVERT: C 370 ASN cc_start: 0.8047 (t0) cc_final: 0.7782 (t0) REVERT: C 440 ASN cc_start: 0.8709 (m-40) cc_final: 0.8075 (p0) REVERT: C 533 LEU cc_start: 0.8576 (tp) cc_final: 0.8299 (tp) REVERT: C 543 PHE cc_start: 0.8609 (m-80) cc_final: 0.8325 (m-80) REVERT: C 581 THR cc_start: 0.8166 (m) cc_final: 0.7849 (p) REVERT: C 583 GLU cc_start: 0.8434 (mp0) cc_final: 0.8098 (mp0) REVERT: C 613 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7194 (mp10) REVERT: C 657 ASN cc_start: 0.8537 (m-40) cc_final: 0.8163 (m-40) REVERT: C 693 ILE cc_start: 0.8199 (pt) cc_final: 0.7867 (mp) REVERT: C 699 LEU cc_start: 0.8262 (pt) cc_final: 0.7907 (pt) REVERT: C 710 ASN cc_start: 0.8351 (p0) cc_final: 0.8054 (m-40) REVERT: C 727 LEU cc_start: 0.8385 (mt) cc_final: 0.8068 (mt) REVERT: C 730 SER cc_start: 0.7028 (p) cc_final: 0.6670 (t) REVERT: C 731 MET cc_start: 0.8410 (ptt) cc_final: 0.8031 (ptt) REVERT: C 740 MET cc_start: 0.7251 (tpp) cc_final: 0.6811 (tpp) REVERT: C 751 ASN cc_start: 0.8686 (p0) cc_final: 0.8441 (p0) REVERT: C 763 LEU cc_start: 0.8994 (mt) cc_final: 0.8782 (mt) REVERT: C 767 LEU cc_start: 0.9083 (mm) cc_final: 0.8785 (pp) REVERT: C 772 VAL cc_start: 0.8617 (t) cc_final: 0.7851 (p) REVERT: C 776 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8885 (ttpt) REVERT: C 790 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7839 (mmtm) REVERT: C 802 PHE cc_start: 0.9157 (m-10) cc_final: 0.8701 (m-10) REVERT: C 805 ILE cc_start: 0.8504 (mp) cc_final: 0.8275 (tp) REVERT: C 866 THR cc_start: 0.7515 (p) cc_final: 0.6672 (p) REVERT: C 872 GLN cc_start: 0.8940 (tp40) cc_final: 0.8655 (tp-100) REVERT: C 873 TYR cc_start: 0.8641 (m-10) cc_final: 0.8405 (m-10) REVERT: C 894 LEU cc_start: 0.7755 (mt) cc_final: 0.7465 (mm) REVERT: C 902 MET cc_start: 0.8293 (tmm) cc_final: 0.7881 (tmm) REVERT: C 905 ARG cc_start: 0.8950 (mtt-85) cc_final: 0.8474 (tpp80) REVERT: C 918 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C 921 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8274 (mtpp) REVERT: C 925 ASN cc_start: 0.8563 (m-40) cc_final: 0.8305 (m-40) REVERT: C 926 GLN cc_start: 0.8715 (mt0) cc_final: 0.8331 (mt0) REVERT: C 947 LYS cc_start: 0.8478 (mttt) cc_final: 0.8215 (ptpp) REVERT: C 949 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7708 (tp40) REVERT: C 953 ASN cc_start: 0.8375 (m-40) cc_final: 0.8017 (m-40) REVERT: C 964 LYS cc_start: 0.8552 (tttt) cc_final: 0.8029 (ptpt) REVERT: C 965 GLN cc_start: 0.8791 (tp40) cc_final: 0.8206 (mm-40) REVERT: C 1005 GLN cc_start: 0.7999 (pp30) cc_final: 0.7780 (pp30) REVERT: C 1013 ILE cc_start: 0.8890 (mt) cc_final: 0.8529 (mm) REVERT: C 1014 ARG cc_start: 0.8448 (mtt90) cc_final: 0.7770 (ptp-110) REVERT: C 1017 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 1028 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8973 (mmtp) REVERT: C 1029 MET cc_start: 0.8796 (tpp) cc_final: 0.8337 (tpp) REVERT: C 1081 ILE cc_start: 0.7896 (mt) cc_final: 0.7629 (mt) REVERT: C 1084 ASP cc_start: 0.6589 (m-30) cc_final: 0.6374 (m-30) REVERT: C 1088 HIS cc_start: 0.6953 (m90) cc_final: 0.6580 (m-70) REVERT: C 1103 PHE cc_start: 0.7681 (m-80) cc_final: 0.7480 (m-80) REVERT: C 1127 ASP cc_start: 0.8587 (m-30) cc_final: 0.8279 (m-30) outliers start: 13 outliers final: 2 residues processed: 781 average time/residue: 0.3874 time to fit residues: 467.4939 Evaluate side-chains 689 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 686 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 164 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 300 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 317 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122545 restraints weight = 55244.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127334 restraints weight = 34897.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.130779 restraints weight = 24457.598| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26624 Z= 0.234 Angle : 0.844 19.880 36353 Z= 0.416 Chirality : 0.055 0.730 4208 Planarity : 0.006 0.099 4627 Dihedral : 9.662 103.356 4458 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % 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: -0.68 (0.14), residues: 3207 helix: 1.05 (0.20), residues: 678 sheet: -0.22 (0.19), residues: 664 loop : -1.13 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 436 HIS 0.013 0.002 HIS B 655 PHE 0.026 0.002 PHE C 559 TYR 0.024 0.002 TYR C 741 ARG 0.019 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 34) link_NAG-ASN : angle 5.30790 ( 102) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.76183 ( 30) hydrogen bonds : bond 0.05734 ( 873) hydrogen bonds : angle 6.58322 ( 2436) SS BOND : bond 0.00656 ( 41) SS BOND : angle 1.96663 ( 82) covalent geometry : bond 0.00460 (26536) covalent geometry : angle 0.79083 (36139) Misc. bond : bond 0.00274 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 768 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8074 (ttpt) REVERT: A 49 HIS cc_start: 0.7760 (t70) cc_final: 0.7327 (t-90) REVERT: A 80 ASP cc_start: 0.8153 (t0) cc_final: 0.7794 (t70) REVERT: A 91 TYR cc_start: 0.6978 (t80) cc_final: 0.6177 (t80) REVERT: A 207 HIS cc_start: 0.7056 (t-90) cc_final: 0.5088 (t-90) REVERT: A 224 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8313 (pm20) REVERT: A 273 ARG cc_start: 0.8434 (mmt180) cc_final: 0.8101 (mmt180) REVERT: A 287 ASP cc_start: 0.8525 (t0) cc_final: 0.8125 (p0) REVERT: A 291 CYS cc_start: 0.6281 (t) cc_final: 0.5742 (t) REVERT: A 298 GLU cc_start: 0.8298 (tt0) cc_final: 0.7911 (tt0) REVERT: A 318 PHE cc_start: 0.7776 (t80) cc_final: 0.7543 (t80) REVERT: A 342 PHE cc_start: 0.9138 (m-10) cc_final: 0.8849 (m-10) REVERT: A 532 ASN cc_start: 0.8119 (t0) cc_final: 0.7813 (t0) REVERT: A 535 LYS cc_start: 0.8237 (mttt) cc_final: 0.7879 (mtpt) REVERT: A 562 PHE cc_start: 0.7936 (p90) cc_final: 0.7623 (p90) REVERT: A 583 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 592 PHE cc_start: 0.7206 (t80) cc_final: 0.6871 (t80) REVERT: A 646 ARG cc_start: 0.7943 (tpt90) cc_final: 0.7488 (tpt90) REVERT: A 658 ASN cc_start: 0.7440 (t0) cc_final: 0.7068 (t0) REVERT: A 731 MET cc_start: 0.8183 (pmm) cc_final: 0.7666 (pmm) REVERT: A 737 ASP cc_start: 0.8335 (t0) cc_final: 0.7993 (t70) REVERT: A 740 MET cc_start: 0.8266 (tpp) cc_final: 0.8046 (tpp) REVERT: A 751 ASN cc_start: 0.8388 (m110) cc_final: 0.8074 (m110) REVERT: A 773 GLU cc_start: 0.8721 (tt0) cc_final: 0.8129 (tt0) REVERT: A 777 ASN cc_start: 0.8885 (m-40) cc_final: 0.8634 (m-40) REVERT: A 788 ILE cc_start: 0.8352 (mm) cc_final: 0.7918 (tp) REVERT: A 790 LYS cc_start: 0.8070 (tptt) cc_final: 0.7777 (tptt) REVERT: A 791 THR cc_start: 0.8633 (m) cc_final: 0.8092 (m) REVERT: A 796 ASP cc_start: 0.8016 (m-30) cc_final: 0.7681 (m-30) REVERT: A 818 ILE cc_start: 0.9254 (mt) cc_final: 0.8954 (mm) REVERT: A 866 THR cc_start: 0.7552 (p) cc_final: 0.6769 (m) REVERT: A 870 ILE cc_start: 0.8969 (mt) cc_final: 0.8681 (mt) REVERT: A 873 TYR cc_start: 0.8784 (m-10) cc_final: 0.8198 (m-10) REVERT: A 911 VAL cc_start: 0.7459 (t) cc_final: 0.7187 (m) REVERT: A 919 ASN cc_start: 0.8747 (m110) cc_final: 0.8431 (m110) REVERT: A 921 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8267 (tptp) REVERT: A 926 GLN cc_start: 0.9000 (mt0) cc_final: 0.8501 (mt0) REVERT: A 928 ASN cc_start: 0.8471 (m-40) cc_final: 0.8168 (m-40) REVERT: A 933 LYS cc_start: 0.9055 (mttm) cc_final: 0.8412 (mmmm) REVERT: A 949 GLN cc_start: 0.8562 (pp30) cc_final: 0.8313 (pp30) REVERT: A 957 GLN cc_start: 0.8970 (tt0) cc_final: 0.8334 (tm-30) REVERT: A 964 LYS cc_start: 0.8886 (mttt) cc_final: 0.8427 (tptp) REVERT: A 965 GLN cc_start: 0.8983 (mm110) cc_final: 0.8733 (mm110) REVERT: A 979 ASP cc_start: 0.8707 (t0) cc_final: 0.8487 (t0) REVERT: A 991 VAL cc_start: 0.8012 (p) cc_final: 0.7482 (t) REVERT: A 995 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8465 (tpp80) REVERT: A 1005 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 1009 THR cc_start: 0.8874 (m) cc_final: 0.8374 (p) REVERT: A 1014 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.8462 (mmm-85) REVERT: A 1023 ASN cc_start: 0.8474 (t0) cc_final: 0.8217 (t0) REVERT: A 1036 GLN cc_start: 0.6752 (tt0) cc_final: 0.6318 (tt0) REVERT: A 1038 LYS cc_start: 0.8745 (mttt) cc_final: 0.8267 (mtpt) REVERT: A 1045 LYS cc_start: 0.8465 (mppt) cc_final: 0.8021 (mmtm) REVERT: A 1049 LEU cc_start: 0.8921 (mt) cc_final: 0.8691 (mt) REVERT: A 1081 ILE cc_start: 0.8925 (mm) cc_final: 0.7899 (tp) REVERT: A 1086 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8641 (mmpt) REVERT: A 1088 HIS cc_start: 0.7741 (m-70) cc_final: 0.6943 (m-70) REVERT: A 1091 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7054 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8827 (m90) cc_final: 0.8597 (m90) REVERT: A 1109 PHE cc_start: 0.7898 (t80) cc_final: 0.7371 (t80) REVERT: A 1114 ILE cc_start: 0.8985 (mp) cc_final: 0.8716 (tp) REVERT: A 1121 PHE cc_start: 0.7523 (p90) cc_final: 0.7198 (p90) REVERT: B 43 PHE cc_start: 0.7749 (p90) cc_final: 0.7352 (p90) REVERT: B 44 ARG cc_start: 0.7661 (mtt90) cc_final: 0.7108 (mpt-90) REVERT: B 52 GLN cc_start: 0.8267 (mp10) cc_final: 0.8017 (mp10) REVERT: B 53 ASP cc_start: 0.6891 (t0) cc_final: 0.6196 (t0) REVERT: B 54 LEU cc_start: 0.8092 (mp) cc_final: 0.7273 (tt) REVERT: B 65 PHE cc_start: 0.8304 (m-80) cc_final: 0.7469 (m-80) REVERT: B 92 PHE cc_start: 0.7931 (t80) cc_final: 0.7246 (t80) REVERT: B 99 ASN cc_start: 0.8589 (t0) cc_final: 0.7819 (t0) REVERT: B 187 LYS cc_start: 0.7714 (pttm) cc_final: 0.7494 (pttm) REVERT: B 190 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7477 (mmt180) REVERT: B 192 PHE cc_start: 0.6135 (m-80) cc_final: 0.5858 (m-80) REVERT: B 224 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7763 (pm20) REVERT: B 353 TRP cc_start: 0.7820 (p90) cc_final: 0.6836 (p90) REVERT: B 364 ASP cc_start: 0.8302 (t0) cc_final: 0.7931 (t0) REVERT: B 398 ASP cc_start: 0.6738 (m-30) cc_final: 0.6235 (m-30) REVERT: B 409 GLN cc_start: 0.8887 (mt0) cc_final: 0.7962 (mt0) REVERT: B 529 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7655 (ttmm) REVERT: B 535 LYS cc_start: 0.8235 (tppp) cc_final: 0.7724 (tppt) REVERT: B 557 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7344 (mtmm) REVERT: B 578 ASP cc_start: 0.7849 (p0) cc_final: 0.7425 (t0) REVERT: B 582 LEU cc_start: 0.9102 (mt) cc_final: 0.8870 (mt) REVERT: B 583 GLU cc_start: 0.8702 (mm-30) cc_final: 0.7781 (tp30) REVERT: B 702 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 714 ILE cc_start: 0.8504 (mt) cc_final: 0.8034 (mp) REVERT: B 725 GLU cc_start: 0.7627 (tt0) cc_final: 0.6883 (tm-30) REVERT: B 727 LEU cc_start: 0.7700 (mt) cc_final: 0.6855 (mt) REVERT: B 740 MET cc_start: 0.9242 (tpt) cc_final: 0.8712 (tpt) REVERT: B 758 SER cc_start: 0.8906 (t) cc_final: 0.8602 (m) REVERT: B 762 GLN cc_start: 0.8403 (pp30) cc_final: 0.7987 (pp30) REVERT: B 763 LEU cc_start: 0.8626 (mt) cc_final: 0.8359 (mm) REVERT: B 776 LYS cc_start: 0.8810 (tptp) cc_final: 0.8428 (tptp) REVERT: B 779 GLN cc_start: 0.8540 (tp40) cc_final: 0.7815 (tm-30) REVERT: B 780 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7493 (tp30) REVERT: B 805 ILE cc_start: 0.8679 (mt) cc_final: 0.8295 (tp) REVERT: B 815 ARG cc_start: 0.7122 (mtm180) cc_final: 0.6660 (mtp85) REVERT: B 867 ASP cc_start: 0.8053 (t0) cc_final: 0.7586 (t0) REVERT: B 917 TYR cc_start: 0.7981 (m-80) cc_final: 0.7298 (m-10) REVERT: B 921 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8478 (mtpp) REVERT: B 926 GLN cc_start: 0.8777 (mt0) cc_final: 0.8426 (tp40) REVERT: B 934 ILE cc_start: 0.8453 (mm) cc_final: 0.8223 (mm) REVERT: B 935 GLN cc_start: 0.8944 (tt0) cc_final: 0.8385 (tm-30) REVERT: B 939 SER cc_start: 0.6814 (p) cc_final: 0.6586 (p) REVERT: B 954 GLN cc_start: 0.8244 (pp30) cc_final: 0.7982 (pp30) REVERT: B 955 ASN cc_start: 0.8836 (m110) cc_final: 0.8188 (m110) REVERT: B 957 GLN cc_start: 0.8925 (mt0) cc_final: 0.8699 (tt0) REVERT: B 979 ASP cc_start: 0.8701 (t0) cc_final: 0.8399 (t0) REVERT: B 991 VAL cc_start: 0.9079 (m) cc_final: 0.8783 (t) REVERT: B 996 LEU cc_start: 0.9050 (mt) cc_final: 0.8845 (mt) REVERT: B 1001 LEU cc_start: 0.9111 (mt) cc_final: 0.8870 (mt) REVERT: B 1003 SER cc_start: 0.9182 (m) cc_final: 0.8918 (p) REVERT: B 1005 GLN cc_start: 0.9023 (pt0) cc_final: 0.8368 (pp30) REVERT: B 1017 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8255 (tp30) REVERT: B 1024 LEU cc_start: 0.8857 (tt) cc_final: 0.8464 (tt) REVERT: B 1027 THR cc_start: 0.8703 (m) cc_final: 0.8499 (p) REVERT: B 1028 LYS cc_start: 0.8621 (tppt) cc_final: 0.7641 (tppt) REVERT: B 1031 GLU cc_start: 0.7898 (tt0) cc_final: 0.6916 (tt0) REVERT: B 1045 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7531 (tmmt) REVERT: B 1081 ILE cc_start: 0.7279 (mp) cc_final: 0.6780 (tp) REVERT: B 1113 GLN cc_start: 0.8499 (mt0) cc_final: 0.8131 (mp10) REVERT: C 34 ARG cc_start: 0.7077 (tpp-160) cc_final: 0.5757 (tpp80) REVERT: C 65 PHE cc_start: 0.8552 (m-80) cc_final: 0.7963 (m-80) REVERT: C 135 PHE cc_start: 0.8550 (m-10) cc_final: 0.7567 (t80) REVERT: C 164 ASN cc_start: 0.8175 (t0) cc_final: 0.7944 (t0) REVERT: C 203 ILE cc_start: 0.8236 (tt) cc_final: 0.8008 (tp) REVERT: C 237 ARG cc_start: 0.8467 (ptm-80) cc_final: 0.7905 (mtm110) REVERT: C 267 VAL cc_start: 0.7424 (t) cc_final: 0.6749 (t) REVERT: C 277 LEU cc_start: 0.8104 (mt) cc_final: 0.7802 (pp) REVERT: C 300 LYS cc_start: 0.8068 (mttt) cc_final: 0.7483 (mptt) REVERT: C 318 PHE cc_start: 0.7490 (t80) cc_final: 0.7259 (t80) REVERT: C 440 ASN cc_start: 0.8678 (m-40) cc_final: 0.8009 (p0) REVERT: C 557 LYS cc_start: 0.8967 (mttt) cc_final: 0.8611 (mmmt) REVERT: C 583 GLU cc_start: 0.8675 (mp0) cc_final: 0.8279 (mp0) REVERT: C 657 ASN cc_start: 0.8607 (m-40) cc_final: 0.8267 (m-40) REVERT: C 693 ILE cc_start: 0.8267 (pt) cc_final: 0.7869 (tt) REVERT: C 710 ASN cc_start: 0.8378 (p0) cc_final: 0.8144 (m-40) REVERT: C 712 ILE cc_start: 0.8126 (tp) cc_final: 0.7912 (tp) REVERT: C 723 THR cc_start: 0.8280 (t) cc_final: 0.7813 (p) REVERT: C 727 LEU cc_start: 0.8321 (mt) cc_final: 0.8017 (mt) REVERT: C 731 MET cc_start: 0.8544 (ptt) cc_final: 0.8196 (ptt) REVERT: C 763 LEU cc_start: 0.8977 (mt) cc_final: 0.8742 (mt) REVERT: C 774 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8337 (mm110) REVERT: C 790 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7915 (mmtm) REVERT: C 808 ASP cc_start: 0.8397 (t0) cc_final: 0.8189 (t0) REVERT: C 865 LEU cc_start: 0.8619 (mt) cc_final: 0.7864 (mt) REVERT: C 869 MET cc_start: 0.8457 (mtm) cc_final: 0.7946 (mtm) REVERT: C 901 GLN cc_start: 0.8796 (tt0) cc_final: 0.8228 (tm-30) REVERT: C 902 MET cc_start: 0.8517 (tmm) cc_final: 0.7912 (tmm) REVERT: C 905 ARG cc_start: 0.8977 (mtt-85) cc_final: 0.8307 (mtt-85) REVERT: C 921 LYS cc_start: 0.8496 (mmpt) cc_final: 0.8211 (mtpp) REVERT: C 925 ASN cc_start: 0.8634 (m-40) cc_final: 0.8370 (m-40) REVERT: C 926 GLN cc_start: 0.8670 (mt0) cc_final: 0.8446 (mt0) REVERT: C 947 LYS cc_start: 0.8588 (mttt) cc_final: 0.8324 (ptpp) REVERT: C 949 GLN cc_start: 0.8365 (tp-100) cc_final: 0.7614 (tp40) REVERT: C 953 ASN cc_start: 0.8434 (m-40) cc_final: 0.7934 (m-40) REVERT: C 964 LYS cc_start: 0.8828 (tttt) cc_final: 0.8272 (ptmt) REVERT: C 965 GLN cc_start: 0.8851 (tp40) cc_final: 0.8316 (mm-40) REVERT: C 966 LEU cc_start: 0.8569 (mt) cc_final: 0.8368 (mt) REVERT: C 1013 ILE cc_start: 0.9013 (mt) cc_final: 0.8700 (mm) REVERT: C 1014 ARG cc_start: 0.8694 (mtt90) cc_final: 0.7683 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 1029 MET cc_start: 0.8807 (tpp) cc_final: 0.8492 (tpp) REVERT: C 1053 PRO cc_start: 0.8861 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: C 1081 ILE cc_start: 0.7984 (mt) cc_final: 0.7662 (mm) REVERT: C 1084 ASP cc_start: 0.7006 (m-30) cc_final: 0.6792 (m-30) REVERT: C 1088 HIS cc_start: 0.7328 (m90) cc_final: 0.6704 (m-70) REVERT: C 1089 PHE cc_start: 0.6411 (m-80) cc_final: 0.6124 (m-10) REVERT: C 1103 PHE cc_start: 0.7832 (m-80) cc_final: 0.7481 (m-80) REVERT: C 1105 THR cc_start: 0.7637 (t) cc_final: 0.6696 (m) outliers start: 3 outliers final: 1 residues processed: 771 average time/residue: 0.3787 time to fit residues: 453.7094 Evaluate side-chains 715 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 714 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 243 optimal weight: 0.0770 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.160076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120862 restraints weight = 56202.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125583 restraints weight = 35430.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129028 restraints weight = 24807.442| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26624 Z= 0.203 Angle : 0.788 19.237 36353 Z= 0.389 Chirality : 0.052 0.690 4208 Planarity : 0.005 0.089 4627 Dihedral : 9.468 104.056 4458 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % 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: -0.78 (0.14), residues: 3207 helix: 0.93 (0.20), residues: 673 sheet: -0.20 (0.19), residues: 657 loop : -1.21 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.020 0.002 HIS A 207 PHE 0.033 0.002 PHE A 759 TYR 0.019 0.002 TYR A 917 ARG 0.009 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 34) link_NAG-ASN : angle 5.15945 ( 102) link_BETA1-4 : bond 0.00406 ( 10) link_BETA1-4 : angle 2.00681 ( 30) hydrogen bonds : bond 0.05176 ( 873) hydrogen bonds : angle 6.22936 ( 2436) SS BOND : bond 0.00614 ( 41) SS BOND : angle 2.05541 ( 82) covalent geometry : bond 0.00400 (26536) covalent geometry : angle 0.73243 (36139) Misc. bond : bond 0.00062 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 759 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7526 (t70) cc_final: 0.7286 (t-90) REVERT: A 80 ASP cc_start: 0.8144 (t0) cc_final: 0.7678 (t0) REVERT: A 177 MET cc_start: 0.2888 (mtm) cc_final: 0.1534 (mmp) REVERT: A 224 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8392 (pm20) REVERT: A 273 ARG cc_start: 0.8630 (mmt180) cc_final: 0.8331 (mmt180) REVERT: A 287 ASP cc_start: 0.8459 (t0) cc_final: 0.8223 (t70) REVERT: A 298 GLU cc_start: 0.8344 (tt0) cc_final: 0.7981 (tt0) REVERT: A 318 PHE cc_start: 0.7725 (t80) cc_final: 0.7448 (t80) REVERT: A 342 PHE cc_start: 0.9199 (m-10) cc_final: 0.8881 (m-10) REVERT: A 532 ASN cc_start: 0.8118 (t0) cc_final: 0.7807 (t0) REVERT: A 535 LYS cc_start: 0.8449 (mttt) cc_final: 0.7882 (ptpt) REVERT: A 562 PHE cc_start: 0.7924 (p90) cc_final: 0.7686 (p90) REVERT: A 583 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8410 (mm-30) REVERT: A 646 ARG cc_start: 0.7977 (tpt90) cc_final: 0.7557 (tpt90) REVERT: A 656 VAL cc_start: 0.8572 (t) cc_final: 0.8288 (p) REVERT: A 658 ASN cc_start: 0.7826 (t0) cc_final: 0.7203 (t0) REVERT: A 731 MET cc_start: 0.8074 (pmm) cc_final: 0.7556 (pmm) REVERT: A 740 MET cc_start: 0.7990 (tpp) cc_final: 0.7594 (tpp) REVERT: A 751 ASN cc_start: 0.8374 (m110) cc_final: 0.8036 (m110) REVERT: A 762 GLN cc_start: 0.8641 (pt0) cc_final: 0.8356 (mt0) REVERT: A 767 LEU cc_start: 0.8643 (mt) cc_final: 0.8226 (tp) REVERT: A 772 VAL cc_start: 0.9203 (t) cc_final: 0.8327 (m) REVERT: A 775 ASP cc_start: 0.7832 (t0) cc_final: 0.7300 (t0) REVERT: A 776 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8344 (mmtp) REVERT: A 777 ASN cc_start: 0.8860 (m-40) cc_final: 0.8607 (m-40) REVERT: A 788 ILE cc_start: 0.8299 (mm) cc_final: 0.7877 (tp) REVERT: A 818 ILE cc_start: 0.9224 (mt) cc_final: 0.8998 (pt) REVERT: A 866 THR cc_start: 0.7737 (p) cc_final: 0.6969 (m) REVERT: A 870 ILE cc_start: 0.8935 (mt) cc_final: 0.8624 (mt) REVERT: A 873 TYR cc_start: 0.8715 (m-10) cc_final: 0.8223 (m-80) REVERT: A 902 MET cc_start: 0.8516 (ttm) cc_final: 0.7715 (ttm) REVERT: A 911 VAL cc_start: 0.7439 (t) cc_final: 0.7094 (m) REVERT: A 919 ASN cc_start: 0.8708 (m110) cc_final: 0.8299 (m110) REVERT: A 921 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8289 (tptp) REVERT: A 926 GLN cc_start: 0.9065 (mt0) cc_final: 0.8595 (mt0) REVERT: A 928 ASN cc_start: 0.8452 (m-40) cc_final: 0.8150 (m-40) REVERT: A 933 LYS cc_start: 0.9060 (mttm) cc_final: 0.8402 (mmmm) REVERT: A 949 GLN cc_start: 0.8556 (pp30) cc_final: 0.8233 (pp30) REVERT: A 957 GLN cc_start: 0.9032 (tt0) cc_final: 0.8306 (tm-30) REVERT: A 964 LYS cc_start: 0.8864 (mttt) cc_final: 0.8354 (tptp) REVERT: A 965 GLN cc_start: 0.8886 (mm110) cc_final: 0.8488 (mm-40) REVERT: A 979 ASP cc_start: 0.8664 (t0) cc_final: 0.8428 (t0) REVERT: A 991 VAL cc_start: 0.8173 (p) cc_final: 0.7599 (t) REVERT: A 993 ILE cc_start: 0.9125 (mm) cc_final: 0.8922 (mm) REVERT: A 995 ARG cc_start: 0.8880 (ttm170) cc_final: 0.8484 (tpp80) REVERT: A 1005 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 1009 THR cc_start: 0.8878 (m) cc_final: 0.8508 (p) REVERT: A 1014 ARG cc_start: 0.8855 (mtt-85) cc_final: 0.8389 (tpp80) REVERT: A 1017 GLU cc_start: 0.9089 (tt0) cc_final: 0.8386 (mm-30) REVERT: A 1023 ASN cc_start: 0.8545 (t0) cc_final: 0.8340 (t0) REVERT: A 1038 LYS cc_start: 0.8759 (mttt) cc_final: 0.8155 (mttp) REVERT: A 1041 ASP cc_start: 0.7844 (t0) cc_final: 0.7614 (t0) REVERT: A 1045 LYS cc_start: 0.8506 (mppt) cc_final: 0.8110 (mmtm) REVERT: A 1075 PHE cc_start: 0.7784 (m-80) cc_final: 0.7384 (m-10) REVERT: A 1088 HIS cc_start: 0.7723 (m-70) cc_final: 0.7241 (m-70) REVERT: A 1091 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7124 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8760 (m90) cc_final: 0.8377 (m170) REVERT: A 1109 PHE cc_start: 0.7879 (t80) cc_final: 0.7385 (t80) REVERT: A 1114 ILE cc_start: 0.8995 (mp) cc_final: 0.8690 (tp) REVERT: A 1121 PHE cc_start: 0.7500 (p90) cc_final: 0.7106 (p90) REVERT: B 52 GLN cc_start: 0.8239 (mp10) cc_final: 0.7963 (mp10) REVERT: B 53 ASP cc_start: 0.7092 (t0) cc_final: 0.6438 (t0) REVERT: B 54 LEU cc_start: 0.8218 (mp) cc_final: 0.7377 (tt) REVERT: B 65 PHE cc_start: 0.8193 (m-80) cc_final: 0.7339 (m-80) REVERT: B 92 PHE cc_start: 0.7814 (t80) cc_final: 0.7190 (t80) REVERT: B 99 ASN cc_start: 0.8616 (t0) cc_final: 0.7981 (t0) REVERT: B 187 LYS cc_start: 0.8023 (pttm) cc_final: 0.7734 (pttm) REVERT: B 192 PHE cc_start: 0.6228 (m-80) cc_final: 0.5939 (m-80) REVERT: B 207 HIS cc_start: 0.8500 (m90) cc_final: 0.8106 (m90) REVERT: B 233 ILE cc_start: 0.6529 (pt) cc_final: 0.5440 (tp) REVERT: B 296 LEU cc_start: 0.8911 (tp) cc_final: 0.8303 (tp) REVERT: B 300 LYS cc_start: 0.8677 (mttt) cc_final: 0.8183 (mttt) REVERT: B 306 PHE cc_start: 0.7684 (m-10) cc_final: 0.7185 (m-10) REVERT: B 313 TYR cc_start: 0.8130 (m-80) cc_final: 0.7902 (m-80) REVERT: B 353 TRP cc_start: 0.7726 (p90) cc_final: 0.6849 (p90) REVERT: B 357 ARG cc_start: 0.8443 (mmm160) cc_final: 0.7166 (mmm160) REVERT: B 380 TYR cc_start: 0.8134 (m-80) cc_final: 0.7753 (m-80) REVERT: B 395 VAL cc_start: 0.7989 (t) cc_final: 0.7546 (m) REVERT: B 398 ASP cc_start: 0.6644 (m-30) cc_final: 0.6037 (m-30) REVERT: B 403 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8331 (mmt180) REVERT: B 409 GLN cc_start: 0.8872 (mt0) cc_final: 0.8349 (mt0) REVERT: B 418 ILE cc_start: 0.8914 (pt) cc_final: 0.8692 (mp) REVERT: B 436 TRP cc_start: 0.8138 (p-90) cc_final: 0.7826 (p-90) REVERT: B 521 PRO cc_start: 0.7349 (Cg_endo) cc_final: 0.7114 (Cg_exo) REVERT: B 535 LYS cc_start: 0.8394 (tppp) cc_final: 0.7995 (tppt) REVERT: B 557 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7448 (mtmm) REVERT: B 578 ASP cc_start: 0.7746 (p0) cc_final: 0.7529 (p0) REVERT: B 583 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8219 (tp30) REVERT: B 619 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7920 (mp0) REVERT: B 707 TYR cc_start: 0.6842 (t80) cc_final: 0.6592 (t80) REVERT: B 723 THR cc_start: 0.8275 (m) cc_final: 0.8073 (m) REVERT: B 725 GLU cc_start: 0.7513 (tt0) cc_final: 0.7019 (tm-30) REVERT: B 726 ILE cc_start: 0.8179 (mp) cc_final: 0.7720 (mp) REVERT: B 727 LEU cc_start: 0.7763 (mt) cc_final: 0.6936 (mt) REVERT: B 748 GLU cc_start: 0.8949 (mp0) cc_final: 0.8738 (mp0) REVERT: B 756 TYR cc_start: 0.8061 (m-80) cc_final: 0.7484 (m-80) REVERT: B 758 SER cc_start: 0.8880 (t) cc_final: 0.8608 (m) REVERT: B 762 GLN cc_start: 0.8401 (pp30) cc_final: 0.7984 (pp30) REVERT: B 763 LEU cc_start: 0.8668 (mt) cc_final: 0.8332 (mm) REVERT: B 776 LYS cc_start: 0.8867 (tptp) cc_final: 0.8434 (tptp) REVERT: B 779 GLN cc_start: 0.8531 (tp40) cc_final: 0.7776 (tm-30) REVERT: B 780 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7458 (tp30) REVERT: B 805 ILE cc_start: 0.8747 (mt) cc_final: 0.8219 (tp) REVERT: B 823 PHE cc_start: 0.8236 (m-80) cc_final: 0.7714 (m-80) REVERT: B 867 ASP cc_start: 0.7995 (t0) cc_final: 0.7793 (t0) REVERT: B 869 MET cc_start: 0.8394 (mpp) cc_final: 0.7853 (ptp) REVERT: B 878 LEU cc_start: 0.9256 (mt) cc_final: 0.8986 (tp) REVERT: B 917 TYR cc_start: 0.8101 (m-80) cc_final: 0.7498 (m-10) REVERT: B 921 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8428 (mtpp) REVERT: B 926 GLN cc_start: 0.8725 (mt0) cc_final: 0.8405 (tp40) REVERT: B 934 ILE cc_start: 0.8423 (mm) cc_final: 0.8189 (mm) REVERT: B 935 GLN cc_start: 0.8860 (tt0) cc_final: 0.8250 (tm-30) REVERT: B 939 SER cc_start: 0.6840 (p) cc_final: 0.6637 (p) REVERT: B 954 GLN cc_start: 0.8262 (pp30) cc_final: 0.7967 (pp30) REVERT: B 955 ASN cc_start: 0.8848 (m110) cc_final: 0.8209 (m110) REVERT: B 965 GLN cc_start: 0.8615 (tp-100) cc_final: 0.7916 (tp40) REVERT: B 970 PHE cc_start: 0.6831 (m-10) cc_final: 0.5968 (m-10) REVERT: B 979 ASP cc_start: 0.8693 (t0) cc_final: 0.8385 (t0) REVERT: B 991 VAL cc_start: 0.9036 (m) cc_final: 0.8729 (t) REVERT: B 994 ASP cc_start: 0.8431 (t0) cc_final: 0.8005 (t0) REVERT: B 996 LEU cc_start: 0.9018 (mt) cc_final: 0.8800 (mt) REVERT: B 1003 SER cc_start: 0.9193 (m) cc_final: 0.8869 (p) REVERT: B 1004 LEU cc_start: 0.9187 (mt) cc_final: 0.8981 (mt) REVERT: B 1005 GLN cc_start: 0.8938 (pt0) cc_final: 0.8208 (pp30) REVERT: B 1017 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8167 (pp20) REVERT: B 1024 LEU cc_start: 0.8853 (tt) cc_final: 0.8453 (tt) REVERT: B 1027 THR cc_start: 0.8821 (m) cc_final: 0.8573 (p) REVERT: B 1028 LYS cc_start: 0.8602 (tppt) cc_final: 0.7686 (tppt) REVERT: B 1031 GLU cc_start: 0.7801 (tt0) cc_final: 0.6847 (tt0) REVERT: B 1033 VAL cc_start: 0.7949 (t) cc_final: 0.7663 (t) REVERT: B 1034 LEU cc_start: 0.8023 (mt) cc_final: 0.7718 (mt) REVERT: B 1038 LYS cc_start: 0.9155 (tptt) cc_final: 0.8741 (tptt) REVERT: B 1081 ILE cc_start: 0.7256 (mp) cc_final: 0.6744 (tp) REVERT: B 1096 VAL cc_start: 0.8016 (p) cc_final: 0.7643 (m) REVERT: B 1113 GLN cc_start: 0.8556 (mt0) cc_final: 0.8284 (mp10) REVERT: C 65 PHE cc_start: 0.8526 (m-80) cc_final: 0.7867 (m-80) REVERT: C 104 TRP cc_start: 0.5513 (m-90) cc_final: 0.5005 (m-90) REVERT: C 133 PHE cc_start: 0.6748 (m-80) cc_final: 0.5954 (m-80) REVERT: C 135 PHE cc_start: 0.8529 (m-10) cc_final: 0.7603 (t80) REVERT: C 203 ILE cc_start: 0.8272 (tt) cc_final: 0.7958 (tp) REVERT: C 265 TYR cc_start: 0.7554 (p90) cc_final: 0.7245 (p90) REVERT: C 318 PHE cc_start: 0.7594 (t80) cc_final: 0.7282 (t80) REVERT: C 370 ASN cc_start: 0.8953 (m110) cc_final: 0.8535 (p0) REVERT: C 440 ASN cc_start: 0.8563 (m-40) cc_final: 0.7901 (p0) REVERT: C 535 LYS cc_start: 0.8345 (mppt) cc_final: 0.7930 (ttmm) REVERT: C 552 LEU cc_start: 0.8698 (mm) cc_final: 0.8113 (mm) REVERT: C 554 GLU cc_start: 0.8655 (tt0) cc_final: 0.8228 (tt0) REVERT: C 557 LYS cc_start: 0.9024 (mttt) cc_final: 0.8644 (mmmt) REVERT: C 559 PHE cc_start: 0.7586 (m-10) cc_final: 0.6358 (m-10) REVERT: C 583 GLU cc_start: 0.8716 (mp0) cc_final: 0.8285 (mp0) REVERT: C 657 ASN cc_start: 0.8595 (m-40) cc_final: 0.8306 (m-40) REVERT: C 712 ILE cc_start: 0.8023 (tp) cc_final: 0.7797 (tp) REVERT: C 725 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7156 (tt0) REVERT: C 727 LEU cc_start: 0.8316 (mt) cc_final: 0.7985 (mt) REVERT: C 759 PHE cc_start: 0.8055 (m-80) cc_final: 0.7370 (m-80) REVERT: C 763 LEU cc_start: 0.8920 (mt) cc_final: 0.8708 (mt) REVERT: C 772 VAL cc_start: 0.8807 (m) cc_final: 0.8501 (p) REVERT: C 774 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8308 (mm110) REVERT: C 776 LYS cc_start: 0.9175 (ttpt) cc_final: 0.8974 (ttpt) REVERT: C 790 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7868 (mmtm) REVERT: C 795 LYS cc_start: 0.8880 (mppt) cc_final: 0.8490 (mptt) REVERT: C 796 ASP cc_start: 0.8837 (m-30) cc_final: 0.8182 (m-30) REVERT: C 808 ASP cc_start: 0.8432 (t0) cc_final: 0.8171 (t0) REVERT: C 859 THR cc_start: 0.8363 (t) cc_final: 0.8057 (p) REVERT: C 865 LEU cc_start: 0.8517 (mt) cc_final: 0.8046 (mp) REVERT: C 869 MET cc_start: 0.8483 (mtm) cc_final: 0.8062 (mtm) REVERT: C 872 GLN cc_start: 0.8932 (tp40) cc_final: 0.8599 (tp-100) REVERT: C 901 GLN cc_start: 0.8800 (tt0) cc_final: 0.8102 (tm-30) REVERT: C 902 MET cc_start: 0.8408 (tmm) cc_final: 0.7806 (tmm) REVERT: C 905 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8148 (mtt-85) REVERT: C 921 LYS cc_start: 0.8464 (mmpt) cc_final: 0.8150 (mttm) REVERT: C 925 ASN cc_start: 0.8670 (m-40) cc_final: 0.8433 (m-40) REVERT: C 926 GLN cc_start: 0.8730 (mt0) cc_final: 0.8463 (mt0) REVERT: C 947 LYS cc_start: 0.8711 (mttt) cc_final: 0.8480 (pttt) REVERT: C 949 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8182 (tp-100) REVERT: C 964 LYS cc_start: 0.8906 (tttt) cc_final: 0.8327 (ptmt) REVERT: C 965 GLN cc_start: 0.8776 (tp40) cc_final: 0.8210 (mm-40) REVERT: C 966 LEU cc_start: 0.8704 (mt) cc_final: 0.8478 (mt) REVERT: C 1013 ILE cc_start: 0.8948 (mt) cc_final: 0.8618 (mm) REVERT: C 1017 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8101 (mt-10) REVERT: C 1029 MET cc_start: 0.8864 (tpp) cc_final: 0.8458 (tpp) REVERT: C 1054 GLN cc_start: 0.8098 (mm110) cc_final: 0.7817 (tp40) REVERT: C 1067 TYR cc_start: 0.8226 (t80) cc_final: 0.7845 (t80) REVERT: C 1081 ILE cc_start: 0.8020 (mt) cc_final: 0.7456 (mm) REVERT: C 1088 HIS cc_start: 0.7431 (m90) cc_final: 0.6999 (m-70) REVERT: C 1103 PHE cc_start: 0.7923 (m-80) cc_final: 0.7468 (m-80) REVERT: C 1105 THR cc_start: 0.7380 (t) cc_final: 0.6884 (m) outliers start: 2 outliers final: 0 residues processed: 759 average time/residue: 0.3815 time to fit residues: 446.4525 Evaluate side-chains 712 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 0.2980 chunk 280 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 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 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120376 restraints weight = 56362.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.125387 restraints weight = 35138.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129051 restraints weight = 24531.326| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26624 Z= 0.169 Angle : 0.762 18.551 36353 Z= 0.369 Chirality : 0.051 0.671 4208 Planarity : 0.005 0.082 4627 Dihedral : 9.157 102.528 4458 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.14), residues: 3207 helix: 0.99 (0.20), residues: 667 sheet: -0.14 (0.19), residues: 666 loop : -1.22 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 436 HIS 0.013 0.002 HIS B 66 PHE 0.017 0.002 PHE B1062 TYR 0.021 0.002 TYR A 674 ARG 0.010 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 34) link_NAG-ASN : angle 5.09705 ( 102) link_BETA1-4 : bond 0.00283 ( 10) link_BETA1-4 : angle 1.89112 ( 30) hydrogen bonds : bond 0.04780 ( 873) hydrogen bonds : angle 6.01130 ( 2436) SS BOND : bond 0.00568 ( 41) SS BOND : angle 2.09028 ( 82) covalent geometry : bond 0.00341 (26536) covalent geometry : angle 0.70589 (36139) Misc. bond : bond 0.00313 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7420 (t70) cc_final: 0.6881 (t-90) REVERT: A 56 LEU cc_start: 0.8726 (tp) cc_final: 0.8499 (tp) REVERT: A 80 ASP cc_start: 0.8200 (t0) cc_final: 0.7709 (t0) REVERT: A 104 TRP cc_start: 0.6820 (m-90) cc_final: 0.6494 (m-90) REVERT: A 177 MET cc_start: 0.2698 (mtm) cc_final: 0.1439 (mmp) REVERT: A 224 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8281 (pm20) REVERT: A 240 THR cc_start: 0.8292 (t) cc_final: 0.7601 (t) REVERT: A 273 ARG cc_start: 0.8652 (mmt180) cc_final: 0.8359 (mmt180) REVERT: A 278 LYS cc_start: 0.6737 (tmmt) cc_final: 0.6232 (ptmm) REVERT: A 287 ASP cc_start: 0.8448 (t0) cc_final: 0.8168 (t70) REVERT: A 298 GLU cc_start: 0.8276 (tt0) cc_final: 0.7932 (tt0) REVERT: A 342 PHE cc_start: 0.9229 (m-10) cc_final: 0.8812 (m-10) REVERT: A 374 PHE cc_start: 0.7989 (m-80) cc_final: 0.7625 (m-10) REVERT: A 532 ASN cc_start: 0.8024 (t0) cc_final: 0.7732 (t0) REVERT: A 535 LYS cc_start: 0.8501 (mttt) cc_final: 0.8043 (ptpt) REVERT: A 562 PHE cc_start: 0.7923 (p90) cc_final: 0.7704 (p90) REVERT: A 571 ASP cc_start: 0.7166 (t0) cc_final: 0.6901 (t0) REVERT: A 578 ASP cc_start: 0.8072 (t70) cc_final: 0.7810 (t0) REVERT: A 583 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 643 PHE cc_start: 0.7986 (t80) cc_final: 0.7720 (t80) REVERT: A 658 ASN cc_start: 0.7909 (t0) cc_final: 0.7300 (t0) REVERT: A 702 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7914 (tp30) REVERT: A 708 SER cc_start: 0.7768 (t) cc_final: 0.7457 (p) REVERT: A 731 MET cc_start: 0.8167 (pmm) cc_final: 0.7701 (pmm) REVERT: A 740 MET cc_start: 0.8065 (tpp) cc_final: 0.7374 (tpp) REVERT: A 751 ASN cc_start: 0.8361 (m110) cc_final: 0.8033 (m110) REVERT: A 762 GLN cc_start: 0.8694 (pt0) cc_final: 0.8398 (pt0) REVERT: A 763 LEU cc_start: 0.8717 (mt) cc_final: 0.8460 (mt) REVERT: A 772 VAL cc_start: 0.8996 (t) cc_final: 0.8059 (m) REVERT: A 775 ASP cc_start: 0.7997 (t0) cc_final: 0.7677 (t0) REVERT: A 776 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8228 (mmtp) REVERT: A 777 ASN cc_start: 0.8859 (m-40) cc_final: 0.8639 (m-40) REVERT: A 818 ILE cc_start: 0.9221 (mt) cc_final: 0.8993 (pt) REVERT: A 858 LEU cc_start: 0.8431 (mt) cc_final: 0.8215 (mt) REVERT: A 870 ILE cc_start: 0.8944 (mt) cc_final: 0.8692 (mt) REVERT: A 873 TYR cc_start: 0.8718 (m-10) cc_final: 0.8225 (m-80) REVERT: A 878 LEU cc_start: 0.8948 (tp) cc_final: 0.8680 (tp) REVERT: A 902 MET cc_start: 0.8491 (ttm) cc_final: 0.7815 (ttm) REVERT: A 911 VAL cc_start: 0.7169 (t) cc_final: 0.6871 (m) REVERT: A 919 ASN cc_start: 0.8598 (m110) cc_final: 0.8183 (m110) REVERT: A 921 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8247 (tptp) REVERT: A 926 GLN cc_start: 0.9062 (mt0) cc_final: 0.8572 (mt0) REVERT: A 928 ASN cc_start: 0.8417 (m-40) cc_final: 0.8126 (m-40) REVERT: A 933 LYS cc_start: 0.9025 (mttm) cc_final: 0.8384 (mmmm) REVERT: A 949 GLN cc_start: 0.8616 (pp30) cc_final: 0.8300 (pp30) REVERT: A 957 GLN cc_start: 0.9045 (tt0) cc_final: 0.8326 (tm-30) REVERT: A 964 LYS cc_start: 0.8835 (mttt) cc_final: 0.8291 (tptp) REVERT: A 965 GLN cc_start: 0.8783 (mm110) cc_final: 0.8403 (mm-40) REVERT: A 991 VAL cc_start: 0.8255 (p) cc_final: 0.7721 (t) REVERT: A 993 ILE cc_start: 0.9173 (mm) cc_final: 0.8924 (mm) REVERT: A 995 ARG cc_start: 0.8876 (ttm170) cc_final: 0.8507 (tpp80) REVERT: A 1005 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 1009 THR cc_start: 0.8862 (m) cc_final: 0.8306 (p) REVERT: A 1014 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8585 (mmm-85) REVERT: A 1017 GLU cc_start: 0.9023 (tt0) cc_final: 0.8258 (mm-30) REVERT: A 1038 LYS cc_start: 0.8747 (mttt) cc_final: 0.8150 (mttp) REVERT: A 1045 LYS cc_start: 0.8529 (mppt) cc_final: 0.8166 (mmtm) REVERT: A 1060 VAL cc_start: 0.8775 (t) cc_final: 0.8567 (m) REVERT: A 1077 THR cc_start: 0.8073 (t) cc_final: 0.7734 (t) REVERT: A 1088 HIS cc_start: 0.7793 (m-70) cc_final: 0.7230 (m-70) REVERT: A 1091 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7184 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8696 (m90) cc_final: 0.8333 (m170) REVERT: A 1109 PHE cc_start: 0.7879 (t80) cc_final: 0.7427 (t80) REVERT: A 1114 ILE cc_start: 0.9033 (mp) cc_final: 0.8674 (tp) REVERT: A 1121 PHE cc_start: 0.7465 (p90) cc_final: 0.7124 (p90) REVERT: B 44 ARG cc_start: 0.7971 (mtt90) cc_final: 0.6978 (mtm-85) REVERT: B 52 GLN cc_start: 0.8221 (mp10) cc_final: 0.7923 (mp10) REVERT: B 53 ASP cc_start: 0.7216 (t0) cc_final: 0.6526 (t0) REVERT: B 54 LEU cc_start: 0.8202 (mp) cc_final: 0.7310 (tt) REVERT: B 65 PHE cc_start: 0.8152 (m-80) cc_final: 0.7319 (m-80) REVERT: B 92 PHE cc_start: 0.7754 (t80) cc_final: 0.7146 (t80) REVERT: B 99 ASN cc_start: 0.8706 (t0) cc_final: 0.8047 (t0) REVERT: B 135 PHE cc_start: 0.8630 (m-80) cc_final: 0.8412 (m-80) REVERT: B 153 MET cc_start: 0.6996 (ppp) cc_final: 0.6324 (ppp) REVERT: B 187 LYS cc_start: 0.8255 (pttm) cc_final: 0.7797 (pttm) REVERT: B 192 PHE cc_start: 0.6279 (m-80) cc_final: 0.5990 (m-80) REVERT: B 207 HIS cc_start: 0.8502 (m90) cc_final: 0.8129 (m90) REVERT: B 233 ILE cc_start: 0.6581 (pt) cc_final: 0.5492 (tp) REVERT: B 287 ASP cc_start: 0.7782 (t0) cc_final: 0.7507 (t0) REVERT: B 306 PHE cc_start: 0.7660 (m-10) cc_final: 0.7033 (m-10) REVERT: B 313 TYR cc_start: 0.8156 (m-80) cc_final: 0.7885 (m-80) REVERT: B 331 ASN cc_start: 0.7012 (t0) cc_final: 0.6634 (m-40) REVERT: B 357 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7465 (mmm160) REVERT: B 380 TYR cc_start: 0.8161 (m-80) cc_final: 0.7755 (m-80) REVERT: B 395 VAL cc_start: 0.8065 (t) cc_final: 0.7816 (m) REVERT: B 398 ASP cc_start: 0.6463 (m-30) cc_final: 0.5486 (m-30) REVERT: B 409 GLN cc_start: 0.8895 (mt0) cc_final: 0.8360 (mt0) REVERT: B 418 ILE cc_start: 0.8880 (pt) cc_final: 0.8613 (mp) REVERT: B 436 TRP cc_start: 0.8022 (p-90) cc_final: 0.7517 (p-90) REVERT: B 454 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7941 (tpt-90) REVERT: B 457 ARG cc_start: 0.8625 (tmt-80) cc_final: 0.8216 (tpt90) REVERT: B 535 LYS cc_start: 0.8507 (tppp) cc_final: 0.7849 (tppt) REVERT: B 557 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7418 (mtmm) REVERT: B 619 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7879 (mp0) REVERT: B 712 ILE cc_start: 0.7682 (tt) cc_final: 0.7237 (tp) REVERT: B 748 GLU cc_start: 0.8767 (mp0) cc_final: 0.8555 (mp0) REVERT: B 756 TYR cc_start: 0.8197 (m-80) cc_final: 0.7290 (m-80) REVERT: B 758 SER cc_start: 0.8929 (t) cc_final: 0.8665 (m) REVERT: B 762 GLN cc_start: 0.8373 (pp30) cc_final: 0.7959 (pp30) REVERT: B 763 LEU cc_start: 0.8677 (mt) cc_final: 0.8313 (mm) REVERT: B 773 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 776 LYS cc_start: 0.8837 (tptp) cc_final: 0.8374 (tptp) REVERT: B 779 GLN cc_start: 0.8499 (tp40) cc_final: 0.7702 (tm-30) REVERT: B 780 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7458 (tp30) REVERT: B 805 ILE cc_start: 0.8807 (mt) cc_final: 0.8364 (tp) REVERT: B 811 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8350 (mmmt) REVERT: B 823 PHE cc_start: 0.8246 (m-80) cc_final: 0.7712 (m-80) REVERT: B 869 MET cc_start: 0.8383 (mpp) cc_final: 0.7854 (ptp) REVERT: B 877 LEU cc_start: 0.8914 (mt) cc_final: 0.8690 (mt) REVERT: B 894 LEU cc_start: 0.8103 (mm) cc_final: 0.7860 (mm) REVERT: B 909 ILE cc_start: 0.7672 (mm) cc_final: 0.7421 (pt) REVERT: B 917 TYR cc_start: 0.8186 (m-10) cc_final: 0.7435 (m-10) REVERT: B 921 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8401 (mtpp) REVERT: B 926 GLN cc_start: 0.8745 (mt0) cc_final: 0.8369 (tp40) REVERT: B 934 ILE cc_start: 0.8394 (mm) cc_final: 0.8160 (mm) REVERT: B 935 GLN cc_start: 0.8841 (tt0) cc_final: 0.8238 (tm-30) REVERT: B 954 GLN cc_start: 0.8271 (pp30) cc_final: 0.7969 (pp30) REVERT: B 955 ASN cc_start: 0.8937 (m110) cc_final: 0.8241 (m110) REVERT: B 957 GLN cc_start: 0.9030 (tt0) cc_final: 0.8349 (tp40) REVERT: B 964 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8407 (ttmm) REVERT: B 965 GLN cc_start: 0.8496 (tp-100) cc_final: 0.7786 (tp-100) REVERT: B 970 PHE cc_start: 0.6943 (m-10) cc_final: 0.5993 (m-10) REVERT: B 979 ASP cc_start: 0.8693 (t0) cc_final: 0.8354 (t0) REVERT: B 991 VAL cc_start: 0.9024 (m) cc_final: 0.8722 (t) REVERT: B 994 ASP cc_start: 0.8383 (t0) cc_final: 0.7856 (t0) REVERT: B 996 LEU cc_start: 0.8996 (mt) cc_final: 0.8787 (mt) REVERT: B 1003 SER cc_start: 0.9261 (m) cc_final: 0.8859 (p) REVERT: B 1005 GLN cc_start: 0.8862 (pt0) cc_final: 0.8085 (pp30) REVERT: B 1024 LEU cc_start: 0.8827 (tt) cc_final: 0.8471 (tt) REVERT: B 1027 THR cc_start: 0.8709 (m) cc_final: 0.8491 (p) REVERT: B 1028 LYS cc_start: 0.8563 (tppt) cc_final: 0.7742 (tppt) REVERT: B 1031 GLU cc_start: 0.7853 (tt0) cc_final: 0.6800 (tt0) REVERT: B 1033 VAL cc_start: 0.8084 (t) cc_final: 0.7807 (t) REVERT: B 1038 LYS cc_start: 0.9125 (tptt) cc_final: 0.8709 (tptt) REVERT: B 1045 LYS cc_start: 0.8142 (pptt) cc_final: 0.7694 (pptt) REVERT: B 1077 THR cc_start: 0.7559 (t) cc_final: 0.7355 (t) REVERT: B 1081 ILE cc_start: 0.7242 (mp) cc_final: 0.6715 (tp) REVERT: B 1113 GLN cc_start: 0.8547 (mt0) cc_final: 0.8320 (mp10) REVERT: C 65 PHE cc_start: 0.8429 (m-80) cc_final: 0.7681 (m-80) REVERT: C 164 ASN cc_start: 0.8368 (t0) cc_final: 0.8152 (t0) REVERT: C 197 ILE cc_start: 0.8045 (pt) cc_final: 0.7560 (mm) REVERT: C 203 ILE cc_start: 0.8138 (tt) cc_final: 0.7855 (tp) REVERT: C 206 LYS cc_start: 0.7658 (mmpt) cc_final: 0.7405 (mmtt) REVERT: C 265 TYR cc_start: 0.7575 (p90) cc_final: 0.7143 (p90) REVERT: C 277 LEU cc_start: 0.8120 (mt) cc_final: 0.7864 (mt) REVERT: C 318 PHE cc_start: 0.7723 (t80) cc_final: 0.7337 (t80) REVERT: C 370 ASN cc_start: 0.8980 (m110) cc_final: 0.8571 (p0) REVERT: C 440 ASN cc_start: 0.8552 (m-40) cc_final: 0.7879 (p0) REVERT: C 533 LEU cc_start: 0.8906 (tp) cc_final: 0.8595 (tp) REVERT: C 576 VAL cc_start: 0.8396 (p) cc_final: 0.8159 (m) REVERT: C 657 ASN cc_start: 0.8548 (m-40) cc_final: 0.8335 (m-40) REVERT: C 664 ILE cc_start: 0.7843 (mm) cc_final: 0.7642 (mm) REVERT: C 712 ILE cc_start: 0.7901 (tp) cc_final: 0.7668 (tp) REVERT: C 725 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7188 (tt0) REVERT: C 727 LEU cc_start: 0.8325 (mt) cc_final: 0.7962 (mt) REVERT: C 742 ILE cc_start: 0.9018 (mm) cc_final: 0.8706 (pt) REVERT: C 756 TYR cc_start: 0.7703 (m-80) cc_final: 0.7369 (m-80) REVERT: C 759 PHE cc_start: 0.8055 (m-80) cc_final: 0.7335 (m-80) REVERT: C 763 LEU cc_start: 0.8936 (mt) cc_final: 0.8551 (mt) REVERT: C 772 VAL cc_start: 0.8864 (m) cc_final: 0.8603 (p) REVERT: C 774 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8158 (mm110) REVERT: C 776 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8915 (ttpt) REVERT: C 777 ASN cc_start: 0.8910 (m110) cc_final: 0.8708 (m110) REVERT: C 778 THR cc_start: 0.8836 (m) cc_final: 0.8601 (p) REVERT: C 790 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7881 (mmtm) REVERT: C 796 ASP cc_start: 0.8864 (m-30) cc_final: 0.7832 (t0) REVERT: C 808 ASP cc_start: 0.8422 (t0) cc_final: 0.8141 (t0) REVERT: C 859 THR cc_start: 0.8349 (t) cc_final: 0.8050 (p) REVERT: C 865 LEU cc_start: 0.8631 (mt) cc_final: 0.7948 (mt) REVERT: C 869 MET cc_start: 0.8369 (mtm) cc_final: 0.7927 (mtm) REVERT: C 872 GLN cc_start: 0.8924 (tp40) cc_final: 0.8660 (tp-100) REVERT: C 902 MET cc_start: 0.8461 (tmm) cc_final: 0.7776 (tmm) REVERT: C 909 ILE cc_start: 0.8859 (pt) cc_final: 0.8318 (mm) REVERT: C 921 LYS cc_start: 0.8477 (mmpt) cc_final: 0.8157 (mtpp) REVERT: C 925 ASN cc_start: 0.8650 (m-40) cc_final: 0.8398 (m-40) REVERT: C 926 GLN cc_start: 0.8739 (mt0) cc_final: 0.8447 (mt0) REVERT: C 947 LYS cc_start: 0.8837 (mttt) cc_final: 0.8455 (ptpp) REVERT: C 964 LYS cc_start: 0.8950 (tttt) cc_final: 0.8424 (ptmt) REVERT: C 966 LEU cc_start: 0.8745 (mt) cc_final: 0.8489 (mt) REVERT: C 1013 ILE cc_start: 0.8982 (mt) cc_final: 0.8641 (mm) REVERT: C 1017 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 1028 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8912 (mmtp) REVERT: C 1081 ILE cc_start: 0.8008 (mt) cc_final: 0.7451 (mm) REVERT: C 1088 HIS cc_start: 0.7415 (m90) cc_final: 0.6988 (m-70) REVERT: C 1103 PHE cc_start: 0.7933 (m-80) cc_final: 0.7557 (m-80) REVERT: C 1125 ASN cc_start: 0.8939 (p0) cc_final: 0.8730 (p0) outliers start: 0 outliers final: 0 residues processed: 741 average time/residue: 0.3852 time to fit residues: 441.5967 Evaluate side-chains 695 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 55 optimal weight: 0.0050 chunk 231 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 291 optimal weight: 0.0670 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 271 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.164738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125687 restraints weight = 54707.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130656 restraints weight = 34231.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.134214 restraints weight = 23811.324| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26624 Z= 0.136 Angle : 0.743 18.516 36353 Z= 0.356 Chirality : 0.051 0.658 4208 Planarity : 0.005 0.122 4627 Dihedral : 8.871 100.015 4458 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -0.72 (0.14), residues: 3207 helix: 1.00 (0.20), residues: 679 sheet: -0.10 (0.19), residues: 695 loop : -1.23 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1102 HIS 0.010 0.001 HIS B 66 PHE 0.028 0.001 PHE A 906 TYR 0.037 0.001 TYR B 365 ARG 0.017 0.001 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00892 ( 34) link_NAG-ASN : angle 4.91577 ( 102) link_BETA1-4 : bond 0.00300 ( 10) link_BETA1-4 : angle 1.66069 ( 30) hydrogen bonds : bond 0.04402 ( 873) hydrogen bonds : angle 5.79320 ( 2436) SS BOND : bond 0.00392 ( 41) SS BOND : angle 1.90796 ( 82) covalent geometry : bond 0.00291 (26536) covalent geometry : angle 0.69050 (36139) Misc. bond : bond 0.00190 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 740 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8736 (mmpt) cc_final: 0.7590 (mmmm) REVERT: A 49 HIS cc_start: 0.7239 (t70) cc_final: 0.6946 (t-90) REVERT: A 53 ASP cc_start: 0.8136 (t0) cc_final: 0.7566 (t0) REVERT: A 80 ASP cc_start: 0.8166 (t0) cc_final: 0.7635 (t0) REVERT: A 104 TRP cc_start: 0.6733 (m-90) cc_final: 0.6409 (m-90) REVERT: A 177 MET cc_start: 0.2489 (mtm) cc_final: 0.1344 (mmp) REVERT: A 207 HIS cc_start: 0.8124 (t70) cc_final: 0.6018 (t70) REVERT: A 224 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8350 (pm20) REVERT: A 240 THR cc_start: 0.8246 (t) cc_final: 0.7570 (t) REVERT: A 273 ARG cc_start: 0.8570 (mmt180) cc_final: 0.8293 (mmt180) REVERT: A 287 ASP cc_start: 0.8395 (t0) cc_final: 0.8165 (t70) REVERT: A 298 GLU cc_start: 0.8265 (tt0) cc_final: 0.7901 (tt0) REVERT: A 319 ARG cc_start: 0.7330 (ptt90) cc_final: 0.7100 (ptt90) REVERT: A 342 PHE cc_start: 0.9098 (m-10) cc_final: 0.8751 (m-10) REVERT: A 374 PHE cc_start: 0.7903 (m-80) cc_final: 0.7544 (m-10) REVERT: A 529 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7957 (mmtm) REVERT: A 532 ASN cc_start: 0.7972 (t0) cc_final: 0.7661 (t0) REVERT: A 533 LEU cc_start: 0.8615 (tp) cc_final: 0.8410 (tp) REVERT: A 578 ASP cc_start: 0.7865 (t70) cc_final: 0.7642 (t0) REVERT: A 583 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 658 ASN cc_start: 0.8017 (t0) cc_final: 0.7462 (t0) REVERT: A 702 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7857 (tp30) REVERT: A 708 SER cc_start: 0.7759 (t) cc_final: 0.7467 (p) REVERT: A 737 ASP cc_start: 0.8054 (t0) cc_final: 0.7824 (t0) REVERT: A 740 MET cc_start: 0.7885 (tpp) cc_final: 0.7240 (tpp) REVERT: A 751 ASN cc_start: 0.8344 (m110) cc_final: 0.7996 (m110) REVERT: A 762 GLN cc_start: 0.8686 (pt0) cc_final: 0.8339 (pt0) REVERT: A 763 LEU cc_start: 0.8790 (mt) cc_final: 0.8486 (mt) REVERT: A 770 ILE cc_start: 0.8965 (mt) cc_final: 0.8525 (mt) REVERT: A 772 VAL cc_start: 0.9017 (t) cc_final: 0.8287 (m) REVERT: A 774 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7777 (mm-40) REVERT: A 775 ASP cc_start: 0.7874 (t0) cc_final: 0.7588 (t0) REVERT: A 776 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8178 (mmtp) REVERT: A 788 ILE cc_start: 0.7934 (mm) cc_final: 0.7583 (tp) REVERT: A 797 PHE cc_start: 0.8968 (m-80) cc_final: 0.8550 (m-80) REVERT: A 818 ILE cc_start: 0.9197 (mt) cc_final: 0.8972 (pt) REVERT: A 858 LEU cc_start: 0.8450 (mt) cc_final: 0.8243 (mt) REVERT: A 866 THR cc_start: 0.7907 (p) cc_final: 0.6987 (m) REVERT: A 869 MET cc_start: 0.8995 (mtm) cc_final: 0.7849 (mtm) REVERT: A 870 ILE cc_start: 0.8902 (mt) cc_final: 0.8679 (mt) REVERT: A 873 TYR cc_start: 0.8668 (m-10) cc_final: 0.8192 (m-80) REVERT: A 878 LEU cc_start: 0.8892 (tp) cc_final: 0.8641 (tp) REVERT: A 902 MET cc_start: 0.8510 (ttm) cc_final: 0.7859 (ttm) REVERT: A 911 VAL cc_start: 0.7156 (t) cc_final: 0.6865 (m) REVERT: A 919 ASN cc_start: 0.8595 (m110) cc_final: 0.8139 (m110) REVERT: A 921 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8182 (tptp) REVERT: A 926 GLN cc_start: 0.8992 (mt0) cc_final: 0.8548 (mt0) REVERT: A 928 ASN cc_start: 0.8322 (m-40) cc_final: 0.8031 (m-40) REVERT: A 933 LYS cc_start: 0.8971 (mttm) cc_final: 0.8305 (mmmm) REVERT: A 949 GLN cc_start: 0.8601 (pp30) cc_final: 0.8285 (pp30) REVERT: A 957 GLN cc_start: 0.9042 (tt0) cc_final: 0.8296 (tm-30) REVERT: A 964 LYS cc_start: 0.8799 (mttt) cc_final: 0.8260 (tptp) REVERT: A 991 VAL cc_start: 0.8219 (p) cc_final: 0.7688 (t) REVERT: A 995 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8490 (tpp80) REVERT: A 1005 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8110 (tp40) REVERT: A 1009 THR cc_start: 0.8828 (m) cc_final: 0.8407 (p) REVERT: A 1017 GLU cc_start: 0.8970 (tt0) cc_final: 0.8100 (mm-30) REVERT: A 1041 ASP cc_start: 0.7819 (t0) cc_final: 0.7596 (t0) REVERT: A 1045 LYS cc_start: 0.8577 (mppt) cc_final: 0.8221 (mmtm) REVERT: A 1077 THR cc_start: 0.8134 (t) cc_final: 0.7861 (t) REVERT: A 1084 ASP cc_start: 0.8948 (p0) cc_final: 0.8655 (p0) REVERT: A 1086 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8528 (mmmt) REVERT: A 1088 HIS cc_start: 0.7739 (m-70) cc_final: 0.7164 (m-70) REVERT: A 1089 PHE cc_start: 0.7026 (m-80) cc_final: 0.6743 (m-80) REVERT: A 1101 HIS cc_start: 0.8547 (m90) cc_final: 0.8142 (m-70) REVERT: A 1102 TRP cc_start: 0.7926 (m100) cc_final: 0.7720 (m100) REVERT: A 1109 PHE cc_start: 0.7787 (t80) cc_final: 0.7327 (t80) REVERT: A 1114 ILE cc_start: 0.9032 (mp) cc_final: 0.8663 (tp) REVERT: B 44 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7213 (mtt-85) REVERT: B 52 GLN cc_start: 0.8192 (mp10) cc_final: 0.7908 (mp10) REVERT: B 53 ASP cc_start: 0.7269 (t0) cc_final: 0.6660 (t0) REVERT: B 54 LEU cc_start: 0.8224 (mp) cc_final: 0.7889 (mp) REVERT: B 65 PHE cc_start: 0.8058 (m-80) cc_final: 0.7252 (m-80) REVERT: B 92 PHE cc_start: 0.7711 (t80) cc_final: 0.7128 (t80) REVERT: B 99 ASN cc_start: 0.8695 (t0) cc_final: 0.8025 (t0) REVERT: B 192 PHE cc_start: 0.6197 (m-80) cc_final: 0.5940 (m-80) REVERT: B 207 HIS cc_start: 0.8408 (m90) cc_final: 0.8073 (m90) REVERT: B 233 ILE cc_start: 0.6472 (pt) cc_final: 0.5521 (tp) REVERT: B 287 ASP cc_start: 0.7732 (t0) cc_final: 0.7501 (t0) REVERT: B 300 LYS cc_start: 0.8648 (mttt) cc_final: 0.8152 (mttt) REVERT: B 304 LYS cc_start: 0.9088 (mtmm) cc_final: 0.8225 (tppt) REVERT: B 306 PHE cc_start: 0.7655 (m-10) cc_final: 0.6981 (m-10) REVERT: B 309 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8401 (pp20) REVERT: B 313 TYR cc_start: 0.8148 (m-80) cc_final: 0.7542 (m-80) REVERT: B 331 ASN cc_start: 0.6950 (t0) cc_final: 0.6513 (m-40) REVERT: B 353 TRP cc_start: 0.7969 (p90) cc_final: 0.6627 (p90) REVERT: B 357 ARG cc_start: 0.8260 (mmm160) cc_final: 0.6723 (tpp-160) REVERT: B 380 TYR cc_start: 0.8150 (m-80) cc_final: 0.7708 (m-80) REVERT: B 395 VAL cc_start: 0.8036 (t) cc_final: 0.7733 (m) REVERT: B 409 GLN cc_start: 0.8944 (mt0) cc_final: 0.8358 (tt0) REVERT: B 418 ILE cc_start: 0.8813 (pt) cc_final: 0.8483 (mp) REVERT: B 436 TRP cc_start: 0.7947 (p-90) cc_final: 0.7524 (p-90) REVERT: B 454 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: B 557 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7366 (mtmm) REVERT: B 578 ASP cc_start: 0.7840 (p0) cc_final: 0.7339 (p0) REVERT: B 583 GLU cc_start: 0.8750 (mp0) cc_final: 0.8457 (mp0) REVERT: B 619 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7864 (mp0) REVERT: B 712 ILE cc_start: 0.7775 (tt) cc_final: 0.7392 (tp) REVERT: B 722 VAL cc_start: 0.7956 (t) cc_final: 0.7732 (t) REVERT: B 740 MET cc_start: 0.9276 (tpp) cc_final: 0.8975 (tpp) REVERT: B 762 GLN cc_start: 0.8349 (pp30) cc_final: 0.7925 (pp30) REVERT: B 763 LEU cc_start: 0.8661 (mt) cc_final: 0.8270 (mm) REVERT: B 776 LYS cc_start: 0.8767 (tptp) cc_final: 0.8293 (tptp) REVERT: B 779 GLN cc_start: 0.8461 (tp40) cc_final: 0.7643 (tm-30) REVERT: B 780 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7375 (tp30) REVERT: B 805 ILE cc_start: 0.8809 (mt) cc_final: 0.8385 (tp) REVERT: B 815 ARG cc_start: 0.7399 (mtm180) cc_final: 0.6946 (mtt-85) REVERT: B 823 PHE cc_start: 0.8190 (m-80) cc_final: 0.7675 (m-80) REVERT: B 869 MET cc_start: 0.8310 (mpp) cc_final: 0.7842 (ptp) REVERT: B 877 LEU cc_start: 0.8973 (mt) cc_final: 0.8767 (mt) REVERT: B 894 LEU cc_start: 0.8054 (mm) cc_final: 0.7838 (mm) REVERT: B 917 TYR cc_start: 0.8102 (m-10) cc_final: 0.6757 (m-10) REVERT: B 921 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8358 (mmmt) REVERT: B 926 GLN cc_start: 0.8654 (mt0) cc_final: 0.8268 (tp40) REVERT: B 934 ILE cc_start: 0.8284 (mm) cc_final: 0.8052 (mm) REVERT: B 954 GLN cc_start: 0.8236 (pp30) cc_final: 0.7925 (pp30) REVERT: B 955 ASN cc_start: 0.8941 (m110) cc_final: 0.8196 (m110) REVERT: B 957 GLN cc_start: 0.9024 (tt0) cc_final: 0.8734 (tt0) REVERT: B 960 ASN cc_start: 0.8481 (m-40) cc_final: 0.8254 (m-40) REVERT: B 964 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8323 (mmtt) REVERT: B 965 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7858 (tp40) REVERT: B 970 PHE cc_start: 0.6897 (m-10) cc_final: 0.6556 (m-10) REVERT: B 991 VAL cc_start: 0.8944 (m) cc_final: 0.8653 (t) REVERT: B 994 ASP cc_start: 0.8049 (t0) cc_final: 0.7757 (t0) REVERT: B 1003 SER cc_start: 0.9181 (m) cc_final: 0.8823 (p) REVERT: B 1004 LEU cc_start: 0.9132 (mt) cc_final: 0.8923 (mt) REVERT: B 1005 GLN cc_start: 0.8826 (pt0) cc_final: 0.7989 (pp30) REVERT: B 1024 LEU cc_start: 0.8878 (tt) cc_final: 0.8527 (tt) REVERT: B 1031 GLU cc_start: 0.7764 (tt0) cc_final: 0.6819 (tt0) REVERT: B 1038 LYS cc_start: 0.9104 (tptt) cc_final: 0.8695 (tptt) REVERT: B 1074 ASN cc_start: 0.6999 (m-40) cc_final: 0.6789 (m-40) REVERT: B 1077 THR cc_start: 0.7446 (t) cc_final: 0.7230 (t) REVERT: B 1109 PHE cc_start: 0.7271 (t80) cc_final: 0.7067 (t80) REVERT: C 65 PHE cc_start: 0.8393 (m-80) cc_final: 0.7626 (m-80) REVERT: C 164 ASN cc_start: 0.8358 (t0) cc_final: 0.8153 (t0) REVERT: C 197 ILE cc_start: 0.7943 (pt) cc_final: 0.7402 (mm) REVERT: C 203 ILE cc_start: 0.8069 (tt) cc_final: 0.7809 (tp) REVERT: C 206 LYS cc_start: 0.7492 (mmmt) cc_final: 0.7262 (mmtt) REVERT: C 265 TYR cc_start: 0.7476 (p90) cc_final: 0.7167 (p90) REVERT: C 277 LEU cc_start: 0.8054 (mt) cc_final: 0.7611 (pp) REVERT: C 300 LYS cc_start: 0.7909 (mttt) cc_final: 0.7258 (mptt) REVERT: C 318 PHE cc_start: 0.7652 (t80) cc_final: 0.7144 (t80) REVERT: C 370 ASN cc_start: 0.8943 (m110) cc_final: 0.8531 (p0) REVERT: C 377 PHE cc_start: 0.7931 (t80) cc_final: 0.7605 (t80) REVERT: C 440 ASN cc_start: 0.8531 (m-40) cc_final: 0.7844 (p0) REVERT: C 533 LEU cc_start: 0.8887 (tp) cc_final: 0.8640 (tp) REVERT: C 557 LYS cc_start: 0.8992 (mppt) cc_final: 0.8607 (mppt) REVERT: C 576 VAL cc_start: 0.8335 (p) cc_final: 0.8120 (m) REVERT: C 583 GLU cc_start: 0.8451 (mp0) cc_final: 0.8093 (mp0) REVERT: C 657 ASN cc_start: 0.8518 (m-40) cc_final: 0.8310 (m-40) REVERT: C 664 ILE cc_start: 0.7807 (mm) cc_final: 0.7453 (mm) REVERT: C 725 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7053 (tt0) REVERT: C 727 LEU cc_start: 0.8319 (mt) cc_final: 0.7917 (mt) REVERT: C 742 ILE cc_start: 0.8953 (mm) cc_final: 0.8619 (pt) REVERT: C 763 LEU cc_start: 0.8871 (mt) cc_final: 0.8545 (mt) REVERT: C 772 VAL cc_start: 0.8827 (m) cc_final: 0.8617 (p) REVERT: C 776 LYS cc_start: 0.9155 (ttpt) cc_final: 0.8824 (ttpt) REVERT: C 778 THR cc_start: 0.8817 (m) cc_final: 0.8565 (p) REVERT: C 790 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7852 (mmtm) REVERT: C 796 ASP cc_start: 0.8742 (m-30) cc_final: 0.7758 (t0) REVERT: C 808 ASP cc_start: 0.8403 (t0) cc_final: 0.8137 (t0) REVERT: C 824 ASN cc_start: 0.8724 (m110) cc_final: 0.8515 (m110) REVERT: C 865 LEU cc_start: 0.8570 (mt) cc_final: 0.8078 (mp) REVERT: C 869 MET cc_start: 0.8485 (mtm) cc_final: 0.8064 (mtm) REVERT: C 872 GLN cc_start: 0.8932 (tp40) cc_final: 0.8559 (tp-100) REVERT: C 902 MET cc_start: 0.8251 (tmm) cc_final: 0.7767 (tmm) REVERT: C 909 ILE cc_start: 0.8838 (pt) cc_final: 0.8361 (mm) REVERT: C 921 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8124 (mtpp) REVERT: C 925 ASN cc_start: 0.8672 (m-40) cc_final: 0.8418 (m-40) REVERT: C 926 GLN cc_start: 0.8659 (mt0) cc_final: 0.8382 (mt0) REVERT: C 947 LYS cc_start: 0.8876 (mttt) cc_final: 0.8451 (ptpp) REVERT: C 964 LYS cc_start: 0.8959 (tttt) cc_final: 0.8417 (ptmt) REVERT: C 988 GLU cc_start: 0.8384 (mp0) cc_final: 0.8105 (mp0) REVERT: C 992 GLN cc_start: 0.8466 (pp30) cc_final: 0.8229 (pp30) REVERT: C 1012 LEU cc_start: 0.9244 (mt) cc_final: 0.8957 (mm) REVERT: C 1013 ILE cc_start: 0.8988 (mt) cc_final: 0.8659 (mm) REVERT: C 1017 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 1028 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8622 (mmtp) REVERT: C 1081 ILE cc_start: 0.7892 (mt) cc_final: 0.7462 (mm) REVERT: C 1088 HIS cc_start: 0.7386 (m90) cc_final: 0.6946 (m-70) REVERT: C 1103 PHE cc_start: 0.8001 (m-80) cc_final: 0.7479 (m-80) REVERT: C 1125 ASN cc_start: 0.8973 (p0) cc_final: 0.8770 (p0) outliers start: 0 outliers final: 0 residues processed: 740 average time/residue: 0.3881 time to fit residues: 445.1653 Evaluate side-chains 684 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 239 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 260 optimal weight: 0.2980 chunk 307 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119006 restraints weight = 56584.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123768 restraints weight = 35936.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.127222 restraints weight = 25352.046| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26624 Z= 0.193 Angle : 0.764 17.236 36353 Z= 0.375 Chirality : 0.051 0.681 4208 Planarity : 0.005 0.097 4627 Dihedral : 8.819 95.958 4458 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.14), residues: 3207 helix: 0.75 (0.20), residues: 678 sheet: -0.29 (0.19), residues: 690 loop : -1.26 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 64 HIS 0.013 0.002 HIS B 66 PHE 0.029 0.002 PHE C 906 TYR 0.023 0.002 TYR A 674 ARG 0.011 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00829 ( 34) link_NAG-ASN : angle 4.71595 ( 102) link_BETA1-4 : bond 0.00202 ( 10) link_BETA1-4 : angle 1.66322 ( 30) hydrogen bonds : bond 0.04733 ( 873) hydrogen bonds : angle 5.88381 ( 2436) SS BOND : bond 0.00371 ( 41) SS BOND : angle 1.86705 ( 82) covalent geometry : bond 0.00384 (26536) covalent geometry : angle 0.71726 (36139) Misc. bond : bond 0.00102 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8865 (mmpt) cc_final: 0.7784 (mmmm) REVERT: A 49 HIS cc_start: 0.7406 (t70) cc_final: 0.7094 (t-90) REVERT: A 53 ASP cc_start: 0.8387 (t0) cc_final: 0.8029 (t0) REVERT: A 80 ASP cc_start: 0.8349 (t0) cc_final: 0.7845 (t0) REVERT: A 104 TRP cc_start: 0.7180 (m-90) cc_final: 0.6769 (m-90) REVERT: A 177 MET cc_start: 0.2550 (mtm) cc_final: 0.1373 (mmp) REVERT: A 190 ARG cc_start: 0.7118 (mmt-90) cc_final: 0.6367 (mmm160) REVERT: A 224 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8345 (pm20) REVERT: A 240 THR cc_start: 0.8390 (t) cc_final: 0.7793 (t) REVERT: A 269 TYR cc_start: 0.7582 (m-80) cc_final: 0.7286 (m-80) REVERT: A 273 ARG cc_start: 0.8761 (mmt180) cc_final: 0.8519 (mmt180) REVERT: A 287 ASP cc_start: 0.8471 (t0) cc_final: 0.8269 (t70) REVERT: A 291 CYS cc_start: 0.6285 (t) cc_final: 0.5649 (t) REVERT: A 298 GLU cc_start: 0.8273 (tt0) cc_final: 0.7866 (tt0) REVERT: A 303 LEU cc_start: 0.8962 (tp) cc_final: 0.8661 (tp) REVERT: A 319 ARG cc_start: 0.7358 (ptt90) cc_final: 0.7089 (ptt90) REVERT: A 342 PHE cc_start: 0.9136 (m-10) cc_final: 0.8854 (t80) REVERT: A 532 ASN cc_start: 0.8021 (t0) cc_final: 0.7763 (t0) REVERT: A 533 LEU cc_start: 0.8691 (tp) cc_final: 0.8440 (tp) REVERT: A 578 ASP cc_start: 0.8139 (t70) cc_final: 0.7859 (t0) REVERT: A 583 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 643 PHE cc_start: 0.8289 (t80) cc_final: 0.8055 (t80) REVERT: A 658 ASN cc_start: 0.8076 (t0) cc_final: 0.7516 (t0) REVERT: A 737 ASP cc_start: 0.7998 (t0) cc_final: 0.7781 (t0) REVERT: A 740 MET cc_start: 0.7958 (tpp) cc_final: 0.7299 (tpp) REVERT: A 748 GLU cc_start: 0.7757 (mp0) cc_final: 0.7413 (mp0) REVERT: A 751 ASN cc_start: 0.8394 (m110) cc_final: 0.8041 (m110) REVERT: A 762 GLN cc_start: 0.8757 (pt0) cc_final: 0.8426 (pt0) REVERT: A 763 LEU cc_start: 0.8901 (mt) cc_final: 0.8630 (mt) REVERT: A 770 ILE cc_start: 0.9049 (mt) cc_final: 0.8609 (mt) REVERT: A 772 VAL cc_start: 0.8991 (t) cc_final: 0.8603 (m) REVERT: A 774 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7823 (mm-40) REVERT: A 776 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8219 (mmtp) REVERT: A 788 ILE cc_start: 0.7927 (mm) cc_final: 0.7589 (tp) REVERT: A 797 PHE cc_start: 0.8931 (m-80) cc_final: 0.8441 (m-80) REVERT: A 818 ILE cc_start: 0.9260 (mt) cc_final: 0.9024 (pt) REVERT: A 823 PHE cc_start: 0.8485 (t80) cc_final: 0.8283 (t80) REVERT: A 858 LEU cc_start: 0.8440 (mt) cc_final: 0.8218 (mt) REVERT: A 870 ILE cc_start: 0.9004 (mt) cc_final: 0.8780 (mt) REVERT: A 873 TYR cc_start: 0.8664 (m-10) cc_final: 0.8208 (m-80) REVERT: A 878 LEU cc_start: 0.8946 (tp) cc_final: 0.8649 (tp) REVERT: A 902 MET cc_start: 0.8582 (ttm) cc_final: 0.7387 (tmm) REVERT: A 911 VAL cc_start: 0.7131 (t) cc_final: 0.6808 (m) REVERT: A 918 GLU cc_start: 0.8188 (pt0) cc_final: 0.7986 (pt0) REVERT: A 919 ASN cc_start: 0.8668 (m110) cc_final: 0.8276 (m110) REVERT: A 921 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8344 (tptp) REVERT: A 926 GLN cc_start: 0.9060 (mt0) cc_final: 0.8610 (mt0) REVERT: A 928 ASN cc_start: 0.8428 (m-40) cc_final: 0.8117 (m-40) REVERT: A 933 LYS cc_start: 0.9078 (mttm) cc_final: 0.8419 (mmmm) REVERT: A 945 LEU cc_start: 0.8152 (mt) cc_final: 0.7933 (mt) REVERT: A 949 GLN cc_start: 0.8643 (pp30) cc_final: 0.8376 (pp30) REVERT: A 957 GLN cc_start: 0.9037 (tt0) cc_final: 0.8411 (tm-30) REVERT: A 964 LYS cc_start: 0.8874 (mttt) cc_final: 0.8330 (tptp) REVERT: A 965 GLN cc_start: 0.8867 (mt0) cc_final: 0.8650 (mt0) REVERT: A 991 VAL cc_start: 0.8428 (p) cc_final: 0.7900 (t) REVERT: A 993 ILE cc_start: 0.9170 (mm) cc_final: 0.8931 (mm) REVERT: A 995 ARG cc_start: 0.8891 (ttm170) cc_final: 0.8539 (tpp80) REVERT: A 1005 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8228 (tp40) REVERT: A 1009 THR cc_start: 0.8845 (m) cc_final: 0.8424 (p) REVERT: A 1014 ARG cc_start: 0.9042 (mtt-85) cc_final: 0.8738 (mmm-85) REVERT: A 1023 ASN cc_start: 0.8805 (t0) cc_final: 0.8442 (m-40) REVERT: A 1041 ASP cc_start: 0.7885 (t0) cc_final: 0.7680 (t0) REVERT: A 1045 LYS cc_start: 0.8567 (mppt) cc_final: 0.8196 (mmtm) REVERT: A 1077 THR cc_start: 0.8274 (t) cc_final: 0.8006 (t) REVERT: A 1084 ASP cc_start: 0.9030 (p0) cc_final: 0.8734 (p0) REVERT: A 1086 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8691 (mmmt) REVERT: A 1088 HIS cc_start: 0.7813 (m-70) cc_final: 0.7283 (m-70) REVERT: A 1091 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7268 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8635 (m90) cc_final: 0.8273 (m-70) REVERT: A 1109 PHE cc_start: 0.7986 (t80) cc_final: 0.7496 (t80) REVERT: A 1114 ILE cc_start: 0.9044 (mp) cc_final: 0.8689 (tp) REVERT: A 1121 PHE cc_start: 0.7424 (p90) cc_final: 0.7082 (p90) REVERT: B 52 GLN cc_start: 0.8238 (mp10) cc_final: 0.8010 (mp10) REVERT: B 53 ASP cc_start: 0.7327 (t0) cc_final: 0.6683 (t0) REVERT: B 54 LEU cc_start: 0.8276 (mp) cc_final: 0.7391 (tt) REVERT: B 65 PHE cc_start: 0.8387 (m-80) cc_final: 0.7703 (m-80) REVERT: B 99 ASN cc_start: 0.8791 (t0) cc_final: 0.8037 (t0) REVERT: B 135 PHE cc_start: 0.8639 (m-80) cc_final: 0.8412 (m-80) REVERT: B 187 LYS cc_start: 0.8500 (pttm) cc_final: 0.8289 (pttm) REVERT: B 190 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7957 (mmt180) REVERT: B 233 ILE cc_start: 0.6743 (pt) cc_final: 0.5845 (tp) REVERT: B 277 LEU cc_start: 0.7629 (mm) cc_final: 0.7386 (mm) REVERT: B 285 ILE cc_start: 0.8456 (mt) cc_final: 0.8211 (mt) REVERT: B 313 TYR cc_start: 0.8225 (m-80) cc_final: 0.7855 (m-80) REVERT: B 353 TRP cc_start: 0.7861 (p90) cc_final: 0.6991 (p90) REVERT: B 380 TYR cc_start: 0.8255 (m-80) cc_final: 0.7820 (m-80) REVERT: B 382 VAL cc_start: 0.8297 (p) cc_final: 0.7837 (p) REVERT: B 395 VAL cc_start: 0.8219 (t) cc_final: 0.7883 (m) REVERT: B 409 GLN cc_start: 0.8966 (mt0) cc_final: 0.8355 (tt0) REVERT: B 418 ILE cc_start: 0.8887 (pt) cc_final: 0.8623 (pt) REVERT: B 436 TRP cc_start: 0.8105 (p-90) cc_final: 0.7632 (p-90) REVERT: B 454 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7924 (tpt-90) REVERT: B 541 PHE cc_start: 0.7493 (p90) cc_final: 0.7224 (p90) REVERT: B 557 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7548 (mtmm) REVERT: B 619 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7841 (mp0) REVERT: B 712 ILE cc_start: 0.7850 (tt) cc_final: 0.7428 (tp) REVERT: B 725 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6589 (tm-30) REVERT: B 758 SER cc_start: 0.8999 (m) cc_final: 0.8734 (t) REVERT: B 759 PHE cc_start: 0.8024 (m-80) cc_final: 0.7622 (m-80) REVERT: B 762 GLN cc_start: 0.8333 (pp30) cc_final: 0.7967 (pp30) REVERT: B 763 LEU cc_start: 0.8674 (mt) cc_final: 0.8264 (mm) REVERT: B 770 ILE cc_start: 0.8911 (mt) cc_final: 0.8641 (mt) REVERT: B 773 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8146 (mt-10) REVERT: B 776 LYS cc_start: 0.8820 (tptp) cc_final: 0.8371 (tptp) REVERT: B 778 THR cc_start: 0.8786 (m) cc_final: 0.8421 (p) REVERT: B 779 GLN cc_start: 0.8544 (tp40) cc_final: 0.7773 (tm-30) REVERT: B 780 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7529 (tp30) REVERT: B 786 LYS cc_start: 0.8332 (mppt) cc_final: 0.7999 (mppt) REVERT: B 805 ILE cc_start: 0.8831 (mt) cc_final: 0.8452 (tp) REVERT: B 811 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8624 (mmmt) REVERT: B 823 PHE cc_start: 0.8338 (m-80) cc_final: 0.7851 (m-80) REVERT: B 877 LEU cc_start: 0.8891 (mt) cc_final: 0.8669 (mt) REVERT: B 917 TYR cc_start: 0.8159 (m-10) cc_final: 0.7370 (m-10) REVERT: B 921 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8343 (mmmt) REVERT: B 926 GLN cc_start: 0.8784 (mt0) cc_final: 0.8388 (tp40) REVERT: B 934 ILE cc_start: 0.8278 (mm) cc_final: 0.8048 (mm) REVERT: B 935 GLN cc_start: 0.8929 (tt0) cc_final: 0.8326 (tm-30) REVERT: B 954 GLN cc_start: 0.8321 (pp30) cc_final: 0.8019 (pp30) REVERT: B 955 ASN cc_start: 0.8941 (m110) cc_final: 0.8160 (m110) REVERT: B 957 GLN cc_start: 0.9043 (tt0) cc_final: 0.8788 (tt0) REVERT: B 964 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8536 (ttmm) REVERT: B 965 GLN cc_start: 0.8610 (tp-100) cc_final: 0.7869 (tp40) REVERT: B 970 PHE cc_start: 0.6900 (m-10) cc_final: 0.6478 (m-10) REVERT: B 991 VAL cc_start: 0.9007 (m) cc_final: 0.8720 (t) REVERT: B 994 ASP cc_start: 0.8377 (t0) cc_final: 0.8013 (t0) REVERT: B 1003 SER cc_start: 0.9245 (m) cc_final: 0.8897 (p) REVERT: B 1005 GLN cc_start: 0.8911 (pt0) cc_final: 0.8134 (pp30) REVERT: B 1028 LYS cc_start: 0.8500 (tppt) cc_final: 0.7606 (tppt) REVERT: B 1031 GLU cc_start: 0.7822 (tt0) cc_final: 0.6867 (tt0) REVERT: B 1033 VAL cc_start: 0.8009 (t) cc_final: 0.7659 (t) REVERT: B 1038 LYS cc_start: 0.9157 (tptt) cc_final: 0.8751 (tptt) REVERT: B 1074 ASN cc_start: 0.7107 (m-40) cc_final: 0.6848 (m-40) REVERT: B 1081 ILE cc_start: 0.7051 (mp) cc_final: 0.6680 (tp) REVERT: C 64 TRP cc_start: 0.7602 (t-100) cc_final: 0.7392 (t-100) REVERT: C 65 PHE cc_start: 0.8438 (m-80) cc_final: 0.7609 (m-80) REVERT: C 99 ASN cc_start: 0.8937 (m-40) cc_final: 0.8609 (m-40) REVERT: C 104 TRP cc_start: 0.5594 (m-90) cc_final: 0.5060 (m-90) REVERT: C 164 ASN cc_start: 0.8367 (t0) cc_final: 0.8156 (t0) REVERT: C 190 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7908 (mtt180) REVERT: C 197 ILE cc_start: 0.7872 (pt) cc_final: 0.7478 (mm) REVERT: C 203 ILE cc_start: 0.8179 (tt) cc_final: 0.7899 (tp) REVERT: C 265 TYR cc_start: 0.7523 (p90) cc_final: 0.7166 (p90) REVERT: C 267 VAL cc_start: 0.7558 (t) cc_final: 0.6376 (t) REVERT: C 277 LEU cc_start: 0.8163 (mt) cc_final: 0.7860 (mt) REVERT: C 318 PHE cc_start: 0.7825 (t80) cc_final: 0.7329 (t80) REVERT: C 370 ASN cc_start: 0.8990 (m110) cc_final: 0.8625 (p0) REVERT: C 378 LYS cc_start: 0.7919 (tptp) cc_final: 0.7591 (tptp) REVERT: C 436 TRP cc_start: 0.8041 (p-90) cc_final: 0.7584 (p-90) REVERT: C 440 ASN cc_start: 0.8593 (m-40) cc_final: 0.7829 (p0) REVERT: C 535 LYS cc_start: 0.8538 (mppt) cc_final: 0.8039 (ttmm) REVERT: C 554 GLU cc_start: 0.8667 (tt0) cc_final: 0.8297 (tt0) REVERT: C 576 VAL cc_start: 0.8440 (p) cc_final: 0.8221 (m) REVERT: C 583 GLU cc_start: 0.8534 (mp0) cc_final: 0.8076 (mp0) REVERT: C 664 ILE cc_start: 0.7945 (mm) cc_final: 0.7625 (mm) REVERT: C 727 LEU cc_start: 0.8420 (mt) cc_final: 0.8065 (mt) REVERT: C 742 ILE cc_start: 0.8947 (mm) cc_final: 0.8626 (pt) REVERT: C 751 ASN cc_start: 0.8364 (p0) cc_final: 0.8129 (p0) REVERT: C 755 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8651 (mm-40) REVERT: C 756 TYR cc_start: 0.7960 (m-80) cc_final: 0.7667 (m-80) REVERT: C 759 PHE cc_start: 0.7774 (m-80) cc_final: 0.7411 (m-80) REVERT: C 763 LEU cc_start: 0.8982 (mt) cc_final: 0.8697 (mt) REVERT: C 778 THR cc_start: 0.8824 (m) cc_final: 0.8579 (p) REVERT: C 790 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7849 (mmtm) REVERT: C 796 ASP cc_start: 0.8809 (m-30) cc_final: 0.7931 (t0) REVERT: C 808 ASP cc_start: 0.8381 (t0) cc_final: 0.8068 (t0) REVERT: C 859 THR cc_start: 0.8345 (t) cc_final: 0.8105 (p) REVERT: C 865 LEU cc_start: 0.8587 (mt) cc_final: 0.7973 (mt) REVERT: C 869 MET cc_start: 0.8450 (mtm) cc_final: 0.7998 (mtm) REVERT: C 872 GLN cc_start: 0.8950 (tp40) cc_final: 0.8617 (tp-100) REVERT: C 878 LEU cc_start: 0.8768 (mt) cc_final: 0.8559 (mm) REVERT: C 902 MET cc_start: 0.8429 (tmm) cc_final: 0.7976 (tmm) REVERT: C 905 ARG cc_start: 0.8860 (mtt-85) cc_final: 0.8300 (mtt-85) REVERT: C 909 ILE cc_start: 0.8786 (pt) cc_final: 0.8296 (mm) REVERT: C 921 LYS cc_start: 0.8481 (mmpt) cc_final: 0.8103 (mtpp) REVERT: C 925 ASN cc_start: 0.8796 (m-40) cc_final: 0.8519 (m-40) REVERT: C 926 GLN cc_start: 0.8667 (mt0) cc_final: 0.8409 (mt0) REVERT: C 947 LYS cc_start: 0.8992 (mttt) cc_final: 0.8589 (mtmt) REVERT: C 964 LYS cc_start: 0.8991 (tttt) cc_final: 0.8426 (ptmt) REVERT: C 1012 LEU cc_start: 0.9239 (mt) cc_final: 0.8959 (mm) REVERT: C 1013 ILE cc_start: 0.9005 (mt) cc_final: 0.8642 (mm) REVERT: C 1017 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 1034 LEU cc_start: 0.8436 (mt) cc_final: 0.8233 (mt) REVERT: C 1054 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7312 (tp40) REVERT: C 1072 GLU cc_start: 0.8453 (pm20) cc_final: 0.8060 (pm20) REVERT: C 1081 ILE cc_start: 0.8028 (mt) cc_final: 0.7421 (mp) REVERT: C 1084 ASP cc_start: 0.7241 (m-30) cc_final: 0.7038 (m-30) REVERT: C 1088 HIS cc_start: 0.7418 (m90) cc_final: 0.7041 (m-70) REVERT: C 1103 PHE cc_start: 0.8064 (m-80) cc_final: 0.7659 (m-80) REVERT: C 1125 ASN cc_start: 0.9039 (p0) cc_final: 0.8758 (p0) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 0.3843 time to fit residues: 430.1978 Evaluate side-chains 700 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 38 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 205 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 207 HIS ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.159383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119090 restraints weight = 55957.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123849 restraints weight = 35580.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.127297 restraints weight = 25153.248| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26624 Z= 0.182 Angle : 0.763 18.793 36353 Z= 0.374 Chirality : 0.051 0.656 4208 Planarity : 0.005 0.082 4627 Dihedral : 8.687 94.847 4458 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % 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: -0.90 (0.14), residues: 3207 helix: 0.76 (0.20), residues: 678 sheet: -0.19 (0.20), residues: 660 loop : -1.30 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 353 HIS 0.010 0.001 HIS B 66 PHE 0.022 0.002 PHE B 559 TYR 0.024 0.002 TYR B 365 ARG 0.025 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 34) link_NAG-ASN : angle 4.63318 ( 102) link_BETA1-4 : bond 0.00458 ( 10) link_BETA1-4 : angle 1.80120 ( 30) hydrogen bonds : bond 0.04575 ( 873) hydrogen bonds : angle 5.86909 ( 2436) SS BOND : bond 0.00356 ( 41) SS BOND : angle 1.96963 ( 82) covalent geometry : bond 0.00361 (26536) covalent geometry : angle 0.71659 (36139) Misc. bond : bond 0.00069 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 719 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8924 (mmpt) cc_final: 0.7896 (mmmm) REVERT: A 49 HIS cc_start: 0.7332 (t70) cc_final: 0.6681 (t70) REVERT: A 53 ASP cc_start: 0.8496 (t0) cc_final: 0.8141 (t0) REVERT: A 58 PHE cc_start: 0.8270 (m-10) cc_final: 0.8015 (m-80) REVERT: A 80 ASP cc_start: 0.8300 (t0) cc_final: 0.7806 (t0) REVERT: A 100 ILE cc_start: 0.8624 (mm) cc_final: 0.8294 (tp) REVERT: A 104 TRP cc_start: 0.7084 (m-90) cc_final: 0.6644 (m-90) REVERT: A 177 MET cc_start: 0.2366 (mtm) cc_final: 0.1274 (mmp) REVERT: A 190 ARG cc_start: 0.6847 (mmt-90) cc_final: 0.6412 (mmm160) REVERT: A 224 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8414 (pm20) REVERT: A 278 LYS cc_start: 0.7146 (tmmt) cc_final: 0.6186 (ptmm) REVERT: A 287 ASP cc_start: 0.8408 (t0) cc_final: 0.8092 (t70) REVERT: A 291 CYS cc_start: 0.6237 (t) cc_final: 0.5572 (t) REVERT: A 298 GLU cc_start: 0.8293 (tt0) cc_final: 0.7878 (tt0) REVERT: A 303 LEU cc_start: 0.8954 (tp) cc_final: 0.8641 (tp) REVERT: A 319 ARG cc_start: 0.7360 (ptt90) cc_final: 0.7047 (ptt90) REVERT: A 342 PHE cc_start: 0.9151 (m-10) cc_final: 0.8820 (m-10) REVERT: A 532 ASN cc_start: 0.8001 (t0) cc_final: 0.7717 (t0) REVERT: A 533 LEU cc_start: 0.8652 (tp) cc_final: 0.8424 (tp) REVERT: A 578 ASP cc_start: 0.8204 (t70) cc_final: 0.7931 (t0) REVERT: A 583 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8390 (mm-30) REVERT: A 643 PHE cc_start: 0.8282 (t80) cc_final: 0.7980 (t80) REVERT: A 658 ASN cc_start: 0.8110 (t0) cc_final: 0.7571 (t0) REVERT: A 737 ASP cc_start: 0.7967 (t0) cc_final: 0.7708 (t0) REVERT: A 740 MET cc_start: 0.7960 (tpp) cc_final: 0.7249 (tpp) REVERT: A 751 ASN cc_start: 0.8391 (m110) cc_final: 0.8017 (m110) REVERT: A 762 GLN cc_start: 0.8819 (pt0) cc_final: 0.8530 (pt0) REVERT: A 763 LEU cc_start: 0.8937 (mt) cc_final: 0.8666 (mt) REVERT: A 770 ILE cc_start: 0.9127 (mt) cc_final: 0.8754 (mt) REVERT: A 772 VAL cc_start: 0.8887 (t) cc_final: 0.8556 (m) REVERT: A 774 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7843 (mm-40) REVERT: A 776 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8256 (mmtp) REVERT: A 788 ILE cc_start: 0.7873 (mm) cc_final: 0.7603 (tp) REVERT: A 797 PHE cc_start: 0.8945 (m-80) cc_final: 0.8458 (m-80) REVERT: A 818 ILE cc_start: 0.9242 (mt) cc_final: 0.9028 (pt) REVERT: A 823 PHE cc_start: 0.8488 (t80) cc_final: 0.8280 (t80) REVERT: A 869 MET cc_start: 0.8965 (mtm) cc_final: 0.7907 (mtm) REVERT: A 870 ILE cc_start: 0.8987 (mt) cc_final: 0.8769 (mt) REVERT: A 873 TYR cc_start: 0.8689 (m-10) cc_final: 0.8186 (m-80) REVERT: A 878 LEU cc_start: 0.8919 (tp) cc_final: 0.8611 (tp) REVERT: A 902 MET cc_start: 0.8570 (ttm) cc_final: 0.7403 (tmm) REVERT: A 911 VAL cc_start: 0.7110 (t) cc_final: 0.6795 (m) REVERT: A 918 GLU cc_start: 0.8167 (pt0) cc_final: 0.7952 (pt0) REVERT: A 919 ASN cc_start: 0.8595 (m110) cc_final: 0.8214 (m110) REVERT: A 921 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8316 (tptp) REVERT: A 926 GLN cc_start: 0.9044 (mt0) cc_final: 0.8597 (mt0) REVERT: A 928 ASN cc_start: 0.8407 (m-40) cc_final: 0.8100 (m-40) REVERT: A 933 LYS cc_start: 0.9086 (mttm) cc_final: 0.8436 (mmmm) REVERT: A 945 LEU cc_start: 0.8154 (mt) cc_final: 0.7916 (mt) REVERT: A 957 GLN cc_start: 0.9050 (tt0) cc_final: 0.8176 (tp40) REVERT: A 964 LYS cc_start: 0.8872 (mttt) cc_final: 0.8363 (tptp) REVERT: A 965 GLN cc_start: 0.8933 (mt0) cc_final: 0.8674 (mt0) REVERT: A 991 VAL cc_start: 0.8496 (p) cc_final: 0.8004 (t) REVERT: A 993 ILE cc_start: 0.9197 (mm) cc_final: 0.8978 (mm) REVERT: A 995 ARG cc_start: 0.8915 (ttm170) cc_final: 0.8557 (tpp80) REVERT: A 1005 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8304 (tp40) REVERT: A 1009 THR cc_start: 0.8850 (m) cc_final: 0.8524 (p) REVERT: A 1014 ARG cc_start: 0.9014 (mtt-85) cc_final: 0.8589 (tpp80) REVERT: A 1017 GLU cc_start: 0.9045 (tt0) cc_final: 0.8393 (mm-30) REVERT: A 1038 LYS cc_start: 0.8809 (mttt) cc_final: 0.8247 (mttp) REVERT: A 1041 ASP cc_start: 0.7794 (t0) cc_final: 0.7569 (t0) REVERT: A 1045 LYS cc_start: 0.8575 (mppt) cc_final: 0.8188 (mmtm) REVERT: A 1053 PRO cc_start: 0.8403 (Cg_endo) cc_final: 0.7916 (Cg_exo) REVERT: A 1062 PHE cc_start: 0.8093 (m-80) cc_final: 0.6860 (m-80) REVERT: A 1084 ASP cc_start: 0.9002 (p0) cc_final: 0.8716 (p0) REVERT: A 1086 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8670 (mmmt) REVERT: A 1088 HIS cc_start: 0.7826 (m-70) cc_final: 0.7305 (m-70) REVERT: A 1101 HIS cc_start: 0.8643 (m90) cc_final: 0.8231 (m-70) REVERT: A 1109 PHE cc_start: 0.8008 (t80) cc_final: 0.7472 (t80) REVERT: A 1114 ILE cc_start: 0.9029 (mp) cc_final: 0.8646 (tp) REVERT: B 44 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7149 (mtm-85) REVERT: B 52 GLN cc_start: 0.8198 (mp10) cc_final: 0.7989 (mp10) REVERT: B 53 ASP cc_start: 0.7316 (t0) cc_final: 0.6667 (t0) REVERT: B 54 LEU cc_start: 0.8280 (mp) cc_final: 0.7408 (tt) REVERT: B 65 PHE cc_start: 0.8429 (m-80) cc_final: 0.7856 (m-80) REVERT: B 99 ASN cc_start: 0.8872 (t0) cc_final: 0.8349 (t0) REVERT: B 135 PHE cc_start: 0.8652 (m-80) cc_final: 0.8427 (m-80) REVERT: B 187 LYS cc_start: 0.8460 (pttm) cc_final: 0.8241 (pttm) REVERT: B 206 LYS cc_start: 0.7832 (tptp) cc_final: 0.7290 (ptpt) REVERT: B 207 HIS cc_start: 0.8385 (m90) cc_final: 0.7693 (m90) REVERT: B 233 ILE cc_start: 0.6705 (pt) cc_final: 0.5783 (tp) REVERT: B 277 LEU cc_start: 0.7621 (mm) cc_final: 0.7330 (mm) REVERT: B 285 ILE cc_start: 0.8459 (mt) cc_final: 0.8183 (mt) REVERT: B 309 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8504 (mm-30) REVERT: B 313 TYR cc_start: 0.8246 (m-80) cc_final: 0.7824 (m-80) REVERT: B 353 TRP cc_start: 0.7926 (p90) cc_final: 0.6698 (p90) REVERT: B 354 ASN cc_start: 0.8844 (t0) cc_final: 0.8188 (p0) REVERT: B 378 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8873 (mtmt) REVERT: B 395 VAL cc_start: 0.8244 (t) cc_final: 0.7890 (m) REVERT: B 409 GLN cc_start: 0.8985 (mt0) cc_final: 0.8262 (tt0) REVERT: B 418 ILE cc_start: 0.8801 (pt) cc_final: 0.8474 (pt) REVERT: B 444 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8358 (mtpt) REVERT: B 541 PHE cc_start: 0.7581 (p90) cc_final: 0.7307 (p90) REVERT: B 557 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7502 (mtmm) REVERT: B 619 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7767 (mp0) REVERT: B 712 ILE cc_start: 0.7936 (tt) cc_final: 0.7562 (tp) REVERT: B 740 MET cc_start: 0.9377 (tpp) cc_final: 0.8793 (tpt) REVERT: B 758 SER cc_start: 0.9044 (m) cc_final: 0.8762 (t) REVERT: B 759 PHE cc_start: 0.8152 (m-80) cc_final: 0.7751 (m-80) REVERT: B 762 GLN cc_start: 0.8359 (pp30) cc_final: 0.8081 (pp30) REVERT: B 763 LEU cc_start: 0.8635 (mt) cc_final: 0.8268 (mm) REVERT: B 770 ILE cc_start: 0.8900 (mt) cc_final: 0.8630 (mt) REVERT: B 773 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 776 LYS cc_start: 0.8780 (tptp) cc_final: 0.8306 (tptp) REVERT: B 778 THR cc_start: 0.8808 (m) cc_final: 0.8484 (p) REVERT: B 779 GLN cc_start: 0.8545 (tp40) cc_final: 0.7760 (tm-30) REVERT: B 780 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7485 (tp30) REVERT: B 786 LYS cc_start: 0.8389 (mppt) cc_final: 0.8028 (mppt) REVERT: B 805 ILE cc_start: 0.8856 (mt) cc_final: 0.8435 (tp) REVERT: B 823 PHE cc_start: 0.8299 (m-80) cc_final: 0.7786 (m-80) REVERT: B 864 LEU cc_start: 0.8588 (tp) cc_final: 0.8095 (mm) REVERT: B 878 LEU cc_start: 0.9210 (mt) cc_final: 0.8905 (tp) REVERT: B 917 TYR cc_start: 0.8195 (m-10) cc_final: 0.7365 (m-10) REVERT: B 921 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8436 (mtpp) REVERT: B 926 GLN cc_start: 0.8720 (mt0) cc_final: 0.8324 (tp40) REVERT: B 934 ILE cc_start: 0.8306 (mm) cc_final: 0.8079 (mm) REVERT: B 935 GLN cc_start: 0.8931 (tt0) cc_final: 0.8366 (tm-30) REVERT: B 954 GLN cc_start: 0.8352 (pp30) cc_final: 0.8064 (pp30) REVERT: B 955 ASN cc_start: 0.9009 (m110) cc_final: 0.8243 (m110) REVERT: B 957 GLN cc_start: 0.9019 (tt0) cc_final: 0.8695 (tt0) REVERT: B 960 ASN cc_start: 0.8553 (m-40) cc_final: 0.8275 (m-40) REVERT: B 965 GLN cc_start: 0.8511 (tp-100) cc_final: 0.7795 (tp40) REVERT: B 970 PHE cc_start: 0.6856 (m-10) cc_final: 0.6425 (m-10) REVERT: B 991 VAL cc_start: 0.8987 (m) cc_final: 0.8717 (t) REVERT: B 994 ASP cc_start: 0.8434 (t0) cc_final: 0.7967 (t0) REVERT: B 1003 SER cc_start: 0.9244 (m) cc_final: 0.8852 (p) REVERT: B 1005 GLN cc_start: 0.8913 (pt0) cc_final: 0.8137 (pp30) REVERT: B 1031 GLU cc_start: 0.7775 (tt0) cc_final: 0.6874 (tt0) REVERT: B 1038 LYS cc_start: 0.9164 (tptt) cc_final: 0.8744 (tptt) REVERT: B 1050 MET cc_start: 0.7027 (ptp) cc_final: 0.6729 (ptp) REVERT: B 1073 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7148 (mtpp) REVERT: B 1074 ASN cc_start: 0.7148 (m-40) cc_final: 0.6889 (m-40) REVERT: B 1077 THR cc_start: 0.7471 (t) cc_final: 0.7258 (t) REVERT: B 1081 ILE cc_start: 0.7438 (mp) cc_final: 0.7074 (tp) REVERT: B 1139 ASP cc_start: 0.6972 (p0) cc_final: 0.6751 (p0) REVERT: C 58 PHE cc_start: 0.8573 (m-80) cc_final: 0.8138 (m-80) REVERT: C 64 TRP cc_start: 0.7606 (t-100) cc_final: 0.7357 (t-100) REVERT: C 65 PHE cc_start: 0.8394 (m-80) cc_final: 0.7510 (m-80) REVERT: C 99 ASN cc_start: 0.8931 (m-40) cc_final: 0.8720 (m-40) REVERT: C 104 TRP cc_start: 0.5594 (m-90) cc_final: 0.4972 (m-90) REVERT: C 164 ASN cc_start: 0.8393 (t0) cc_final: 0.8178 (t0) REVERT: C 197 ILE cc_start: 0.7929 (pt) cc_final: 0.7400 (mm) REVERT: C 203 ILE cc_start: 0.8138 (tt) cc_final: 0.7866 (tp) REVERT: C 265 TYR cc_start: 0.7482 (p90) cc_final: 0.7201 (p90) REVERT: C 271 GLN cc_start: 0.8166 (mp10) cc_final: 0.7866 (mp10) REVERT: C 277 LEU cc_start: 0.8152 (mt) cc_final: 0.7865 (mt) REVERT: C 290 ASP cc_start: 0.6063 (t0) cc_final: 0.5794 (t0) REVERT: C 318 PHE cc_start: 0.7842 (t80) cc_final: 0.7347 (t80) REVERT: C 370 ASN cc_start: 0.8980 (m110) cc_final: 0.8584 (p0) REVERT: C 378 LYS cc_start: 0.7897 (tptp) cc_final: 0.7436 (tptp) REVERT: C 436 TRP cc_start: 0.8114 (p-90) cc_final: 0.7685 (p-90) REVERT: C 440 ASN cc_start: 0.8592 (m-40) cc_final: 0.7810 (p0) REVERT: C 535 LYS cc_start: 0.8561 (mppt) cc_final: 0.8064 (ttmm) REVERT: C 554 GLU cc_start: 0.8629 (tt0) cc_final: 0.8269 (tt0) REVERT: C 557 LYS cc_start: 0.9021 (mppt) cc_final: 0.8518 (mmmt) REVERT: C 576 VAL cc_start: 0.8405 (p) cc_final: 0.8173 (m) REVERT: C 583 GLU cc_start: 0.8506 (mp0) cc_final: 0.8188 (mp0) REVERT: C 664 ILE cc_start: 0.7887 (mm) cc_final: 0.7548 (mm) REVERT: C 727 LEU cc_start: 0.8402 (mt) cc_final: 0.8020 (mt) REVERT: C 741 TYR cc_start: 0.8449 (t80) cc_final: 0.8152 (t80) REVERT: C 742 ILE cc_start: 0.8955 (mm) cc_final: 0.8572 (pt) REVERT: C 756 TYR cc_start: 0.7954 (m-80) cc_final: 0.7645 (m-80) REVERT: C 759 PHE cc_start: 0.7613 (m-80) cc_final: 0.7345 (m-80) REVERT: C 763 LEU cc_start: 0.8951 (mt) cc_final: 0.8735 (mt) REVERT: C 778 THR cc_start: 0.8798 (m) cc_final: 0.8517 (p) REVERT: C 790 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7849 (mmtm) REVERT: C 796 ASP cc_start: 0.8771 (m-30) cc_final: 0.7922 (t0) REVERT: C 808 ASP cc_start: 0.8378 (t0) cc_final: 0.8019 (t0) REVERT: C 859 THR cc_start: 0.8347 (t) cc_final: 0.8120 (p) REVERT: C 865 LEU cc_start: 0.8489 (mt) cc_final: 0.8195 (mp) REVERT: C 869 MET cc_start: 0.8510 (mtm) cc_final: 0.8043 (mtm) REVERT: C 872 GLN cc_start: 0.8893 (tp40) cc_final: 0.8618 (tp40) REVERT: C 901 GLN cc_start: 0.8698 (tt0) cc_final: 0.8147 (tm-30) REVERT: C 902 MET cc_start: 0.8386 (tmm) cc_final: 0.7888 (tmm) REVERT: C 905 ARG cc_start: 0.8860 (mtt-85) cc_final: 0.8263 (mtt-85) REVERT: C 909 ILE cc_start: 0.8750 (pt) cc_final: 0.8245 (mm) REVERT: C 921 LYS cc_start: 0.8461 (mmpt) cc_final: 0.8114 (mtpp) REVERT: C 925 ASN cc_start: 0.8792 (m-40) cc_final: 0.8587 (m-40) REVERT: C 926 GLN cc_start: 0.8669 (mt0) cc_final: 0.8407 (mt0) REVERT: C 936 ASP cc_start: 0.8538 (t0) cc_final: 0.8327 (t0) REVERT: C 947 LYS cc_start: 0.9000 (mttt) cc_final: 0.8586 (mtmt) REVERT: C 964 LYS cc_start: 0.9010 (tttt) cc_final: 0.8469 (ptmt) REVERT: C 988 GLU cc_start: 0.8282 (mp0) cc_final: 0.7810 (mp0) REVERT: C 992 GLN cc_start: 0.8479 (pp30) cc_final: 0.8196 (pp30) REVERT: C 1012 LEU cc_start: 0.9250 (mt) cc_final: 0.9015 (mm) REVERT: C 1013 ILE cc_start: 0.9009 (mt) cc_final: 0.8642 (mm) REVERT: C 1014 ARG cc_start: 0.8886 (mtt90) cc_final: 0.7898 (ttm110) REVERT: C 1017 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 1034 LEU cc_start: 0.8421 (mt) cc_final: 0.8196 (mt) REVERT: C 1050 MET cc_start: 0.6004 (ppp) cc_final: 0.5427 (ppp) REVERT: C 1052 PHE cc_start: 0.6831 (m-80) cc_final: 0.6459 (m-80) REVERT: C 1054 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7498 (tp40) REVERT: C 1067 TYR cc_start: 0.8145 (t80) cc_final: 0.7808 (t80) REVERT: C 1072 GLU cc_start: 0.8466 (pm20) cc_final: 0.8126 (pm20) REVERT: C 1081 ILE cc_start: 0.7935 (mt) cc_final: 0.7352 (mp) REVERT: C 1088 HIS cc_start: 0.7348 (m90) cc_final: 0.6859 (m-70) REVERT: C 1089 PHE cc_start: 0.6311 (m-80) cc_final: 0.5921 (m-80) REVERT: C 1103 PHE cc_start: 0.8038 (m-80) cc_final: 0.7476 (m-80) REVERT: C 1125 ASN cc_start: 0.9041 (p0) cc_final: 0.8687 (p0) outliers start: 4 outliers final: 0 residues processed: 720 average time/residue: 0.3675 time to fit residues: 410.9354 Evaluate side-chains 683 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 683 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 317 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 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 = 0.4285 r_free = 0.4285 target = 0.158409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.117639 restraints weight = 56748.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122628 restraints weight = 35507.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.126236 restraints weight = 24861.850| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26624 Z= 0.184 Angle : 0.763 17.322 36353 Z= 0.373 Chirality : 0.051 0.685 4208 Planarity : 0.006 0.113 4627 Dihedral : 8.588 91.446 4458 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 0.07 % Allowed : 0.82 % Favored : 99.11 % 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: -0.95 (0.14), residues: 3207 helix: 0.77 (0.20), residues: 679 sheet: -0.29 (0.20), residues: 667 loop : -1.33 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 353 HIS 0.007 0.001 HIS A1048 PHE 0.017 0.002 PHE C 906 TYR 0.026 0.002 TYR A 674 ARG 0.019 0.001 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 34) link_NAG-ASN : angle 4.52343 ( 102) link_BETA1-4 : bond 0.00249 ( 10) link_BETA1-4 : angle 1.63623 ( 30) hydrogen bonds : bond 0.04632 ( 873) hydrogen bonds : angle 5.85345 ( 2436) SS BOND : bond 0.00330 ( 41) SS BOND : angle 1.91479 ( 82) covalent geometry : bond 0.00368 (26536) covalent geometry : angle 0.71892 (36139) Misc. bond : bond 0.00087 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 730 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7362 (t70) cc_final: 0.6717 (t70) REVERT: A 53 ASP cc_start: 0.8602 (t0) cc_final: 0.8011 (t0) REVERT: A 58 PHE cc_start: 0.8273 (m-10) cc_final: 0.7989 (m-80) REVERT: A 80 ASP cc_start: 0.8381 (t0) cc_final: 0.7935 (t0) REVERT: A 100 ILE cc_start: 0.8682 (mm) cc_final: 0.8362 (tp) REVERT: A 104 TRP cc_start: 0.7141 (m-90) cc_final: 0.6740 (m-90) REVERT: A 177 MET cc_start: 0.2371 (mtm) cc_final: 0.1214 (mmp) REVERT: A 190 ARG cc_start: 0.6948 (mmt-90) cc_final: 0.6441 (mmm160) REVERT: A 224 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8383 (pm20) REVERT: A 269 TYR cc_start: 0.7590 (m-80) cc_final: 0.7326 (m-80) REVERT: A 273 ARG cc_start: 0.8764 (mmt180) cc_final: 0.8410 (mmt-90) REVERT: A 287 ASP cc_start: 0.8425 (t0) cc_final: 0.8186 (t70) REVERT: A 291 CYS cc_start: 0.6327 (t) cc_final: 0.5692 (t) REVERT: A 298 GLU cc_start: 0.8297 (tt0) cc_final: 0.7860 (tt0) REVERT: A 303 LEU cc_start: 0.8971 (tp) cc_final: 0.8670 (tp) REVERT: A 319 ARG cc_start: 0.7362 (ptt90) cc_final: 0.6976 (ptt90) REVERT: A 342 PHE cc_start: 0.9173 (m-10) cc_final: 0.8854 (m-10) REVERT: A 437 ASN cc_start: 0.8396 (t0) cc_final: 0.8058 (t0) REVERT: A 532 ASN cc_start: 0.8015 (t0) cc_final: 0.7753 (t0) REVERT: A 558 LYS cc_start: 0.8871 (pttt) cc_final: 0.8403 (mmtt) REVERT: A 571 ASP cc_start: 0.7557 (t0) cc_final: 0.7174 (t0) REVERT: A 578 ASP cc_start: 0.8348 (t70) cc_final: 0.8059 (t0) REVERT: A 583 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 643 PHE cc_start: 0.8396 (t80) cc_final: 0.8051 (t80) REVERT: A 658 ASN cc_start: 0.8113 (t0) cc_final: 0.7553 (t0) REVERT: A 690 GLN cc_start: 0.6747 (mm-40) cc_final: 0.6077 (pm20) REVERT: A 737 ASP cc_start: 0.8039 (t0) cc_final: 0.7723 (t0) REVERT: A 740 MET cc_start: 0.7995 (tpp) cc_final: 0.7278 (tpp) REVERT: A 748 GLU cc_start: 0.7773 (mp0) cc_final: 0.7316 (mp0) REVERT: A 751 ASN cc_start: 0.8400 (m110) cc_final: 0.8018 (m110) REVERT: A 762 GLN cc_start: 0.8791 (pt0) cc_final: 0.8535 (pt0) REVERT: A 763 LEU cc_start: 0.8928 (mt) cc_final: 0.8688 (mt) REVERT: A 770 ILE cc_start: 0.9152 (mt) cc_final: 0.8780 (mt) REVERT: A 772 VAL cc_start: 0.8840 (t) cc_final: 0.8465 (m) REVERT: A 774 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7873 (mm-40) REVERT: A 776 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8204 (mmtp) REVERT: A 788 ILE cc_start: 0.7935 (mm) cc_final: 0.7662 (tp) REVERT: A 797 PHE cc_start: 0.8920 (m-80) cc_final: 0.8685 (m-80) REVERT: A 818 ILE cc_start: 0.9263 (mt) cc_final: 0.9050 (pt) REVERT: A 858 LEU cc_start: 0.8415 (mt) cc_final: 0.8153 (mt) REVERT: A 869 MET cc_start: 0.8949 (mtm) cc_final: 0.7926 (mtm) REVERT: A 870 ILE cc_start: 0.9011 (mt) cc_final: 0.8743 (mt) REVERT: A 873 TYR cc_start: 0.8645 (m-10) cc_final: 0.8125 (m-80) REVERT: A 878 LEU cc_start: 0.8992 (tp) cc_final: 0.8701 (tp) REVERT: A 902 MET cc_start: 0.8577 (ttm) cc_final: 0.7445 (tmm) REVERT: A 911 VAL cc_start: 0.7112 (t) cc_final: 0.6768 (m) REVERT: A 918 GLU cc_start: 0.8137 (pt0) cc_final: 0.7921 (pt0) REVERT: A 919 ASN cc_start: 0.8563 (m110) cc_final: 0.8147 (m110) REVERT: A 921 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8334 (tptp) REVERT: A 926 GLN cc_start: 0.9033 (mt0) cc_final: 0.8620 (mt0) REVERT: A 928 ASN cc_start: 0.8418 (m-40) cc_final: 0.8105 (m-40) REVERT: A 933 LYS cc_start: 0.9108 (mttm) cc_final: 0.8461 (mmmm) REVERT: A 945 LEU cc_start: 0.8162 (mt) cc_final: 0.7936 (mt) REVERT: A 949 GLN cc_start: 0.8649 (pp30) cc_final: 0.8420 (pp30) REVERT: A 957 GLN cc_start: 0.9041 (tt0) cc_final: 0.8457 (tm-30) REVERT: A 962 LEU cc_start: 0.8982 (tp) cc_final: 0.8661 (tt) REVERT: A 964 LYS cc_start: 0.8928 (mttt) cc_final: 0.8426 (tptp) REVERT: A 965 GLN cc_start: 0.8902 (mt0) cc_final: 0.8552 (mt0) REVERT: A 977 LEU cc_start: 0.9075 (tp) cc_final: 0.8814 (tt) REVERT: A 988 GLU cc_start: 0.8053 (mp0) cc_final: 0.7707 (pm20) REVERT: A 991 VAL cc_start: 0.8558 (p) cc_final: 0.8082 (t) REVERT: A 993 ILE cc_start: 0.9204 (mm) cc_final: 0.8537 (tp) REVERT: A 995 ARG cc_start: 0.8902 (ttm170) cc_final: 0.8601 (tpp80) REVERT: A 1005 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8240 (tp40) REVERT: A 1009 THR cc_start: 0.8800 (m) cc_final: 0.8576 (p) REVERT: A 1014 ARG cc_start: 0.9039 (mtt-85) cc_final: 0.8578 (tpp80) REVERT: A 1038 LYS cc_start: 0.8814 (mttt) cc_final: 0.8235 (mttp) REVERT: A 1045 LYS cc_start: 0.8563 (mppt) cc_final: 0.8230 (mmtm) REVERT: A 1049 LEU cc_start: 0.8981 (mt) cc_final: 0.8760 (mt) REVERT: A 1053 PRO cc_start: 0.8407 (Cg_endo) cc_final: 0.8061 (Cg_exo) REVERT: A 1062 PHE cc_start: 0.8060 (m-80) cc_final: 0.7411 (m-80) REVERT: A 1081 ILE cc_start: 0.8854 (mm) cc_final: 0.7885 (tp) REVERT: A 1084 ASP cc_start: 0.8990 (p0) cc_final: 0.8711 (p0) REVERT: A 1086 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8667 (mmmt) REVERT: A 1088 HIS cc_start: 0.7796 (m-70) cc_final: 0.7236 (m-70) REVERT: A 1101 HIS cc_start: 0.8753 (m90) cc_final: 0.8276 (m-70) REVERT: A 1109 PHE cc_start: 0.8074 (t80) cc_final: 0.7568 (t80) REVERT: A 1111 GLU cc_start: 0.7654 (tt0) cc_final: 0.7435 (tt0) REVERT: A 1114 ILE cc_start: 0.9012 (mp) cc_final: 0.8643 (tp) REVERT: A 1135 ASN cc_start: 0.8590 (m110) cc_final: 0.8025 (m-40) REVERT: B 53 ASP cc_start: 0.7335 (t0) cc_final: 0.6680 (t0) REVERT: B 54 LEU cc_start: 0.8303 (mp) cc_final: 0.7454 (tt) REVERT: B 65 PHE cc_start: 0.8571 (m-80) cc_final: 0.7812 (m-80) REVERT: B 99 ASN cc_start: 0.8946 (t0) cc_final: 0.8471 (t0) REVERT: B 135 PHE cc_start: 0.8670 (m-80) cc_final: 0.8435 (m-80) REVERT: B 187 LYS cc_start: 0.8646 (pttm) cc_final: 0.8428 (pttm) REVERT: B 207 HIS cc_start: 0.8256 (m-70) cc_final: 0.7835 (m-70) REVERT: B 233 ILE cc_start: 0.6842 (pt) cc_final: 0.5921 (tp) REVERT: B 277 LEU cc_start: 0.7628 (mm) cc_final: 0.7377 (mm) REVERT: B 285 ILE cc_start: 0.8492 (mt) cc_final: 0.8219 (mt) REVERT: B 300 LYS cc_start: 0.8712 (mttt) cc_final: 0.8201 (mttm) REVERT: B 309 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8317 (pp20) REVERT: B 313 TYR cc_start: 0.8260 (m-80) cc_final: 0.7442 (m-80) REVERT: B 351 TYR cc_start: 0.7385 (p90) cc_final: 0.6889 (p90) REVERT: B 353 TRP cc_start: 0.7845 (p90) cc_final: 0.6855 (p90) REVERT: B 354 ASN cc_start: 0.8733 (t0) cc_final: 0.8183 (p0) REVERT: B 378 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8898 (mtmt) REVERT: B 409 GLN cc_start: 0.8985 (mt0) cc_final: 0.8427 (tt0) REVERT: B 418 ILE cc_start: 0.8842 (pt) cc_final: 0.8598 (mt) REVERT: B 436 TRP cc_start: 0.8212 (p-90) cc_final: 0.7402 (p-90) REVERT: B 444 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8398 (mtpt) REVERT: B 454 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.7979 (ttp-170) REVERT: B 509 ARG cc_start: 0.6602 (mmt180) cc_final: 0.5893 (mmm-85) REVERT: B 541 PHE cc_start: 0.7637 (p90) cc_final: 0.7397 (p90) REVERT: B 557 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7589 (mtmm) REVERT: B 619 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 725 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6815 (tm-30) REVERT: B 740 MET cc_start: 0.9395 (tpp) cc_final: 0.8735 (tpt) REVERT: B 756 TYR cc_start: 0.8349 (m-80) cc_final: 0.8139 (m-80) REVERT: B 758 SER cc_start: 0.9066 (m) cc_final: 0.8784 (t) REVERT: B 759 PHE cc_start: 0.8149 (m-80) cc_final: 0.7699 (m-80) REVERT: B 762 GLN cc_start: 0.8321 (pp30) cc_final: 0.8016 (pp30) REVERT: B 763 LEU cc_start: 0.8615 (mt) cc_final: 0.8221 (mm) REVERT: B 764 ASN cc_start: 0.8716 (m110) cc_final: 0.8506 (m110) REVERT: B 776 LYS cc_start: 0.8764 (tptp) cc_final: 0.8210 (tptp) REVERT: B 778 THR cc_start: 0.8825 (m) cc_final: 0.8470 (p) REVERT: B 779 GLN cc_start: 0.8526 (tp40) cc_final: 0.7737 (tm-30) REVERT: B 780 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7506 (tp30) REVERT: B 786 LYS cc_start: 0.8404 (mppt) cc_final: 0.8019 (mppt) REVERT: B 800 PHE cc_start: 0.8320 (m-80) cc_final: 0.7961 (m-80) REVERT: B 805 ILE cc_start: 0.8822 (mt) cc_final: 0.8478 (tp) REVERT: B 823 PHE cc_start: 0.8181 (m-80) cc_final: 0.7696 (m-80) REVERT: B 864 LEU cc_start: 0.8619 (tp) cc_final: 0.8101 (mm) REVERT: B 877 LEU cc_start: 0.8899 (mt) cc_final: 0.8679 (mt) REVERT: B 917 TYR cc_start: 0.8183 (m-10) cc_final: 0.7332 (m-10) REVERT: B 921 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8443 (mtpp) REVERT: B 926 GLN cc_start: 0.8576 (mt0) cc_final: 0.8153 (tp40) REVERT: B 934 ILE cc_start: 0.8303 (mm) cc_final: 0.8091 (mm) REVERT: B 935 GLN cc_start: 0.8919 (tt0) cc_final: 0.8303 (tm-30) REVERT: B 954 GLN cc_start: 0.8335 (pp30) cc_final: 0.8033 (pp30) REVERT: B 955 ASN cc_start: 0.9019 (m110) cc_final: 0.8207 (m110) REVERT: B 957 GLN cc_start: 0.9036 (tt0) cc_final: 0.8738 (tt0) REVERT: B 960 ASN cc_start: 0.8528 (m-40) cc_final: 0.8272 (m-40) REVERT: B 965 GLN cc_start: 0.8504 (tp-100) cc_final: 0.7705 (tp-100) REVERT: B 991 VAL cc_start: 0.8967 (m) cc_final: 0.8687 (t) REVERT: B 994 ASP cc_start: 0.8380 (t0) cc_final: 0.7954 (t0) REVERT: B 996 LEU cc_start: 0.8945 (mt) cc_final: 0.8730 (mt) REVERT: B 1003 SER cc_start: 0.9223 (m) cc_final: 0.8814 (p) REVERT: B 1004 LEU cc_start: 0.9234 (mt) cc_final: 0.9032 (mt) REVERT: B 1005 GLN cc_start: 0.8893 (pt0) cc_final: 0.8115 (pp30) REVERT: B 1008 VAL cc_start: 0.9060 (m) cc_final: 0.8848 (m) REVERT: B 1028 LYS cc_start: 0.8430 (tppt) cc_final: 0.7449 (tppt) REVERT: B 1031 GLU cc_start: 0.7799 (tt0) cc_final: 0.6868 (tt0) REVERT: B 1033 VAL cc_start: 0.7857 (t) cc_final: 0.7494 (t) REVERT: B 1038 LYS cc_start: 0.9164 (tptt) cc_final: 0.8755 (tptt) REVERT: B 1073 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7251 (mtpp) REVERT: B 1074 ASN cc_start: 0.7150 (m-40) cc_final: 0.6899 (m-40) REVERT: B 1081 ILE cc_start: 0.7409 (mp) cc_final: 0.7105 (tp) REVERT: C 64 TRP cc_start: 0.7387 (t-100) cc_final: 0.7001 (t-100) REVERT: C 66 HIS cc_start: 0.7618 (m170) cc_final: 0.7144 (m170) REVERT: C 99 ASN cc_start: 0.8953 (m-40) cc_final: 0.8747 (m-40) REVERT: C 104 TRP cc_start: 0.5687 (m-90) cc_final: 0.5055 (m-90) REVERT: C 164 ASN cc_start: 0.8412 (t0) cc_final: 0.8210 (t0) REVERT: C 197 ILE cc_start: 0.7876 (pt) cc_final: 0.7427 (mm) REVERT: C 203 ILE cc_start: 0.8103 (tt) cc_final: 0.7873 (tp) REVERT: C 265 TYR cc_start: 0.7432 (p90) cc_final: 0.7153 (p90) REVERT: C 267 VAL cc_start: 0.7676 (t) cc_final: 0.6667 (t) REVERT: C 271 GLN cc_start: 0.8097 (mp10) cc_final: 0.7752 (mp10) REVERT: C 273 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6309 (mtm-85) REVERT: C 277 LEU cc_start: 0.8209 (mt) cc_final: 0.7902 (mt) REVERT: C 318 PHE cc_start: 0.7811 (t80) cc_final: 0.7231 (t80) REVERT: C 370 ASN cc_start: 0.9031 (m110) cc_final: 0.8691 (p0) REVERT: C 378 LYS cc_start: 0.7901 (tptp) cc_final: 0.7560 (tptp) REVERT: C 436 TRP cc_start: 0.7995 (p-90) cc_final: 0.7440 (p-90) REVERT: C 440 ASN cc_start: 0.8605 (m-40) cc_final: 0.8029 (p0) REVERT: C 535 LYS cc_start: 0.8609 (mppt) cc_final: 0.8135 (ttmm) REVERT: C 554 GLU cc_start: 0.8609 (tt0) cc_final: 0.8269 (tt0) REVERT: C 557 LYS cc_start: 0.9045 (mppt) cc_final: 0.8617 (tptt) REVERT: C 576 VAL cc_start: 0.8407 (p) cc_final: 0.8182 (m) REVERT: C 664 ILE cc_start: 0.7840 (mm) cc_final: 0.7482 (mm) REVERT: C 725 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7347 (tt0) REVERT: C 727 LEU cc_start: 0.8416 (mt) cc_final: 0.8001 (mt) REVERT: C 735 SER cc_start: 0.8606 (t) cc_final: 0.8194 (p) REVERT: C 742 ILE cc_start: 0.8924 (mm) cc_final: 0.8598 (pt) REVERT: C 756 TYR cc_start: 0.8015 (m-80) cc_final: 0.7504 (m-80) REVERT: C 759 PHE cc_start: 0.7621 (m-80) cc_final: 0.7240 (m-80) REVERT: C 763 LEU cc_start: 0.8940 (mt) cc_final: 0.8655 (mt) REVERT: C 777 ASN cc_start: 0.8890 (m110) cc_final: 0.8641 (m110) REVERT: C 778 THR cc_start: 0.8802 (m) cc_final: 0.8505 (p) REVERT: C 779 GLN cc_start: 0.8620 (mt0) cc_final: 0.7869 (tp40) REVERT: C 790 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7836 (mmtm) REVERT: C 796 ASP cc_start: 0.8790 (m-30) cc_final: 0.7909 (t0) REVERT: C 808 ASP cc_start: 0.8354 (t0) cc_final: 0.7986 (t0) REVERT: C 859 THR cc_start: 0.8355 (t) cc_final: 0.7829 (p) REVERT: C 865 LEU cc_start: 0.8496 (mt) cc_final: 0.8066 (mm) REVERT: C 869 MET cc_start: 0.8533 (mtm) cc_final: 0.8064 (mtm) REVERT: C 872 GLN cc_start: 0.8904 (tp40) cc_final: 0.8603 (tp40) REVERT: C 901 GLN cc_start: 0.8713 (tt0) cc_final: 0.7894 (tm-30) REVERT: C 902 MET cc_start: 0.8436 (tmm) cc_final: 0.7814 (tmm) REVERT: C 909 ILE cc_start: 0.8743 (pt) cc_final: 0.8269 (mm) REVERT: C 921 LYS cc_start: 0.8476 (mmpt) cc_final: 0.8101 (mtpp) REVERT: C 925 ASN cc_start: 0.8799 (m-40) cc_final: 0.8588 (m-40) REVERT: C 926 GLN cc_start: 0.8678 (mt0) cc_final: 0.8400 (mt0) REVERT: C 936 ASP cc_start: 0.8510 (t0) cc_final: 0.8293 (t0) REVERT: C 947 LYS cc_start: 0.9095 (mttt) cc_final: 0.8632 (mtmt) REVERT: C 964 LYS cc_start: 0.9018 (tttt) cc_final: 0.8482 (ptmt) REVERT: C 992 GLN cc_start: 0.8466 (pp30) cc_final: 0.8231 (pp30) REVERT: C 1012 LEU cc_start: 0.9255 (mt) cc_final: 0.9054 (mm) REVERT: C 1013 ILE cc_start: 0.9026 (mt) cc_final: 0.8399 (tp) REVERT: C 1014 ARG cc_start: 0.8769 (mtt90) cc_final: 0.7818 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8132 (mt-10) REVERT: C 1052 PHE cc_start: 0.6950 (m-80) cc_final: 0.6325 (m-10) REVERT: C 1067 TYR cc_start: 0.8161 (t80) cc_final: 0.7844 (t80) REVERT: C 1072 GLU cc_start: 0.8468 (pm20) cc_final: 0.8157 (pm20) REVERT: C 1081 ILE cc_start: 0.7965 (mt) cc_final: 0.7376 (mp) REVERT: C 1088 HIS cc_start: 0.7362 (m90) cc_final: 0.7002 (m-70) REVERT: C 1103 PHE cc_start: 0.7994 (m-80) cc_final: 0.7572 (m-80) outliers start: 2 outliers final: 0 residues processed: 730 average time/residue: 0.3787 time to fit residues: 429.9021 Evaluate side-chains 687 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 264 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.159964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119373 restraints weight = 56117.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124420 restraints weight = 35044.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.128085 restraints weight = 24465.987| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26624 Z= 0.150 Angle : 0.755 17.627 36353 Z= 0.364 Chirality : 0.051 0.658 4208 Planarity : 0.005 0.073 4627 Dihedral : 8.422 90.101 4458 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.14), residues: 3207 helix: 0.78 (0.20), residues: 686 sheet: -0.23 (0.20), residues: 664 loop : -1.32 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 436 HIS 0.008 0.001 HIS A1048 PHE 0.021 0.002 PHE A 374 TYR 0.024 0.002 TYR B 365 ARG 0.016 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 34) link_NAG-ASN : angle 4.40845 ( 102) link_BETA1-4 : bond 0.00271 ( 10) link_BETA1-4 : angle 1.60104 ( 30) hydrogen bonds : bond 0.04367 ( 873) hydrogen bonds : angle 5.77031 ( 2436) SS BOND : bond 0.00347 ( 41) SS BOND : angle 1.88721 ( 82) covalent geometry : bond 0.00316 (26536) covalent geometry : angle 0.71264 (36139) Misc. bond : bond 0.00048 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 728 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8340 (mmpt) REVERT: A 49 HIS cc_start: 0.7354 (t70) cc_final: 0.6723 (t70) REVERT: A 58 PHE cc_start: 0.8265 (m-10) cc_final: 0.8006 (m-80) REVERT: A 80 ASP cc_start: 0.8338 (t0) cc_final: 0.7842 (t0) REVERT: A 100 ILE cc_start: 0.8639 (mm) cc_final: 0.8306 (tp) REVERT: A 104 TRP cc_start: 0.7054 (m-90) cc_final: 0.6628 (m-90) REVERT: A 177 MET cc_start: 0.2228 (mtm) cc_final: 0.1149 (mmp) REVERT: A 190 ARG cc_start: 0.6841 (mmt-90) cc_final: 0.6346 (mmm160) REVERT: A 223 LEU cc_start: 0.8429 (mt) cc_final: 0.8163 (mt) REVERT: A 269 TYR cc_start: 0.7550 (m-80) cc_final: 0.7268 (m-80) REVERT: A 273 ARG cc_start: 0.8684 (mmt180) cc_final: 0.8447 (mmt180) REVERT: A 287 ASP cc_start: 0.8380 (t0) cc_final: 0.8091 (t70) REVERT: A 291 CYS cc_start: 0.6312 (t) cc_final: 0.5671 (t) REVERT: A 298 GLU cc_start: 0.8268 (tt0) cc_final: 0.7827 (tt0) REVERT: A 303 LEU cc_start: 0.8970 (tp) cc_final: 0.8680 (tp) REVERT: A 342 PHE cc_start: 0.9152 (m-10) cc_final: 0.8841 (m-10) REVERT: A 374 PHE cc_start: 0.8318 (m-10) cc_final: 0.7929 (m-80) REVERT: A 437 ASN cc_start: 0.8420 (t0) cc_final: 0.8192 (t0) REVERT: A 529 LYS cc_start: 0.8129 (mppt) cc_final: 0.7852 (mmmt) REVERT: A 532 ASN cc_start: 0.7895 (t0) cc_final: 0.7640 (t0) REVERT: A 552 LEU cc_start: 0.8008 (mt) cc_final: 0.7798 (mt) REVERT: A 571 ASP cc_start: 0.7488 (t0) cc_final: 0.7049 (t0) REVERT: A 578 ASP cc_start: 0.8306 (t70) cc_final: 0.8030 (t0) REVERT: A 583 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 643 PHE cc_start: 0.8309 (t80) cc_final: 0.7989 (t80) REVERT: A 646 ARG cc_start: 0.8113 (tpt90) cc_final: 0.7759 (tpt90) REVERT: A 658 ASN cc_start: 0.8155 (t0) cc_final: 0.7457 (t0) REVERT: A 708 SER cc_start: 0.7741 (t) cc_final: 0.7466 (p) REVERT: A 740 MET cc_start: 0.7957 (tpp) cc_final: 0.7279 (tpp) REVERT: A 751 ASN cc_start: 0.8375 (m110) cc_final: 0.8001 (m110) REVERT: A 762 GLN cc_start: 0.8760 (pt0) cc_final: 0.8486 (pt0) REVERT: A 763 LEU cc_start: 0.8943 (mt) cc_final: 0.8684 (mt) REVERT: A 770 ILE cc_start: 0.9212 (mt) cc_final: 0.8897 (mt) REVERT: A 772 VAL cc_start: 0.8826 (t) cc_final: 0.8605 (m) REVERT: A 774 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7878 (mm-40) REVERT: A 776 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8235 (mmtp) REVERT: A 788 ILE cc_start: 0.7794 (mm) cc_final: 0.7521 (tp) REVERT: A 797 PHE cc_start: 0.8929 (m-80) cc_final: 0.8672 (m-80) REVERT: A 818 ILE cc_start: 0.9236 (mt) cc_final: 0.9017 (pt) REVERT: A 823 PHE cc_start: 0.8421 (t80) cc_final: 0.8196 (t80) REVERT: A 866 THR cc_start: 0.7932 (p) cc_final: 0.7662 (t) REVERT: A 869 MET cc_start: 0.8843 (mtm) cc_final: 0.7915 (mtm) REVERT: A 870 ILE cc_start: 0.8970 (mt) cc_final: 0.8728 (mt) REVERT: A 873 TYR cc_start: 0.8574 (m-10) cc_final: 0.8151 (m-80) REVERT: A 877 LEU cc_start: 0.8823 (mt) cc_final: 0.8569 (tp) REVERT: A 878 LEU cc_start: 0.8982 (tp) cc_final: 0.8712 (tt) REVERT: A 902 MET cc_start: 0.8567 (ttm) cc_final: 0.7225 (tmm) REVERT: A 911 VAL cc_start: 0.7099 (t) cc_final: 0.6750 (m) REVERT: A 919 ASN cc_start: 0.8484 (m110) cc_final: 0.8095 (m110) REVERT: A 921 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8299 (tptp) REVERT: A 926 GLN cc_start: 0.9018 (mt0) cc_final: 0.8606 (mt0) REVERT: A 928 ASN cc_start: 0.8365 (m-40) cc_final: 0.8059 (m-40) REVERT: A 933 LYS cc_start: 0.9095 (mttm) cc_final: 0.8762 (mttm) REVERT: A 945 LEU cc_start: 0.8144 (mt) cc_final: 0.7915 (mt) REVERT: A 949 GLN cc_start: 0.8640 (pp30) cc_final: 0.8397 (pp30) REVERT: A 957 GLN cc_start: 0.9012 (tt0) cc_final: 0.8468 (tm-30) REVERT: A 964 LYS cc_start: 0.8885 (mttt) cc_final: 0.8373 (tptp) REVERT: A 965 GLN cc_start: 0.8809 (mt0) cc_final: 0.8590 (mt0) REVERT: A 977 LEU cc_start: 0.9043 (tp) cc_final: 0.8753 (tt) REVERT: A 988 GLU cc_start: 0.8007 (mp0) cc_final: 0.7639 (pm20) REVERT: A 991 VAL cc_start: 0.8561 (p) cc_final: 0.8079 (t) REVERT: A 993 ILE cc_start: 0.9212 (mm) cc_final: 0.8538 (tp) REVERT: A 995 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8598 (tpp80) REVERT: A 1005 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8234 (tp40) REVERT: A 1009 THR cc_start: 0.8762 (m) cc_final: 0.8522 (p) REVERT: A 1014 ARG cc_start: 0.9024 (mtt-85) cc_final: 0.8549 (tpp80) REVERT: A 1038 LYS cc_start: 0.8834 (mttt) cc_final: 0.8222 (ttmm) REVERT: A 1041 ASP cc_start: 0.7733 (t0) cc_final: 0.7508 (t0) REVERT: A 1045 LYS cc_start: 0.8619 (mppt) cc_final: 0.8184 (mppt) REVERT: A 1073 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7363 (mmmm) REVERT: A 1081 ILE cc_start: 0.8780 (mm) cc_final: 0.7869 (tp) REVERT: A 1083 HIS cc_start: 0.8276 (t-90) cc_final: 0.7818 (t-90) REVERT: A 1084 ASP cc_start: 0.8942 (p0) cc_final: 0.8631 (p0) REVERT: A 1086 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8611 (mmmt) REVERT: A 1088 HIS cc_start: 0.7797 (m-70) cc_final: 0.7196 (m-70) REVERT: A 1101 HIS cc_start: 0.8709 (m90) cc_final: 0.8217 (m-70) REVERT: A 1109 PHE cc_start: 0.8073 (t80) cc_final: 0.7549 (t80) REVERT: A 1111 GLU cc_start: 0.7705 (tt0) cc_final: 0.7449 (tt0) REVERT: A 1114 ILE cc_start: 0.8985 (mp) cc_final: 0.8592 (tp) REVERT: B 44 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7104 (mtt-85) REVERT: B 53 ASP cc_start: 0.7350 (t0) cc_final: 0.6687 (t0) REVERT: B 54 LEU cc_start: 0.8363 (mp) cc_final: 0.7499 (tt) REVERT: B 65 PHE cc_start: 0.8551 (m-80) cc_final: 0.7800 (m-80) REVERT: B 99 ASN cc_start: 0.8950 (t0) cc_final: 0.8507 (t0) REVERT: B 135 PHE cc_start: 0.8653 (m-80) cc_final: 0.8391 (m-80) REVERT: B 206 LYS cc_start: 0.7667 (tptp) cc_final: 0.7080 (ptpt) REVERT: B 207 HIS cc_start: 0.8224 (m-70) cc_final: 0.7393 (m-70) REVERT: B 233 ILE cc_start: 0.6765 (pt) cc_final: 0.5863 (tp) REVERT: B 277 LEU cc_start: 0.7639 (mm) cc_final: 0.7386 (mm) REVERT: B 293 LEU cc_start: 0.8073 (tt) cc_final: 0.7834 (tt) REVERT: B 313 TYR cc_start: 0.8246 (m-80) cc_final: 0.7796 (m-80) REVERT: B 351 TYR cc_start: 0.7392 (p90) cc_final: 0.6887 (p90) REVERT: B 353 TRP cc_start: 0.7845 (p90) cc_final: 0.6851 (p90) REVERT: B 354 ASN cc_start: 0.8917 (t0) cc_final: 0.8146 (p0) REVERT: B 380 TYR cc_start: 0.8202 (m-80) cc_final: 0.7879 (m-80) REVERT: B 403 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8510 (mmt180) REVERT: B 409 GLN cc_start: 0.8996 (mt0) cc_final: 0.8514 (tt0) REVERT: B 418 ILE cc_start: 0.8778 (pt) cc_final: 0.8527 (mt) REVERT: B 436 TRP cc_start: 0.8120 (p-90) cc_final: 0.7626 (p-90) REVERT: B 444 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8424 (mtpt) REVERT: B 541 PHE cc_start: 0.7684 (p90) cc_final: 0.7404 (p90) REVERT: B 557 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7488 (mtmm) REVERT: B 568 ASP cc_start: 0.8335 (p0) cc_final: 0.8128 (p0) REVERT: B 619 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7761 (mp0) REVERT: B 712 ILE cc_start: 0.7826 (tt) cc_final: 0.7622 (tp) REVERT: B 723 THR cc_start: 0.8195 (m) cc_final: 0.7799 (m) REVERT: B 725 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6810 (tm-30) REVERT: B 740 MET cc_start: 0.9393 (tpp) cc_final: 0.9111 (tpp) REVERT: B 758 SER cc_start: 0.9033 (m) cc_final: 0.8750 (t) REVERT: B 759 PHE cc_start: 0.8072 (m-80) cc_final: 0.7618 (m-80) REVERT: B 762 GLN cc_start: 0.8306 (pp30) cc_final: 0.8005 (pp30) REVERT: B 763 LEU cc_start: 0.8623 (mt) cc_final: 0.8238 (mm) REVERT: B 764 ASN cc_start: 0.8701 (m110) cc_final: 0.8495 (m110) REVERT: B 776 LYS cc_start: 0.8698 (tptp) cc_final: 0.8147 (tptp) REVERT: B 778 THR cc_start: 0.8806 (m) cc_final: 0.8490 (p) REVERT: B 779 GLN cc_start: 0.8478 (tp40) cc_final: 0.7707 (tm-30) REVERT: B 780 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7405 (tp30) REVERT: B 786 LYS cc_start: 0.8410 (mppt) cc_final: 0.7988 (mppt) REVERT: B 800 PHE cc_start: 0.8335 (m-80) cc_final: 0.7959 (m-80) REVERT: B 805 ILE cc_start: 0.8833 (mt) cc_final: 0.8513 (tp) REVERT: B 811 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8465 (mmmt) REVERT: B 823 PHE cc_start: 0.8140 (m-80) cc_final: 0.7732 (m-80) REVERT: B 864 LEU cc_start: 0.8618 (tp) cc_final: 0.8081 (mm) REVERT: B 907 ASN cc_start: 0.8270 (t0) cc_final: 0.8034 (t0) REVERT: B 917 TYR cc_start: 0.8204 (m-10) cc_final: 0.7307 (m-10) REVERT: B 921 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8379 (mtpp) REVERT: B 926 GLN cc_start: 0.8581 (mt0) cc_final: 0.8155 (tp40) REVERT: B 934 ILE cc_start: 0.8284 (mm) cc_final: 0.8065 (mm) REVERT: B 935 GLN cc_start: 0.8872 (tt0) cc_final: 0.8638 (tt0) REVERT: B 954 GLN cc_start: 0.8289 (pp30) cc_final: 0.7991 (pp30) REVERT: B 955 ASN cc_start: 0.9012 (m110) cc_final: 0.8189 (m110) REVERT: B 957 GLN cc_start: 0.9115 (tt0) cc_final: 0.8304 (tp40) REVERT: B 960 ASN cc_start: 0.8494 (m-40) cc_final: 0.8210 (m-40) REVERT: B 965 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7626 (tp40) REVERT: B 970 PHE cc_start: 0.6787 (m-10) cc_final: 0.6277 (m-10) REVERT: B 994 ASP cc_start: 0.8172 (t0) cc_final: 0.7859 (t0) REVERT: B 996 LEU cc_start: 0.8913 (mt) cc_final: 0.8703 (mt) REVERT: B 1008 VAL cc_start: 0.9044 (m) cc_final: 0.8809 (m) REVERT: B 1031 GLU cc_start: 0.7827 (tt0) cc_final: 0.6900 (tt0) REVERT: B 1038 LYS cc_start: 0.9143 (tptt) cc_final: 0.8744 (tptt) REVERT: B 1050 MET cc_start: 0.6791 (ptp) cc_final: 0.6503 (ptp) REVERT: B 1073 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7191 (mtpp) REVERT: B 1074 ASN cc_start: 0.7139 (m-40) cc_final: 0.6880 (m-40) REVERT: B 1081 ILE cc_start: 0.7274 (mp) cc_final: 0.6997 (tt) REVERT: B 1106 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 1109 PHE cc_start: 0.7643 (t80) cc_final: 0.7080 (t80) REVERT: B 1111 GLU cc_start: 0.8094 (pp20) cc_final: 0.7562 (pm20) REVERT: C 64 TRP cc_start: 0.7315 (t-100) cc_final: 0.6997 (t-100) REVERT: C 65 PHE cc_start: 0.8275 (m-80) cc_final: 0.7495 (m-80) REVERT: C 66 HIS cc_start: 0.7414 (m-70) cc_final: 0.7064 (m-70) REVERT: C 99 ASN cc_start: 0.8867 (m-40) cc_final: 0.8415 (m-40) REVERT: C 104 TRP cc_start: 0.5648 (m-90) cc_final: 0.5055 (m-90) REVERT: C 197 ILE cc_start: 0.7781 (pt) cc_final: 0.7395 (mm) REVERT: C 203 ILE cc_start: 0.8009 (tt) cc_final: 0.7800 (pt) REVERT: C 267 VAL cc_start: 0.7721 (t) cc_final: 0.7506 (t) REVERT: C 277 LEU cc_start: 0.8128 (mt) cc_final: 0.7810 (mt) REVERT: C 318 PHE cc_start: 0.7783 (t80) cc_final: 0.7151 (t80) REVERT: C 370 ASN cc_start: 0.9013 (m110) cc_final: 0.8659 (p0) REVERT: C 378 LYS cc_start: 0.7918 (tptp) cc_final: 0.7640 (tptp) REVERT: C 406 GLU cc_start: 0.8952 (pm20) cc_final: 0.8750 (pm20) REVERT: C 436 TRP cc_start: 0.8013 (p-90) cc_final: 0.7105 (p-90) REVERT: C 440 ASN cc_start: 0.8637 (m-40) cc_final: 0.8029 (p0) REVERT: C 535 LYS cc_start: 0.8553 (mppt) cc_final: 0.8065 (ttmm) REVERT: C 554 GLU cc_start: 0.8591 (tt0) cc_final: 0.8236 (tt0) REVERT: C 557 LYS cc_start: 0.9038 (mppt) cc_final: 0.8528 (mmmt) REVERT: C 564 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8092 (mm110) REVERT: C 664 ILE cc_start: 0.7806 (mm) cc_final: 0.7427 (mm) REVERT: C 693 ILE cc_start: 0.8287 (tt) cc_final: 0.7982 (tt) REVERT: C 707 TYR cc_start: 0.7426 (t80) cc_final: 0.6012 (t80) REVERT: C 727 LEU cc_start: 0.8392 (mt) cc_final: 0.8054 (mt) REVERT: C 740 MET cc_start: 0.7004 (tpp) cc_final: 0.6647 (tpt) REVERT: C 742 ILE cc_start: 0.8856 (mm) cc_final: 0.8625 (pt) REVERT: C 756 TYR cc_start: 0.7919 (m-80) cc_final: 0.7609 (m-80) REVERT: C 759 PHE cc_start: 0.7522 (m-80) cc_final: 0.7242 (m-80) REVERT: C 777 ASN cc_start: 0.8996 (m110) cc_final: 0.8747 (m110) REVERT: C 778 THR cc_start: 0.8789 (m) cc_final: 0.8523 (p) REVERT: C 779 GLN cc_start: 0.8619 (mt0) cc_final: 0.7848 (tp40) REVERT: C 790 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7846 (mmtm) REVERT: C 796 ASP cc_start: 0.8726 (m-30) cc_final: 0.7879 (t0) REVERT: C 808 ASP cc_start: 0.8319 (t0) cc_final: 0.7951 (t0) REVERT: C 859 THR cc_start: 0.8328 (t) cc_final: 0.8084 (p) REVERT: C 865 LEU cc_start: 0.8445 (mt) cc_final: 0.8059 (mp) REVERT: C 869 MET cc_start: 0.8389 (mtm) cc_final: 0.8068 (mtm) REVERT: C 872 GLN cc_start: 0.8877 (tp40) cc_final: 0.8534 (tp40) REVERT: C 895 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8078 (mm110) REVERT: C 901 GLN cc_start: 0.8701 (tt0) cc_final: 0.8083 (tm-30) REVERT: C 902 MET cc_start: 0.8360 (tmm) cc_final: 0.7844 (tmm) REVERT: C 905 ARG cc_start: 0.8850 (mtt-85) cc_final: 0.8332 (mtt-85) REVERT: C 909 ILE cc_start: 0.8729 (pt) cc_final: 0.8235 (mm) REVERT: C 921 LYS cc_start: 0.8475 (mmpt) cc_final: 0.8091 (mtpp) REVERT: C 925 ASN cc_start: 0.8786 (m-40) cc_final: 0.8561 (m-40) REVERT: C 926 GLN cc_start: 0.8675 (mt0) cc_final: 0.8398 (mt0) REVERT: C 936 ASP cc_start: 0.8471 (t0) cc_final: 0.8256 (t0) REVERT: C 947 LYS cc_start: 0.9093 (mttt) cc_final: 0.8571 (mtmt) REVERT: C 953 ASN cc_start: 0.8575 (m-40) cc_final: 0.8264 (m-40) REVERT: C 964 LYS cc_start: 0.8963 (tttt) cc_final: 0.8459 (ptmt) REVERT: C 992 GLN cc_start: 0.8424 (pp30) cc_final: 0.8187 (pp30) REVERT: C 1013 ILE cc_start: 0.9025 (mt) cc_final: 0.8342 (tp) REVERT: C 1014 ARG cc_start: 0.8830 (mtt90) cc_final: 0.8040 (mtp85) REVERT: C 1017 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8040 (mt-10) REVERT: C 1034 LEU cc_start: 0.8349 (mt) cc_final: 0.8149 (mt) REVERT: C 1052 PHE cc_start: 0.7059 (m-80) cc_final: 0.6369 (m-10) REVERT: C 1072 GLU cc_start: 0.8418 (pm20) cc_final: 0.8068 (pm20) REVERT: C 1081 ILE cc_start: 0.7923 (mt) cc_final: 0.7297 (mp) REVERT: C 1088 HIS cc_start: 0.7295 (m90) cc_final: 0.6791 (m-70) REVERT: C 1089 PHE cc_start: 0.6228 (m-10) cc_final: 0.5871 (m-80) REVERT: C 1103 PHE cc_start: 0.7974 (m-80) cc_final: 0.7489 (m-80) outliers start: 2 outliers final: 0 residues processed: 728 average time/residue: 0.3927 time to fit residues: 447.3332 Evaluate side-chains 686 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 103 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 901 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 = 0.4269 r_free = 0.4269 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117465 restraints weight = 56067.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122173 restraints weight = 35645.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125597 restraints weight = 25187.665| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26624 Z= 0.200 Angle : 0.778 17.358 36353 Z= 0.385 Chirality : 0.051 0.668 4208 Planarity : 0.005 0.072 4627 Dihedral : 8.432 87.382 4458 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 0.07 % Allowed : 0.25 % Favored : 99.68 % 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: -1.02 (0.14), residues: 3207 helix: 0.68 (0.20), residues: 686 sheet: -0.33 (0.20), residues: 664 loop : -1.37 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 436 HIS 0.008 0.001 HIS A1048 PHE 0.038 0.002 PHE C 906 TYR 0.025 0.002 TYR B 365 ARG 0.018 0.001 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 34) link_NAG-ASN : angle 4.40423 ( 102) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.61558 ( 30) hydrogen bonds : bond 0.04655 ( 873) hydrogen bonds : angle 5.87078 ( 2436) SS BOND : bond 0.00381 ( 41) SS BOND : angle 1.90825 ( 82) covalent geometry : bond 0.00400 (26536) covalent geometry : angle 0.73683 (36139) Misc. bond : bond 0.00051 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10983.97 seconds wall clock time: 193 minutes 2.73 seconds (11582.73 seconds total)