Starting phenix.real_space_refine on Mon Aug 25 07:40:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p9y_17578/08_2025/8p9y_17578_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p9y_17578/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p9y_17578/08_2025/8p9y_17578_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p9y_17578/08_2025/8p9y_17578_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p9y_17578/08_2025/8p9y_17578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p9y_17578/08_2025/8p9y_17578.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 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: 6.49, per 1000 atoms: 0.25 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 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: 6.68 Time building geometry restraints manager: 3.22 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 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 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 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: 8.380 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.600 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- 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 : 59.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.036 0.003 ARG C 273 TYR 0.050 0.005 TYR A 266 PHE 0.049 0.006 PHE B 464 TRP 0.043 0.005 TRP A 64 HIS 0.023 0.003 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.01192 (26536) covalent geometry : angle 1.52864 (36139) SS BOND : bond 0.34551 ( 41) SS BOND : angle 11.05693 ( 82) hydrogen bonds : bond 0.27868 ( 873) hydrogen bonds : angle 9.59373 ( 2436) Misc. bond : bond 0.20283 ( 3) link_BETA1-4 : bond 0.00175 ( 10) link_BETA1-4 : angle 2.07411 ( 30) link_NAG-ASN : bond 0.04276 ( 34) link_NAG-ASN : angle 12.20058 ( 102) *********************** 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 : 0.952 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: symmetry clash REVERT: A 54 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6298 (mp) REVERT: A 57 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.7849 (Cg_endo) REVERT: A 80 ASP cc_start: 0.8130 (t0) cc_final: 0.7830 (t70) REVERT: A 224 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8377 (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: 0.7058 (tp) REVERT: A 544 ASN cc_start: 0.7902 (m-40) cc_final: 0.7609 (p0) REVERT: A 732 THR cc_start: 0.8109 (p) cc_final: 0.7491 (t) REVERT: A 733 LYS cc_start: 0.8600 (mttt) cc_final: 0.7983 (mttm) REVERT: A 765 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7831 (ttp-170) REVERT: A 778 THR cc_start: 0.8196 (m) cc_final: 0.7945 (p) REVERT: A 788 ILE cc_start: 0.8117 (mm) cc_final: 0.7857 (mm) REVERT: A 866 THR cc_start: 0.5962 (p) cc_final: 0.5269 (m) REVERT: A 877 LEU cc_start: 0.8666 (mt) cc_final: 0.8290 (mm) REVERT: A 878 LEU cc_start: 0.8403 (tt) cc_final: 0.8143 (tt) REVERT: A 905 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7855 (mmm-85) REVERT: A 921 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7600 (tptp) REVERT: A 926 GLN cc_start: 0.8414 (mt0) cc_final: 0.7743 (mt0) REVERT: A 954 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6963 (tp-100) REVERT: A 957 GLN cc_start: 0.8503 (tt0) cc_final: 0.8095 (tm-30) REVERT: A 964 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8179 (tptm) REVERT: A 965 GLN cc_start: 0.8548 (mm110) cc_final: 0.8240 (mm-40) REVERT: A 991 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7023 (t) REVERT: A 995 ARG cc_start: 0.8480 (ttm170) cc_final: 0.8036 (tpp80) REVERT: A 997 ILE cc_start: 0.8761 (mt) cc_final: 0.8492 (mt) REVERT: A 1014 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7742 (mmm-85) REVERT: A 1019 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6380 (tpp80) REVERT: A 1023 ASN cc_start: 0.7704 (t0) cc_final: 0.7473 (t0) REVERT: A 1038 LYS cc_start: 0.8281 (mttt) cc_final: 0.7732 (ttmm) REVERT: A 1045 LYS cc_start: 0.7576 (tttp) cc_final: 0.7165 (tttp) REVERT: A 1106 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: A 1128 VAL cc_start: 0.7931 (p) cc_final: 0.7513 (m) REVERT: B 65 PHE cc_start: 0.8460 (m-80) cc_final: 0.8005 (m-80) REVERT: B 141 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4526 (tt) REVERT: B 187 LYS cc_start: 0.8195 (tptp) cc_final: 0.7824 (ptmt) REVERT: B 220 PHE cc_start: 0.3216 (OUTLIER) cc_final: 0.1400 (t80) REVERT: B 233 ILE cc_start: 0.5802 (pt) cc_final: 0.3979 (mt) REVERT: B 266 TYR cc_start: 0.6351 (m-10) cc_final: 0.5729 (m-10) REVERT: B 289 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 293 LEU cc_start: 0.8513 (tp) cc_final: 0.8184 (tt) REVERT: B 378 LYS cc_start: 0.6964 (ptmm) cc_final: 0.6735 (ttpp) REVERT: B 398 ASP cc_start: 0.6972 (m-30) cc_final: 0.6392 (m-30) REVERT: B 454 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.7896 (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: 0.8114 (tp) REVERT: B 613 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5420 (tp40) REVERT: B 714 ILE cc_start: 0.8592 (mt) cc_final: 0.8351 (mp) REVERT: B 752 LEU cc_start: 0.8771 (mm) cc_final: 0.8493 (mm) REVERT: B 776 LYS cc_start: 0.8689 (tptp) cc_final: 0.8308 (tptp) REVERT: B 779 GLN cc_start: 0.7953 (tp40) cc_final: 0.7602 (tm-30) REVERT: B 814 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6896 (mmtt) REVERT: B 858 LEU cc_start: 0.7823 (mt) cc_final: 0.7582 (pp) REVERT: B 870 ILE cc_start: 0.8219 (mt) cc_final: 0.7983 (tt) REVERT: B 902 MET cc_start: 0.6910 (mmm) cc_final: 0.6593 (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: 0.7867 (tp40) REVERT: B 936 ASP cc_start: 0.6888 (t0) cc_final: 0.6686 (t0) REVERT: B 949 GLN cc_start: 0.7841 (tp40) cc_final: 0.7628 (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: 0.8151 (ttmm) REVERT: B 966 LEU cc_start: 0.8460 (tp) cc_final: 0.8255 (pp) REVERT: B 970 PHE cc_start: 0.7114 (m-80) cc_final: 0.6662 (m-80) REVERT: B 1118 ASP cc_start: 0.8215 (p0) cc_final: 0.7924 (p0) REVERT: B 1133 VAL cc_start: 0.7628 (m) cc_final: 0.7377 (p) REVERT: C 34 ARG cc_start: 0.5779 (tpp-160) cc_final: 0.5483 (mmm160) REVERT: C 55 PHE cc_start: 0.3913 (OUTLIER) cc_final: 0.3543 (m-10) REVERT: C 66 HIS cc_start: 0.6937 (m170) cc_final: 0.5587 (m170) REVERT: C 96 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6018 (mm-30) REVERT: C 206 LYS cc_start: 0.7266 (tptm) cc_final: 0.6908 (tptm) REVERT: C 212 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7126 (mp) REVERT: C 235 ILE cc_start: 0.8503 (mt) cc_final: 0.7985 (mt) REVERT: C 276 LEU cc_start: 0.5838 (tp) cc_final: 0.5045 (tp) REVERT: C 277 LEU cc_start: 0.7204 (mt) cc_final: 0.6735 (mt) REVERT: C 308 VAL cc_start: 0.7258 (t) cc_final: 0.6993 (p) REVERT: C 370 ASN cc_start: 0.8169 (t0) cc_final: 0.7834 (t0) REVERT: C 406 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: C 436 TRP cc_start: 0.7329 (p-90) cc_final: 0.6926 (p-90) REVERT: C 440 ASN cc_start: 0.8834 (m-40) cc_final: 0.8244 (p0) REVERT: C 463 PRO cc_start: 0.6203 (Cg_endo) cc_final: 0.5998 (Cg_exo) REVERT: C 559 PHE cc_start: 0.7908 (m-10) cc_final: 0.7370 (m-80) REVERT: C 563 GLN cc_start: 0.7940 (mt0) cc_final: 0.7648 (mt0) REVERT: C 581 THR cc_start: 0.7540 (m) cc_final: 0.7193 (m) REVERT: C 588 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6068 (t) REVERT: C 611 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4737 (tt) REVERT: C 618 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7829 (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: 0.8258 (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: 0.7764 (mt) REVERT: C 752 LEU cc_start: 0.8861 (mp) cc_final: 0.7897 (mm) REVERT: C 773 GLU cc_start: 0.8000 (tt0) cc_final: 0.7041 (tt0) REVERT: C 776 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8592 (ttpt) REVERT: C 824 ASN cc_start: 0.9195 (m110) cc_final: 0.8832 (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: 0.8137 (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: 0.7245 (tpp80) REVERT: C 918 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7736 (mt-10) REVERT: C 920 GLN cc_start: 0.8221 (tt0) cc_final: 0.7975 (tt0) REVERT: C 921 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: C 926 GLN cc_start: 0.8790 (mt0) cc_final: 0.8536 (pt0) REVERT: C 1013 ILE cc_start: 0.8644 (mt) cc_final: 0.8109 (mm) REVERT: C 1017 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 1021 SER cc_start: 0.8867 (t) cc_final: 0.8409 (p) REVERT: C 1039 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7691 (ttm110) REVERT: C 1083 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.4444 (t-90) REVERT: C 1092 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3721 (pp20) outliers start: 211 outliers final: 75 residues processed: 981 average time/residue: 0.1875 time to fit residues: 286.7044 Evaluate side-chains 786 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 687 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 762 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 641 ASN B 764 ASN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.175287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133731 restraints weight = 54985.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.138853 restraints weight = 34359.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.142699 restraints weight = 24005.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145468 restraints weight = 17997.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.147544 restraints weight = 14328.794| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26624 Z= 0.214 Angle : 0.931 19.401 36353 Z= 0.450 Chirality : 0.058 1.013 4208 Planarity : 0.006 0.116 4627 Dihedral : 9.818 104.736 4458 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.46 % Allowed : 5.17 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3207 helix: 1.61 (0.19), residues: 682 sheet: 0.20 (0.20), residues: 622 loop : -1.04 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1107 TYR 0.025 0.002 TYR C 453 PHE 0.035 0.003 PHE B 275 TRP 0.023 0.002 TRP A 64 HIS 0.016 0.002 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00458 (26536) covalent geometry : angle 0.86489 (36139) SS BOND : bond 0.00716 ( 41) SS BOND : angle 3.28915 ( 82) hydrogen bonds : bond 0.06324 ( 873) hydrogen bonds : angle 7.09211 ( 2436) Misc. bond : bond 0.00414 ( 3) link_BETA1-4 : bond 0.00713 ( 10) link_BETA1-4 : angle 2.42579 ( 30) link_NAG-ASN : bond 0.01010 ( 34) link_NAG-ASN : angle 5.76360 ( 102) *********************** 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 782 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 769 time to evaluate : 0.960 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: A 41 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7859 (ttpt) REVERT: A 49 HIS cc_start: 0.7718 (t-90) cc_final: 0.7399 (t-90) REVERT: A 57 PRO cc_start: 0.8457 (Cg_exo) cc_final: 0.7413 (Cg_endo) REVERT: A 80 ASP cc_start: 0.8079 (t0) cc_final: 0.7768 (t70) REVERT: A 224 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8215 (pm20) REVERT: A 271 GLN cc_start: 0.8181 (mp10) cc_final: 0.7973 (pm20) REVERT: A 273 ARG cc_start: 0.6874 (mtt-85) cc_final: 0.6638 (mtt-85) REVERT: A 287 ASP cc_start: 0.8376 (t0) cc_final: 0.8152 (t0) REVERT: A 298 GLU cc_start: 0.8274 (tt0) cc_final: 0.7843 (tt0) REVERT: A 318 PHE cc_start: 0.7558 (t80) cc_final: 0.7250 (t80) REVERT: A 342 PHE cc_start: 0.9047 (m-10) cc_final: 0.8743 (m-10) REVERT: A 532 ASN cc_start: 0.7912 (t0) cc_final: 0.7569 (t0) REVERT: A 567 ARG cc_start: 0.6249 (ptp-110) cc_final: 0.5622 (ttp-110) REVERT: A 571 ASP cc_start: 0.6615 (t0) cc_final: 0.6251 (t0) REVERT: A 656 VAL cc_start: 0.8633 (m) cc_final: 0.8372 (p) REVERT: A 658 ASN cc_start: 0.7434 (t0) cc_final: 0.7036 (t0) REVERT: A 740 MET cc_start: 0.8200 (tpp) cc_final: 0.7893 (tpp) REVERT: A 751 ASN cc_start: 0.8366 (m110) cc_final: 0.8056 (m110) REVERT: A 762 GLN cc_start: 0.8507 (mm110) cc_final: 0.7789 (mm-40) REVERT: A 765 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7796 (ttp-170) REVERT: A 787 GLN cc_start: 0.7643 (pm20) cc_final: 0.7092 (pp30) REVERT: A 796 ASP cc_start: 0.8004 (m-30) cc_final: 0.7646 (m-30) REVERT: A 823 PHE cc_start: 0.8545 (t80) cc_final: 0.8206 (t80) REVERT: A 869 MET cc_start: 0.8888 (mtm) cc_final: 0.8141 (ptp) REVERT: A 912 THR cc_start: 0.7373 (p) cc_final: 0.7157 (p) REVERT: A 919 ASN cc_start: 0.8726 (m110) cc_final: 0.8403 (m110) REVERT: A 921 LYS cc_start: 0.8692 (mmtt) cc_final: 0.7955 (tptp) REVERT: A 926 GLN cc_start: 0.8919 (mt0) cc_final: 0.8362 (mt0) REVERT: A 928 ASN cc_start: 0.8348 (m-40) cc_final: 0.8075 (m-40) REVERT: A 933 LYS cc_start: 0.9021 (mttm) cc_final: 0.8391 (mmmm) REVERT: A 957 GLN cc_start: 0.8857 (tt0) cc_final: 0.8166 (tm-30) REVERT: A 964 LYS cc_start: 0.8868 (mttt) cc_final: 0.8373 (tptp) REVERT: A 965 GLN cc_start: 0.8834 (mm110) cc_final: 0.8615 (mm-40) REVERT: A 991 VAL cc_start: 0.7629 (p) cc_final: 0.6945 (t) REVERT: A 995 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8352 (tpp80) REVERT: A 1009 THR cc_start: 0.8851 (m) cc_final: 0.8636 (p) REVERT: A 1014 ARG cc_start: 0.8469 (mtt-85) cc_final: 0.8068 (mmm-85) REVERT: A 1023 ASN cc_start: 0.8421 (t0) cc_final: 0.8162 (t0) REVERT: A 1024 LEU cc_start: 0.8439 (tp) cc_final: 0.8171 (pp) REVERT: A 1038 LYS cc_start: 0.8663 (mttt) cc_final: 0.8060 (mttm) REVERT: A 1064 HIS cc_start: 0.7659 (m170) cc_final: 0.7083 (m170) REVERT: A 1088 HIS cc_start: 0.7732 (m-70) cc_final: 0.7180 (m-70) REVERT: A 1105 THR cc_start: 0.6783 (t) cc_final: 0.6558 (m) REVERT: A 1114 ILE cc_start: 0.8948 (mp) cc_final: 0.8718 (tp) REVERT: B 65 PHE cc_start: 0.8110 (m-80) cc_final: 0.7293 (m-80) REVERT: B 92 PHE cc_start: 0.7720 (t80) cc_final: 0.7507 (t80) REVERT: B 224 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7598 (pm20) REVERT: B 277 LEU cc_start: 0.7703 (mm) cc_final: 0.7384 (mm) REVERT: B 287 ASP cc_start: 0.7462 (t0) cc_final: 0.6514 (p0) REVERT: B 300 LYS cc_start: 0.8648 (mttt) cc_final: 0.8218 (mttm) REVERT: B 309 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8274 (mm-30) REVERT: B 329 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5359 (m-10) REVERT: B 331 ASN cc_start: 0.6869 (t0) cc_final: 0.6470 (m-40) REVERT: B 357 ARG cc_start: 0.7455 (mmm160) cc_final: 0.6872 (mmm160) REVERT: B 378 LYS cc_start: 0.7868 (ptmm) cc_final: 0.6979 (ttpp) REVERT: B 398 ASP cc_start: 0.6635 (m-30) cc_final: 0.5923 (m-30) REVERT: B 409 GLN cc_start: 0.8741 (mt0) cc_final: 0.7850 (mt0) REVERT: B 509 ARG cc_start: 0.7248 (tmm160) cc_final: 0.6663 (mmm160) REVERT: B 529 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7390 (tptp) REVERT: B 535 LYS cc_start: 0.8069 (tppp) cc_final: 0.7843 (tppt) REVERT: B 557 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7337 (mtmm) REVERT: B 578 ASP cc_start: 0.7716 (p0) cc_final: 0.7493 (p0) REVERT: B 583 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7947 (tp30) REVERT: B 702 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 714 ILE cc_start: 0.8693 (mt) cc_final: 0.8423 (mp) REVERT: B 725 GLU cc_start: 0.7709 (tt0) cc_final: 0.7257 (tm-30) REVERT: B 727 LEU cc_start: 0.7557 (mt) cc_final: 0.6730 (mt) REVERT: B 740 MET cc_start: 0.9085 (tpt) cc_final: 0.8376 (tpt) REVERT: B 756 TYR cc_start: 0.8072 (m-80) cc_final: 0.7525 (m-80) REVERT: B 758 SER cc_start: 0.8782 (t) cc_final: 0.8561 (m) REVERT: B 776 LYS cc_start: 0.9041 (tptp) cc_final: 0.8418 (tptp) REVERT: B 779 GLN cc_start: 0.8428 (tp40) cc_final: 0.7861 (tp-100) REVERT: B 780 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7428 (tp30) REVERT: B 785 VAL cc_start: 0.8136 (m) cc_final: 0.7920 (p) REVERT: B 814 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7197 (mmtt) REVERT: B 823 PHE cc_start: 0.7529 (m-80) cc_final: 0.7306 (m-80) REVERT: B 860 VAL cc_start: 0.8644 (t) cc_final: 0.8436 (p) REVERT: B 869 MET cc_start: 0.8323 (mpp) cc_final: 0.7895 (ptp) REVERT: B 909 ILE cc_start: 0.8032 (pt) cc_final: 0.7800 (mm) REVERT: B 917 TYR cc_start: 0.7868 (m-80) cc_final: 0.7070 (m-10) REVERT: B 921 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8464 (mtpp) REVERT: B 926 GLN cc_start: 0.8654 (mt0) cc_final: 0.8420 (tp40) REVERT: B 928 ASN cc_start: 0.8442 (m-40) cc_final: 0.8231 (m-40) REVERT: B 934 ILE cc_start: 0.8448 (mm) cc_final: 0.8244 (mm) REVERT: B 954 GLN cc_start: 0.8007 (pp30) cc_final: 0.7787 (pp30) REVERT: B 955 ASN cc_start: 0.8562 (m110) cc_final: 0.7927 (m110) REVERT: B 957 GLN cc_start: 0.8851 (mt0) cc_final: 0.8505 (tt0) REVERT: B 964 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8440 (ttmm) REVERT: B 965 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8386 (tp-100) REVERT: B 991 VAL cc_start: 0.9089 (m) cc_final: 0.8785 (t) REVERT: B 994 ASP cc_start: 0.8353 (t0) cc_final: 0.8027 (t0) REVERT: B 1001 LEU cc_start: 0.9072 (mt) cc_final: 0.8821 (mt) REVERT: B 1017 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8315 (pp20) REVERT: B 1028 LYS cc_start: 0.8150 (tppt) cc_final: 0.7581 (tppt) REVERT: B 1034 LEU cc_start: 0.7933 (mt) cc_final: 0.7732 (mt) REVERT: B 1045 LYS cc_start: 0.7685 (tmmt) cc_final: 0.7466 (tmmt) REVERT: B 1054 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7405 (tp40) REVERT: B 1111 GLU cc_start: 0.7322 (pp20) cc_final: 0.6705 (pm20) REVERT: C 34 ARG cc_start: 0.6653 (tpp-160) cc_final: 0.6185 (tpp80) REVERT: C 37 TYR cc_start: 0.6163 (p90) cc_final: 0.5907 (p90) REVERT: C 43 PHE cc_start: 0.7426 (t80) cc_final: 0.5767 (t80) REVERT: C 65 PHE cc_start: 0.8609 (m-80) cc_final: 0.8033 (m-80) REVERT: C 99 ASN cc_start: 0.8703 (m110) cc_final: 0.8354 (m-40) REVERT: C 104 TRP cc_start: 0.4926 (m-90) cc_final: 0.4546 (m-90) REVERT: C 164 ASN cc_start: 0.8099 (t0) cc_final: 0.7878 (t0) REVERT: C 203 ILE cc_start: 0.8121 (tt) cc_final: 0.7866 (tp) REVERT: C 237 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8105 (mtm110) REVERT: C 240 THR cc_start: 0.7751 (m) cc_final: 0.7275 (t) REVERT: C 277 LEU cc_start: 0.7843 (mt) cc_final: 0.7593 (mt) REVERT: C 356 LYS cc_start: 0.7036 (ttmm) cc_final: 0.6192 (tptp) REVERT: C 440 ASN cc_start: 0.8696 (m-40) cc_final: 0.8066 (p0) REVERT: C 533 LEU cc_start: 0.8560 (tp) cc_final: 0.8274 (tp) REVERT: C 535 LYS cc_start: 0.7943 (mttt) cc_final: 0.7741 (mtmm) REVERT: C 543 PHE cc_start: 0.8579 (m-80) cc_final: 0.8353 (m-80) REVERT: C 581 THR cc_start: 0.8128 (m) cc_final: 0.7825 (p) REVERT: C 583 GLU cc_start: 0.8413 (mp0) cc_final: 0.8007 (mp0) REVERT: C 613 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7179 (mp10) REVERT: C 657 ASN cc_start: 0.8503 (m-40) cc_final: 0.8123 (m-40) REVERT: C 693 ILE cc_start: 0.8179 (pt) cc_final: 0.7833 (mp) REVERT: C 699 LEU cc_start: 0.8278 (pt) cc_final: 0.7927 (pt) REVERT: C 710 ASN cc_start: 0.8363 (p0) cc_final: 0.8059 (m-40) REVERT: C 727 LEU cc_start: 0.8380 (mt) cc_final: 0.8065 (mt) REVERT: C 730 SER cc_start: 0.6907 (p) cc_final: 0.6619 (t) REVERT: C 731 MET cc_start: 0.8419 (ptt) cc_final: 0.8063 (ptt) REVERT: C 740 MET cc_start: 0.7141 (tpp) cc_final: 0.6712 (tpp) REVERT: C 751 ASN cc_start: 0.8662 (p0) cc_final: 0.8417 (p0) REVERT: C 759 PHE cc_start: 0.8195 (m-80) cc_final: 0.7970 (m-10) REVERT: C 772 VAL cc_start: 0.8621 (t) cc_final: 0.7843 (p) REVERT: C 776 LYS cc_start: 0.9158 (ttpt) cc_final: 0.8887 (ttpt) REVERT: C 790 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7883 (mmtm) REVERT: C 802 PHE cc_start: 0.9121 (m-10) cc_final: 0.8669 (m-10) REVERT: C 805 ILE cc_start: 0.8509 (mp) cc_final: 0.8271 (tp) REVERT: C 866 THR cc_start: 0.7485 (p) cc_final: 0.6582 (p) REVERT: C 872 GLN cc_start: 0.8932 (tp40) cc_final: 0.8646 (tp-100) REVERT: C 877 LEU cc_start: 0.8908 (mt) cc_final: 0.8672 (mt) REVERT: C 894 LEU cc_start: 0.7705 (mt) cc_final: 0.7420 (mm) REVERT: C 902 MET cc_start: 0.8265 (tmm) cc_final: 0.7873 (tmm) REVERT: C 905 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8430 (tpp80) REVERT: C 918 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7741 (mt-10) REVERT: C 921 LYS cc_start: 0.8478 (mmpt) cc_final: 0.8244 (mtpp) REVERT: C 925 ASN cc_start: 0.8631 (m-40) cc_final: 0.8362 (m-40) REVERT: C 926 GLN cc_start: 0.8735 (mt0) cc_final: 0.8329 (mt0) REVERT: C 947 LYS cc_start: 0.8470 (mttt) cc_final: 0.8212 (ptpp) REVERT: C 964 LYS cc_start: 0.8521 (tttt) cc_final: 0.7954 (ptpt) REVERT: C 1005 GLN cc_start: 0.8110 (pp30) cc_final: 0.7839 (pp30) REVERT: C 1013 ILE cc_start: 0.8895 (mt) cc_final: 0.8517 (mm) REVERT: C 1014 ARG cc_start: 0.8435 (mtt90) cc_final: 0.7751 (ptp-110) REVERT: C 1017 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 1023 ASN cc_start: 0.8876 (m110) cc_final: 0.8521 (m110) REVERT: C 1028 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8607 (mmmm) REVERT: C 1029 MET cc_start: 0.8748 (tpp) cc_final: 0.8327 (tpp) REVERT: C 1081 ILE cc_start: 0.7837 (mt) cc_final: 0.7559 (mt) REVERT: C 1088 HIS cc_start: 0.6944 (m90) cc_final: 0.6589 (m-70) REVERT: C 1127 ASP cc_start: 0.8458 (p0) cc_final: 0.8243 (p0) outliers start: 13 outliers final: 2 residues processed: 778 average time/residue: 0.1907 time to fit residues: 229.4516 Evaluate side-chains 696 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 693 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 265 optimal weight: 0.5980 chunk 146 optimal weight: 0.0470 chunk 213 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 655 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.167823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127938 restraints weight = 55317.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.132882 restraints weight = 34698.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136509 restraints weight = 24246.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.139112 restraints weight = 18202.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.141046 restraints weight = 14509.441| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4706 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= 0.169 Angle : 0.813 20.091 36353 Z= 0.391 Chirality : 0.054 0.738 4208 Planarity : 0.005 0.098 4627 Dihedral : 9.618 103.942 4458 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.14), residues: 3207 helix: 1.24 (0.20), residues: 676 sheet: 0.03 (0.20), residues: 661 loop : -1.10 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.043 0.002 TYR B 365 PHE 0.029 0.002 PHE C 559 TRP 0.030 0.002 TRP C 436 HIS 0.011 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00352 (26536) covalent geometry : angle 0.75492 (36139) SS BOND : bond 0.00360 ( 41) SS BOND : angle 2.16123 ( 82) hydrogen bonds : bond 0.05315 ( 873) hydrogen bonds : angle 6.48714 ( 2436) Misc. bond : bond 0.00133 ( 3) link_BETA1-4 : bond 0.00361 ( 10) link_BETA1-4 : angle 1.74663 ( 30) link_NAG-ASN : bond 0.00965 ( 34) link_NAG-ASN : angle 5.36743 ( 102) *********************** 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 757 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 754 time to evaluate : 0.976 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: 0.8379 (mmpt) cc_final: 0.7853 (ttpt) REVERT: A 49 HIS cc_start: 0.7730 (t70) cc_final: 0.6934 (t-90) REVERT: A 80 ASP cc_start: 0.8074 (t0) cc_final: 0.7714 (t70) REVERT: A 224 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8258 (pm20) REVERT: A 271 GLN cc_start: 0.8244 (mp10) cc_final: 0.7842 (mp10) REVERT: A 287 ASP cc_start: 0.8412 (t0) cc_final: 0.8009 (p0) REVERT: A 294 ASP cc_start: 0.7210 (m-30) cc_final: 0.6770 (m-30) REVERT: A 298 GLU cc_start: 0.8243 (tt0) cc_final: 0.7874 (tt0) REVERT: A 342 PHE cc_start: 0.9061 (m-10) cc_final: 0.8744 (m-10) REVERT: A 374 PHE cc_start: 0.7612 (m-80) cc_final: 0.6933 (m-80) REVERT: A 562 PHE cc_start: 0.7823 (p90) cc_final: 0.7548 (p90) REVERT: A 592 PHE cc_start: 0.7050 (t80) cc_final: 0.6834 (t80) REVERT: A 646 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7282 (tpt90) REVERT: A 658 ASN cc_start: 0.7427 (t0) cc_final: 0.7020 (t0) REVERT: A 731 MET cc_start: 0.8308 (pmm) cc_final: 0.7888 (pmm) REVERT: A 737 ASP cc_start: 0.8344 (t0) cc_final: 0.7942 (t70) REVERT: A 751 ASN cc_start: 0.8368 (m110) cc_final: 0.8064 (m110) REVERT: A 773 GLU cc_start: 0.8702 (tt0) cc_final: 0.8074 (tt0) REVERT: A 776 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8272 (mmmm) REVERT: A 777 ASN cc_start: 0.8927 (m-40) cc_final: 0.8646 (m110) REVERT: A 787 GLN cc_start: 0.7584 (pm20) cc_final: 0.7120 (pp30) REVERT: A 788 ILE cc_start: 0.8375 (mm) cc_final: 0.8135 (tp) REVERT: A 790 LYS cc_start: 0.7943 (tptt) cc_final: 0.7705 (tptt) REVERT: A 791 THR cc_start: 0.8681 (m) cc_final: 0.8157 (m) REVERT: A 796 ASP cc_start: 0.7994 (m-30) cc_final: 0.7670 (m-30) REVERT: A 818 ILE cc_start: 0.9178 (mt) cc_final: 0.8964 (mt) REVERT: A 869 MET cc_start: 0.8920 (mtm) cc_final: 0.7411 (ptp) REVERT: A 870 ILE cc_start: 0.8918 (mt) cc_final: 0.8544 (mt) REVERT: A 873 TYR cc_start: 0.8670 (m-10) cc_final: 0.8108 (m-10) REVERT: A 902 MET cc_start: 0.8369 (ttm) cc_final: 0.7630 (ttm) REVERT: A 911 VAL cc_start: 0.7376 (t) cc_final: 0.7069 (m) REVERT: A 919 ASN cc_start: 0.8729 (m110) cc_final: 0.8421 (m110) REVERT: A 921 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8058 (tptp) REVERT: A 926 GLN cc_start: 0.8902 (mt0) cc_final: 0.8344 (mt0) REVERT: A 928 ASN cc_start: 0.8366 (m-40) cc_final: 0.8131 (m-40) REVERT: A 933 LYS cc_start: 0.8965 (mttm) cc_final: 0.8284 (mmmm) REVERT: A 949 GLN cc_start: 0.8468 (pp30) cc_final: 0.8245 (pp30) REVERT: A 957 GLN cc_start: 0.8877 (tt0) cc_final: 0.8231 (tm-30) REVERT: A 965 GLN cc_start: 0.8780 (mm110) cc_final: 0.8415 (mm-40) REVERT: A 991 VAL cc_start: 0.7812 (p) cc_final: 0.7196 (t) REVERT: A 995 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8364 (tpp80) REVERT: A 1005 GLN cc_start: 0.8639 (tp40) cc_final: 0.8436 (tp40) REVERT: A 1009 THR cc_start: 0.8746 (m) cc_final: 0.8520 (p) REVERT: A 1014 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8178 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8782 (tt0) cc_final: 0.8564 (tt0) REVERT: A 1023 ASN cc_start: 0.8380 (t0) cc_final: 0.8131 (t0) REVERT: A 1034 LEU cc_start: 0.8275 (mm) cc_final: 0.8040 (mm) REVERT: A 1036 GLN cc_start: 0.6860 (tt0) cc_final: 0.6279 (tt0) REVERT: A 1038 LYS cc_start: 0.8696 (mttt) cc_final: 0.8247 (mtpt) REVERT: A 1045 LYS cc_start: 0.8357 (mppt) cc_final: 0.7872 (mmtm) REVERT: A 1064 HIS cc_start: 0.7455 (m170) cc_final: 0.6871 (m170) REVERT: A 1088 HIS cc_start: 0.7684 (m-70) cc_final: 0.7170 (m-70) REVERT: A 1109 PHE cc_start: 0.7727 (t80) cc_final: 0.7249 (t80) REVERT: A 1114 ILE cc_start: 0.8974 (mp) cc_final: 0.8717 (tp) REVERT: B 54 LEU cc_start: 0.8000 (mp) cc_final: 0.7190 (tt) REVERT: B 65 PHE cc_start: 0.8035 (m-80) cc_final: 0.7192 (m-80) REVERT: B 92 PHE cc_start: 0.7775 (t80) cc_final: 0.7095 (t80) REVERT: B 99 ASN cc_start: 0.8624 (t0) cc_final: 0.7879 (t0) REVERT: B 192 PHE cc_start: 0.5893 (m-80) cc_final: 0.5655 (m-80) REVERT: B 224 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7653 (pm20) REVERT: B 300 LYS cc_start: 0.8560 (mttt) cc_final: 0.8174 (mttt) REVERT: B 309 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 351 TYR cc_start: 0.6889 (p90) cc_final: 0.6643 (p90) REVERT: B 353 TRP cc_start: 0.7463 (p90) cc_final: 0.6449 (p90) REVERT: B 356 LYS cc_start: 0.6843 (mptt) cc_final: 0.6494 (mptt) REVERT: B 398 ASP cc_start: 0.6450 (m-30) cc_final: 0.5967 (m-30) REVERT: B 409 GLN cc_start: 0.8655 (mt0) cc_final: 0.8265 (mt0) REVERT: B 529 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7649 (ttmm) REVERT: B 535 LYS cc_start: 0.8071 (tppp) cc_final: 0.7629 (tppt) REVERT: B 557 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7245 (mtmm) REVERT: B 583 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8157 (tp30) REVERT: B 658 ASN cc_start: 0.7655 (t0) cc_final: 0.7361 (t0) REVERT: B 702 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 714 ILE cc_start: 0.8463 (mt) cc_final: 0.8118 (mm) REVERT: B 725 GLU cc_start: 0.7604 (tt0) cc_final: 0.7093 (tm-30) REVERT: B 727 LEU cc_start: 0.7569 (mt) cc_final: 0.6711 (mt) REVERT: B 735 SER cc_start: 0.8395 (m) cc_final: 0.8180 (m) REVERT: B 740 MET cc_start: 0.9070 (tpt) cc_final: 0.8601 (tpt) REVERT: B 758 SER cc_start: 0.8746 (t) cc_final: 0.8448 (m) REVERT: B 773 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 776 LYS cc_start: 0.8735 (tptp) cc_final: 0.8401 (tptp) REVERT: B 779 GLN cc_start: 0.8462 (tp40) cc_final: 0.7791 (tm-30) REVERT: B 780 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7369 (tp30) REVERT: B 785 VAL cc_start: 0.8543 (m) cc_final: 0.8217 (p) REVERT: B 814 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7144 (mmtt) REVERT: B 867 ASP cc_start: 0.7904 (t0) cc_final: 0.7680 (t0) REVERT: B 902 MET cc_start: 0.8173 (mmm) cc_final: 0.7861 (mmm) REVERT: B 909 ILE cc_start: 0.8022 (pt) cc_final: 0.7754 (mm) REVERT: B 917 TYR cc_start: 0.7876 (m-80) cc_final: 0.7159 (m-10) REVERT: B 921 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8429 (mtpp) REVERT: B 926 GLN cc_start: 0.8674 (mt0) cc_final: 0.8374 (tp40) REVERT: B 934 ILE cc_start: 0.8359 (mm) cc_final: 0.8111 (mm) REVERT: B 935 GLN cc_start: 0.8869 (tt0) cc_final: 0.8276 (tm-30) REVERT: B 954 GLN cc_start: 0.8090 (pp30) cc_final: 0.7854 (pp30) REVERT: B 955 ASN cc_start: 0.8766 (m110) cc_final: 0.8090 (m110) REVERT: B 957 GLN cc_start: 0.8836 (mt0) cc_final: 0.8590 (tt0) REVERT: B 963 VAL cc_start: 0.8787 (t) cc_final: 0.8575 (p) REVERT: B 964 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8375 (ttmm) REVERT: B 979 ASP cc_start: 0.8597 (t0) cc_final: 0.8238 (t0) REVERT: B 991 VAL cc_start: 0.8978 (m) cc_final: 0.8698 (t) REVERT: B 1001 LEU cc_start: 0.9084 (mt) cc_final: 0.8794 (mt) REVERT: B 1005 GLN cc_start: 0.8373 (pp30) cc_final: 0.7993 (pp30) REVERT: B 1017 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 1024 LEU cc_start: 0.8764 (tt) cc_final: 0.8400 (tt) REVERT: B 1028 LYS cc_start: 0.8479 (tppt) cc_final: 0.7695 (tppt) REVERT: B 1038 LYS cc_start: 0.9065 (tptt) cc_final: 0.8750 (tptt) REVERT: B 1045 LYS cc_start: 0.7715 (tmmt) cc_final: 0.7476 (tmmt) REVERT: B 1092 GLU cc_start: 0.6544 (pm20) cc_final: 0.5719 (tp30) REVERT: B 1105 THR cc_start: 0.7072 (t) cc_final: 0.5807 (m) REVERT: B 1106 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 1109 PHE cc_start: 0.6828 (t80) cc_final: 0.5970 (t80) REVERT: B 1114 ILE cc_start: 0.8430 (mm) cc_final: 0.8191 (mm) REVERT: C 65 PHE cc_start: 0.8600 (m-80) cc_final: 0.8016 (m-80) REVERT: C 96 GLU cc_start: 0.6265 (pm20) cc_final: 0.5794 (mp0) REVERT: C 195 LYS cc_start: 0.5981 (ttpp) cc_final: 0.5359 (tttt) REVERT: C 203 ILE cc_start: 0.8140 (tt) cc_final: 0.7890 (tp) REVERT: C 240 THR cc_start: 0.7656 (m) cc_final: 0.7388 (t) REVERT: C 267 VAL cc_start: 0.7507 (t) cc_final: 0.6906 (t) REVERT: C 277 LEU cc_start: 0.7977 (mt) cc_final: 0.7663 (pp) REVERT: C 314 GLN cc_start: 0.6182 (mt0) cc_final: 0.5902 (mt0) REVERT: C 356 LYS cc_start: 0.7201 (ttmm) cc_final: 0.6306 (tptp) REVERT: C 436 TRP cc_start: 0.6793 (p-90) cc_final: 0.6537 (p-90) REVERT: C 440 ASN cc_start: 0.8639 (m-40) cc_final: 0.7979 (p0) REVERT: C 533 LEU cc_start: 0.8672 (tp) cc_final: 0.8373 (tp) REVERT: C 559 PHE cc_start: 0.7323 (m-10) cc_final: 0.5386 (m-10) REVERT: C 583 GLU cc_start: 0.8483 (mp0) cc_final: 0.8159 (mp0) REVERT: C 657 ASN cc_start: 0.8524 (m-40) cc_final: 0.8189 (m-40) REVERT: C 693 ILE cc_start: 0.8213 (pt) cc_final: 0.7901 (mp) REVERT: C 710 ASN cc_start: 0.8355 (p0) cc_final: 0.8099 (m-40) REVERT: C 712 ILE cc_start: 0.8026 (tp) cc_final: 0.7806 (tp) REVERT: C 727 LEU cc_start: 0.8316 (mt) cc_final: 0.8064 (mt) REVERT: C 730 SER cc_start: 0.7018 (p) cc_final: 0.6596 (t) REVERT: C 731 MET cc_start: 0.8614 (ptt) cc_final: 0.7892 (ptt) REVERT: C 774 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7858 (mm-40) REVERT: C 790 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7934 (mmtm) REVERT: C 796 ASP cc_start: 0.8453 (m-30) cc_final: 0.8178 (m-30) REVERT: C 802 PHE cc_start: 0.9088 (m-10) cc_final: 0.8578 (m-10) REVERT: C 865 LEU cc_start: 0.8648 (mt) cc_final: 0.7950 (mt) REVERT: C 866 THR cc_start: 0.7570 (p) cc_final: 0.6311 (p) REVERT: C 869 MET cc_start: 0.8384 (mtm) cc_final: 0.7884 (mtm) REVERT: C 877 LEU cc_start: 0.8854 (mt) cc_final: 0.8643 (mt) REVERT: C 902 MET cc_start: 0.8438 (tmm) cc_final: 0.7933 (tmm) REVERT: C 905 ARG cc_start: 0.8936 (mtt-85) cc_final: 0.8232 (tpp80) REVERT: C 925 ASN cc_start: 0.8623 (m-40) cc_final: 0.8377 (m-40) REVERT: C 926 GLN cc_start: 0.8650 (mt0) cc_final: 0.8374 (mt0) REVERT: C 936 ASP cc_start: 0.8445 (t0) cc_final: 0.8229 (t0) REVERT: C 947 LYS cc_start: 0.8492 (mttt) cc_final: 0.8208 (ptpp) REVERT: C 949 GLN cc_start: 0.8424 (tp40) cc_final: 0.7853 (tp40) REVERT: C 953 ASN cc_start: 0.8581 (m-40) cc_final: 0.7956 (m-40) REVERT: C 962 LEU cc_start: 0.9114 (tp) cc_final: 0.8871 (tp) REVERT: C 964 LYS cc_start: 0.8690 (tttt) cc_final: 0.8125 (ptmt) REVERT: C 965 GLN cc_start: 0.8896 (mt0) cc_final: 0.8628 (mt0) REVERT: C 966 LEU cc_start: 0.8228 (mt) cc_final: 0.7926 (mt) REVERT: C 1005 GLN cc_start: 0.8124 (pp30) cc_final: 0.7802 (pp30) REVERT: C 1013 ILE cc_start: 0.8930 (mt) cc_final: 0.8568 (mm) REVERT: C 1014 ARG cc_start: 0.8589 (mtt90) cc_final: 0.7531 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7950 (mt-10) REVERT: C 1023 ASN cc_start: 0.8820 (m110) cc_final: 0.8478 (m110) REVERT: C 1029 MET cc_start: 0.8699 (tpp) cc_final: 0.8440 (tpp) REVERT: C 1067 TYR cc_start: 0.7908 (t80) cc_final: 0.7678 (t80) REVERT: C 1081 ILE cc_start: 0.7912 (mt) cc_final: 0.7296 (mm) REVERT: C 1088 HIS cc_start: 0.7277 (m90) cc_final: 0.6877 (m-70) outliers start: 3 outliers final: 1 residues processed: 757 average time/residue: 0.1956 time to fit residues: 228.6169 Evaluate side-chains 696 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 695 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 265 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 290 optimal weight: 0.4980 chunk 152 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 762 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 644 GLN ** C 901 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 = 0.4399 r_free = 0.4399 target = 0.167599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128633 restraints weight = 55211.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.133608 restraints weight = 34442.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.137173 restraints weight = 23863.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.139760 restraints weight = 17814.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141627 restraints weight = 14130.660| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26624 Z= 0.152 Angle : 0.765 18.928 36353 Z= 0.366 Chirality : 0.051 0.669 4208 Planarity : 0.005 0.085 4627 Dihedral : 9.358 103.862 4458 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3207 helix: 1.09 (0.20), residues: 675 sheet: -0.10 (0.20), residues: 650 loop : -1.10 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 355 TYR 0.035 0.002 TYR B 365 PHE 0.025 0.002 PHE C 133 TRP 0.028 0.002 TRP C1102 HIS 0.010 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00326 (26536) covalent geometry : angle 0.71066 (36139) SS BOND : bond 0.00301 ( 41) SS BOND : angle 1.91383 ( 82) hydrogen bonds : bond 0.04824 ( 873) hydrogen bonds : angle 6.17161 ( 2436) Misc. bond : bond 0.00075 ( 3) link_BETA1-4 : bond 0.00361 ( 10) link_BETA1-4 : angle 1.65388 ( 30) link_NAG-ASN : bond 0.00877 ( 34) link_NAG-ASN : angle 5.09657 ( 102) *********************** 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 742 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 740 time to evaluate : 0.934 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: A 41 LYS cc_start: 0.8351 (mmpt) cc_final: 0.8065 (mmmm) REVERT: A 49 HIS cc_start: 0.7449 (t70) cc_final: 0.6960 (t-90) REVERT: A 56 LEU cc_start: 0.8240 (mt) cc_final: 0.8007 (mt) REVERT: A 80 ASP cc_start: 0.8102 (t0) cc_final: 0.7736 (t70) REVERT: A 224 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8233 (pm20) REVERT: A 271 GLN cc_start: 0.8172 (mp10) cc_final: 0.7872 (mp10) REVERT: A 273 ARG cc_start: 0.8066 (mmt180) cc_final: 0.7743 (mmt180) REVERT: A 278 LYS cc_start: 0.6358 (tmmt) cc_final: 0.5199 (ptmm) REVERT: A 287 ASP cc_start: 0.8423 (t0) cc_final: 0.8122 (t70) REVERT: A 298 GLU cc_start: 0.8325 (tt0) cc_final: 0.7948 (tt0) REVERT: A 342 PHE cc_start: 0.9110 (m-10) cc_final: 0.8649 (m-10) REVERT: A 357 ARG cc_start: 0.7593 (ptp-170) cc_final: 0.6736 (mtp180) REVERT: A 437 ASN cc_start: 0.8177 (t0) cc_final: 0.7641 (t0) REVERT: A 562 PHE cc_start: 0.7808 (p90) cc_final: 0.7601 (p90) REVERT: A 578 ASP cc_start: 0.7747 (t70) cc_final: 0.7457 (t0) REVERT: A 583 GLU cc_start: 0.7613 (mp0) cc_final: 0.7365 (mp0) REVERT: A 592 PHE cc_start: 0.7284 (t80) cc_final: 0.6943 (t80) REVERT: A 643 PHE cc_start: 0.7600 (t80) cc_final: 0.7196 (t80) REVERT: A 646 ARG cc_start: 0.7722 (tpt90) cc_final: 0.7327 (tpt90) REVERT: A 658 ASN cc_start: 0.7720 (t0) cc_final: 0.6972 (t0) REVERT: A 731 MET cc_start: 0.8316 (pmm) cc_final: 0.7878 (pmm) REVERT: A 740 MET cc_start: 0.8200 (tpp) cc_final: 0.7780 (tpp) REVERT: A 751 ASN cc_start: 0.8323 (m110) cc_final: 0.7993 (m110) REVERT: A 767 LEU cc_start: 0.8543 (mt) cc_final: 0.8109 (tp) REVERT: A 772 VAL cc_start: 0.9210 (t) cc_final: 0.8997 (m) REVERT: A 773 GLU cc_start: 0.8600 (tt0) cc_final: 0.8027 (tt0) REVERT: A 775 ASP cc_start: 0.7864 (t0) cc_final: 0.7444 (t0) REVERT: A 776 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8101 (mmmm) REVERT: A 777 ASN cc_start: 0.8937 (m-40) cc_final: 0.8620 (m110) REVERT: A 788 ILE cc_start: 0.8312 (mm) cc_final: 0.7924 (tp) REVERT: A 796 ASP cc_start: 0.7986 (m-30) cc_final: 0.7699 (m-30) REVERT: A 797 PHE cc_start: 0.8906 (m-80) cc_final: 0.8586 (m-80) REVERT: A 818 ILE cc_start: 0.9158 (mt) cc_final: 0.8851 (mm) REVERT: A 870 ILE cc_start: 0.8905 (mt) cc_final: 0.8671 (mt) REVERT: A 873 TYR cc_start: 0.8696 (m-10) cc_final: 0.8227 (m-80) REVERT: A 902 MET cc_start: 0.8499 (ttm) cc_final: 0.7798 (ttm) REVERT: A 911 VAL cc_start: 0.7409 (t) cc_final: 0.7090 (m) REVERT: A 918 GLU cc_start: 0.8206 (pt0) cc_final: 0.7999 (pt0) REVERT: A 919 ASN cc_start: 0.8708 (m110) cc_final: 0.8352 (m110) REVERT: A 921 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8097 (tptp) REVERT: A 926 GLN cc_start: 0.8968 (mt0) cc_final: 0.8489 (mt0) REVERT: A 928 ASN cc_start: 0.8463 (m-40) cc_final: 0.8178 (m-40) REVERT: A 933 LYS cc_start: 0.8948 (mttm) cc_final: 0.8247 (mmmm) REVERT: A 949 GLN cc_start: 0.8508 (pp30) cc_final: 0.8194 (pp30) REVERT: A 957 GLN cc_start: 0.8946 (tt0) cc_final: 0.8215 (tm-30) REVERT: A 991 VAL cc_start: 0.7904 (p) cc_final: 0.7307 (t) REVERT: A 993 ILE cc_start: 0.9077 (mm) cc_final: 0.8860 (mm) REVERT: A 995 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8371 (tpp80) REVERT: A 1005 GLN cc_start: 0.8692 (tp40) cc_final: 0.8190 (tm-30) REVERT: A 1009 THR cc_start: 0.8847 (m) cc_final: 0.8377 (p) REVERT: A 1014 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8268 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8815 (tt0) cc_final: 0.8571 (tt0) REVERT: A 1023 ASN cc_start: 0.8419 (t0) cc_final: 0.8181 (t0) REVERT: A 1038 LYS cc_start: 0.8733 (mttt) cc_final: 0.8237 (mtpt) REVERT: A 1045 LYS cc_start: 0.8422 (mppt) cc_final: 0.7979 (mmtm) REVERT: A 1084 ASP cc_start: 0.8858 (p0) cc_final: 0.8655 (p0) REVERT: A 1088 HIS cc_start: 0.7635 (m-70) cc_final: 0.7093 (m-70) REVERT: A 1091 ARG cc_start: 0.7387 (mtt180) cc_final: 0.7022 (mtt-85) REVERT: A 1109 PHE cc_start: 0.7755 (t80) cc_final: 0.7243 (t80) REVERT: A 1114 ILE cc_start: 0.8983 (mp) cc_final: 0.8712 (tp) REVERT: A 1121 PHE cc_start: 0.7438 (p90) cc_final: 0.7182 (p90) REVERT: B 52 GLN cc_start: 0.8176 (mp10) cc_final: 0.7890 (mp10) REVERT: B 53 ASP cc_start: 0.6914 (t0) cc_final: 0.6236 (t0) REVERT: B 54 LEU cc_start: 0.8080 (mp) cc_final: 0.7234 (tt) REVERT: B 65 PHE cc_start: 0.8030 (m-80) cc_final: 0.7215 (m-80) REVERT: B 92 PHE cc_start: 0.7693 (t80) cc_final: 0.7063 (t80) REVERT: B 99 ASN cc_start: 0.8608 (t0) cc_final: 0.7974 (t0) REVERT: B 187 LYS cc_start: 0.7453 (pttm) cc_final: 0.7158 (pttm) REVERT: B 192 PHE cc_start: 0.5988 (m-80) cc_final: 0.5768 (m-80) REVERT: B 207 HIS cc_start: 0.8381 (m90) cc_final: 0.7995 (m90) REVERT: B 287 ASP cc_start: 0.7645 (t0) cc_final: 0.7430 (t70) REVERT: B 296 LEU cc_start: 0.8908 (tp) cc_final: 0.8356 (tp) REVERT: B 300 LYS cc_start: 0.8617 (mttt) cc_final: 0.8125 (mttt) REVERT: B 309 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 353 TRP cc_start: 0.7697 (p90) cc_final: 0.6420 (p90) REVERT: B 398 ASP cc_start: 0.6645 (m-30) cc_final: 0.6123 (m-30) REVERT: B 409 GLN cc_start: 0.8860 (mt0) cc_final: 0.8155 (tt0) REVERT: B 444 LYS cc_start: 0.8260 (mtpt) cc_final: 0.8057 (mtpt) REVERT: B 509 ARG cc_start: 0.6397 (mmt180) cc_final: 0.5564 (mmt90) REVERT: B 521 PRO cc_start: 0.7184 (Cg_endo) cc_final: 0.6957 (Cg_exo) REVERT: B 529 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7748 (ttmm) REVERT: B 535 LYS cc_start: 0.8160 (tppp) cc_final: 0.7887 (tppt) REVERT: B 557 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7282 (mtmm) REVERT: B 583 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8028 (tp30) REVERT: B 619 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7871 (mp0) REVERT: B 702 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 712 ILE cc_start: 0.7598 (tt) cc_final: 0.7391 (tp) REVERT: B 714 ILE cc_start: 0.8504 (mt) cc_final: 0.8083 (mm) REVERT: B 725 GLU cc_start: 0.7437 (tt0) cc_final: 0.6881 (tm-30) REVERT: B 726 ILE cc_start: 0.7981 (mp) cc_final: 0.7646 (mp) REVERT: B 727 LEU cc_start: 0.7664 (mt) cc_final: 0.6807 (mt) REVERT: B 740 MET cc_start: 0.9132 (tpt) cc_final: 0.8661 (tpt) REVERT: B 762 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8191 (pp30) REVERT: B 773 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 776 LYS cc_start: 0.8805 (tptp) cc_final: 0.8428 (tptp) REVERT: B 779 GLN cc_start: 0.8446 (tp40) cc_final: 0.7737 (tm-30) REVERT: B 780 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7384 (tp30) REVERT: B 785 VAL cc_start: 0.8663 (m) cc_final: 0.8339 (p) REVERT: B 805 ILE cc_start: 0.8735 (mt) cc_final: 0.8184 (tp) REVERT: B 811 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8236 (mmmt) REVERT: B 814 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7187 (mmtt) REVERT: B 815 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7104 (mtm-85) REVERT: B 823 PHE cc_start: 0.8112 (m-80) cc_final: 0.7664 (m-10) REVERT: B 867 ASP cc_start: 0.7950 (t0) cc_final: 0.7734 (t0) REVERT: B 869 MET cc_start: 0.8292 (mpp) cc_final: 0.7826 (ptp) REVERT: B 877 LEU cc_start: 0.8878 (mt) cc_final: 0.8619 (mt) REVERT: B 917 TYR cc_start: 0.7985 (m-80) cc_final: 0.7296 (m-10) REVERT: B 921 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8401 (mtpp) REVERT: B 926 GLN cc_start: 0.8622 (mt0) cc_final: 0.8317 (tp40) REVERT: B 934 ILE cc_start: 0.8313 (mm) cc_final: 0.8018 (mm) REVERT: B 935 GLN cc_start: 0.8778 (tt0) cc_final: 0.8215 (tm-30) REVERT: B 954 GLN cc_start: 0.8114 (pp30) cc_final: 0.7844 (pp30) REVERT: B 955 ASN cc_start: 0.8779 (m110) cc_final: 0.8151 (m110) REVERT: B 957 GLN cc_start: 0.8832 (mt0) cc_final: 0.8622 (tt0) REVERT: B 979 ASP cc_start: 0.8601 (t0) cc_final: 0.8379 (t0) REVERT: B 991 VAL cc_start: 0.8998 (m) cc_final: 0.8629 (t) REVERT: B 994 ASP cc_start: 0.8240 (t0) cc_final: 0.8014 (t0) REVERT: B 996 LEU cc_start: 0.8947 (mt) cc_final: 0.8739 (mt) REVERT: B 1001 LEU cc_start: 0.9077 (mt) cc_final: 0.8717 (mt) REVERT: B 1005 GLN cc_start: 0.8311 (pp30) cc_final: 0.7978 (pp30) REVERT: B 1017 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8186 (pp20) REVERT: B 1028 LYS cc_start: 0.8500 (tppt) cc_final: 0.7454 (tppt) REVERT: B 1033 VAL cc_start: 0.7753 (t) cc_final: 0.7513 (t) REVERT: B 1038 LYS cc_start: 0.9052 (tptt) cc_final: 0.8706 (tptt) REVERT: B 1045 LYS cc_start: 0.7677 (tmmt) cc_final: 0.7476 (tmmt) REVERT: B 1113 GLN cc_start: 0.7750 (mp10) cc_final: 0.6989 (mp10) REVERT: C 65 PHE cc_start: 0.8527 (m-80) cc_final: 0.7940 (m-80) REVERT: C 96 GLU cc_start: 0.6088 (pm20) cc_final: 0.5868 (mp0) REVERT: C 164 ASN cc_start: 0.8194 (t0) cc_final: 0.7959 (t0) REVERT: C 195 LYS cc_start: 0.5840 (ttpp) cc_final: 0.5620 (tttt) REVERT: C 238 PHE cc_start: 0.8087 (p90) cc_final: 0.6885 (p90) REVERT: C 265 TYR cc_start: 0.7362 (p90) cc_final: 0.7130 (p90) REVERT: C 277 LEU cc_start: 0.7981 (mt) cc_final: 0.7683 (pp) REVERT: C 396 TYR cc_start: 0.7307 (m-80) cc_final: 0.6990 (m-10) REVERT: C 440 ASN cc_start: 0.8656 (m-40) cc_final: 0.8067 (p0) REVERT: C 557 LYS cc_start: 0.8942 (mppt) cc_final: 0.8544 (mppt) REVERT: C 657 ASN cc_start: 0.8559 (m-40) cc_final: 0.8173 (m-40) REVERT: C 693 ILE cc_start: 0.8191 (pt) cc_final: 0.7630 (mp) REVERT: C 712 ILE cc_start: 0.7916 (tp) cc_final: 0.7673 (tp) REVERT: C 723 THR cc_start: 0.8113 (t) cc_final: 0.7626 (p) REVERT: C 727 LEU cc_start: 0.8274 (mt) cc_final: 0.7986 (mt) REVERT: C 731 MET cc_start: 0.8645 (ptt) cc_final: 0.8286 (ptt) REVERT: C 759 PHE cc_start: 0.7744 (m-80) cc_final: 0.7319 (m-80) REVERT: C 772 VAL cc_start: 0.8717 (m) cc_final: 0.8413 (p) REVERT: C 774 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8267 (mm110) REVERT: C 776 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8889 (ttmt) REVERT: C 790 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7947 (mmtm) REVERT: C 796 ASP cc_start: 0.8458 (m-30) cc_final: 0.8247 (m-30) REVERT: C 808 ASP cc_start: 0.8321 (t70) cc_final: 0.8118 (t0) REVERT: C 820 ASP cc_start: 0.7139 (m-30) cc_final: 0.6838 (m-30) REVERT: C 865 LEU cc_start: 0.8576 (mt) cc_final: 0.7914 (mt) REVERT: C 866 THR cc_start: 0.7550 (p) cc_final: 0.6311 (p) REVERT: C 869 MET cc_start: 0.8357 (mtm) cc_final: 0.7586 (mtm) REVERT: C 902 MET cc_start: 0.8426 (tmm) cc_final: 0.7806 (tmm) REVERT: C 905 ARG cc_start: 0.8927 (mtt-85) cc_final: 0.8704 (tpp80) REVERT: C 925 ASN cc_start: 0.8716 (m-40) cc_final: 0.8459 (m-40) REVERT: C 926 GLN cc_start: 0.8665 (mt0) cc_final: 0.8340 (mt0) REVERT: C 936 ASP cc_start: 0.8458 (t0) cc_final: 0.8228 (t0) REVERT: C 947 LYS cc_start: 0.8541 (mttt) cc_final: 0.8234 (ptpp) REVERT: C 964 LYS cc_start: 0.8786 (tttt) cc_final: 0.8228 (ptmt) REVERT: C 965 GLN cc_start: 0.8830 (mt0) cc_final: 0.8088 (mm-40) REVERT: C 1007 TYR cc_start: 0.8952 (t80) cc_final: 0.8747 (t80) REVERT: C 1013 ILE cc_start: 0.8915 (mt) cc_final: 0.8561 (mm) REVERT: C 1014 ARG cc_start: 0.8654 (mtt90) cc_final: 0.7528 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 1023 ASN cc_start: 0.8780 (m110) cc_final: 0.8497 (m110) REVERT: C 1028 LYS cc_start: 0.9122 (mmtp) cc_final: 0.8848 (mmtp) REVERT: C 1029 MET cc_start: 0.8612 (tpp) cc_final: 0.8250 (tpp) REVERT: C 1081 ILE cc_start: 0.7858 (mt) cc_final: 0.7308 (mm) REVERT: C 1088 HIS cc_start: 0.7430 (m90) cc_final: 0.6911 (m-70) REVERT: C 1103 PHE cc_start: 0.7680 (m-80) cc_final: 0.7325 (m-80) outliers start: 2 outliers final: 0 residues processed: 741 average time/residue: 0.1929 time to fit residues: 221.6170 Evaluate side-chains 685 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 684 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 262 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** 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 422 ASN B 655 HIS ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 606 ASN C 755 GLN C 901 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.162482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122398 restraints weight = 55415.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127295 restraints weight = 35119.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130803 restraints weight = 24638.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133336 restraints weight = 18619.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135216 restraints weight = 14920.809| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26624 Z= 0.189 Angle : 0.779 18.246 36353 Z= 0.378 Chirality : 0.051 0.639 4208 Planarity : 0.005 0.105 4627 Dihedral : 9.280 103.826 4458 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 3207 helix: 0.98 (0.20), residues: 675 sheet: -0.16 (0.19), residues: 655 loop : -1.17 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG C 237 TYR 0.024 0.002 TYR B 365 PHE 0.020 0.002 PHE A 374 TRP 0.040 0.003 TRP A1102 HIS 0.010 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00382 (26536) covalent geometry : angle 0.72579 (36139) SS BOND : bond 0.00481 ( 41) SS BOND : angle 1.81582 ( 82) hydrogen bonds : bond 0.04897 ( 873) hydrogen bonds : angle 6.08054 ( 2436) Misc. bond : bond 0.00038 ( 3) link_BETA1-4 : bond 0.00603 ( 10) link_BETA1-4 : angle 1.86294 ( 30) link_NAG-ASN : bond 0.00827 ( 34) link_NAG-ASN : angle 5.11962 ( 102) *********************** 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 736 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 733 time to evaluate : 0.990 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 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: 0.8538 (mmpt) cc_final: 0.8203 (mmmm) REVERT: A 49 HIS cc_start: 0.7487 (t70) cc_final: 0.7076 (t-90) REVERT: A 53 ASP cc_start: 0.7804 (t0) cc_final: 0.7587 (m-30) REVERT: A 56 LEU cc_start: 0.8313 (mt) cc_final: 0.7832 (mt) REVERT: A 80 ASP cc_start: 0.8218 (t0) cc_final: 0.7836 (t70) REVERT: A 91 TYR cc_start: 0.6341 (t80) cc_final: 0.6075 (t80) REVERT: A 100 ILE cc_start: 0.8501 (mm) cc_final: 0.8232 (tp) REVERT: A 221 SER cc_start: 0.8205 (m) cc_final: 0.7461 (t) REVERT: A 224 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8265 (pm20) REVERT: A 269 TYR cc_start: 0.7504 (m-80) cc_final: 0.6419 (m-80) REVERT: A 273 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8143 (mmt180) REVERT: A 287 ASP cc_start: 0.8469 (t0) cc_final: 0.8265 (t70) REVERT: A 298 GLU cc_start: 0.8299 (tt0) cc_final: 0.7943 (tt0) REVERT: A 357 ARG cc_start: 0.7665 (ptp-170) cc_final: 0.7349 (ptp-170) REVERT: A 532 ASN cc_start: 0.7997 (t0) cc_final: 0.7670 (t0) REVERT: A 562 PHE cc_start: 0.7906 (p90) cc_final: 0.7658 (p90) REVERT: A 571 ASP cc_start: 0.6795 (t0) cc_final: 0.6587 (t0) REVERT: A 578 ASP cc_start: 0.7827 (t70) cc_final: 0.7545 (t0) REVERT: A 583 GLU cc_start: 0.7833 (mp0) cc_final: 0.7622 (mp0) REVERT: A 646 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7497 (tpt90) REVERT: A 656 VAL cc_start: 0.8681 (m) cc_final: 0.8390 (p) REVERT: A 658 ASN cc_start: 0.7640 (t0) cc_final: 0.7143 (t0) REVERT: A 702 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7926 (tp30) REVERT: A 740 MET cc_start: 0.8305 (tpp) cc_final: 0.7864 (tpp) REVERT: A 751 ASN cc_start: 0.8371 (m110) cc_final: 0.8044 (m110) REVERT: A 763 LEU cc_start: 0.8813 (mt) cc_final: 0.8552 (mt) REVERT: A 767 LEU cc_start: 0.8563 (mt) cc_final: 0.8118 (tp) REVERT: A 772 VAL cc_start: 0.9124 (t) cc_final: 0.8901 (m) REVERT: A 776 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8063 (mmmm) REVERT: A 777 ASN cc_start: 0.8907 (m-40) cc_final: 0.8657 (m-40) REVERT: A 805 ILE cc_start: 0.8584 (pt) cc_final: 0.8373 (pt) REVERT: A 818 ILE cc_start: 0.9206 (mt) cc_final: 0.8889 (mm) REVERT: A 866 THR cc_start: 0.7887 (p) cc_final: 0.7153 (m) REVERT: A 870 ILE cc_start: 0.8945 (mt) cc_final: 0.8730 (mt) REVERT: A 873 TYR cc_start: 0.8741 (m-10) cc_final: 0.8272 (m-80) REVERT: A 878 LEU cc_start: 0.8974 (tp) cc_final: 0.8758 (tp) REVERT: A 902 MET cc_start: 0.8556 (ttm) cc_final: 0.7868 (ttm) REVERT: A 911 VAL cc_start: 0.7369 (t) cc_final: 0.6980 (m) REVERT: A 914 ASN cc_start: 0.8623 (p0) cc_final: 0.8198 (p0) REVERT: A 918 GLU cc_start: 0.8268 (pt0) cc_final: 0.8033 (pt0) REVERT: A 919 ASN cc_start: 0.8687 (m110) cc_final: 0.8326 (m110) REVERT: A 921 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8194 (tptp) REVERT: A 926 GLN cc_start: 0.9029 (mt0) cc_final: 0.8522 (mt0) REVERT: A 928 ASN cc_start: 0.8521 (m-40) cc_final: 0.8219 (m-40) REVERT: A 933 LYS cc_start: 0.8997 (mttm) cc_final: 0.8328 (mmmm) REVERT: A 949 GLN cc_start: 0.8541 (pp30) cc_final: 0.8244 (pp30) REVERT: A 957 GLN cc_start: 0.9012 (tt0) cc_final: 0.8356 (tm-30) REVERT: A 991 VAL cc_start: 0.8064 (p) cc_final: 0.7521 (t) REVERT: A 995 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8422 (tpp80) REVERT: A 1008 VAL cc_start: 0.9058 (m) cc_final: 0.8841 (p) REVERT: A 1009 THR cc_start: 0.8819 (m) cc_final: 0.8520 (p) REVERT: A 1014 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8434 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8855 (tt0) cc_final: 0.8641 (tt0) REVERT: A 1023 ASN cc_start: 0.8501 (t0) cc_final: 0.8276 (t0) REVERT: A 1038 LYS cc_start: 0.8779 (mttt) cc_final: 0.8289 (mtpt) REVERT: A 1045 LYS cc_start: 0.8505 (mppt) cc_final: 0.8070 (mmtm) REVERT: A 1054 GLN cc_start: 0.6675 (mp10) cc_final: 0.6385 (mp10) REVERT: A 1075 PHE cc_start: 0.7731 (m-80) cc_final: 0.7318 (m-10) REVERT: A 1081 ILE cc_start: 0.8892 (mm) cc_final: 0.8004 (tp) REVERT: A 1088 HIS cc_start: 0.7675 (m-70) cc_final: 0.7069 (m-70) REVERT: A 1101 HIS cc_start: 0.8729 (m90) cc_final: 0.8382 (m170) REVERT: A 1109 PHE cc_start: 0.7848 (t80) cc_final: 0.7321 (t80) REVERT: A 1114 ILE cc_start: 0.9019 (mp) cc_final: 0.8707 (tp) REVERT: B 44 ARG cc_start: 0.7754 (mtt90) cc_final: 0.6890 (mtm-85) REVERT: B 52 GLN cc_start: 0.8215 (mp10) cc_final: 0.7903 (mp10) REVERT: B 53 ASP cc_start: 0.7101 (t0) cc_final: 0.6420 (t0) REVERT: B 54 LEU cc_start: 0.8174 (mp) cc_final: 0.7348 (tt) REVERT: B 65 PHE cc_start: 0.8143 (m-80) cc_final: 0.7287 (m-80) REVERT: B 92 PHE cc_start: 0.7749 (t80) cc_final: 0.7083 (t80) REVERT: B 99 ASN cc_start: 0.8643 (t0) cc_final: 0.7878 (t0) REVERT: B 192 PHE cc_start: 0.6118 (m-80) cc_final: 0.5862 (m-80) REVERT: B 207 HIS cc_start: 0.8502 (m90) cc_final: 0.8148 (m90) REVERT: B 233 ILE cc_start: 0.6422 (pt) cc_final: 0.5335 (tp) REVERT: B 300 LYS cc_start: 0.8633 (mttt) cc_final: 0.8169 (mttt) REVERT: B 353 TRP cc_start: 0.7964 (p90) cc_final: 0.6153 (p90) REVERT: B 354 ASN cc_start: 0.7492 (p0) cc_final: 0.6403 (p0) REVERT: B 374 PHE cc_start: 0.8427 (m-10) cc_final: 0.7903 (m-80) REVERT: B 395 VAL cc_start: 0.7576 (t) cc_final: 0.7298 (m) REVERT: B 398 ASP cc_start: 0.6529 (m-30) cc_final: 0.6227 (m-30) REVERT: B 409 GLN cc_start: 0.8947 (mt0) cc_final: 0.8343 (mt0) REVERT: B 436 TRP cc_start: 0.8291 (p-90) cc_final: 0.7565 (p-90) REVERT: B 529 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7914 (ttmm) REVERT: B 535 LYS cc_start: 0.8294 (tppp) cc_final: 0.7972 (tppt) REVERT: B 557 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7349 (mtmm) REVERT: B 578 ASP cc_start: 0.7920 (t0) cc_final: 0.7541 (t0) REVERT: B 619 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7922 (mp0) REVERT: B 712 ILE cc_start: 0.7759 (tt) cc_final: 0.7558 (tp) REVERT: B 756 TYR cc_start: 0.8124 (m-80) cc_final: 0.7413 (m-80) REVERT: B 773 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 776 LYS cc_start: 0.8858 (tptp) cc_final: 0.8416 (tptp) REVERT: B 779 GLN cc_start: 0.8491 (tp40) cc_final: 0.7743 (tm-30) REVERT: B 780 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7428 (tp30) REVERT: B 805 ILE cc_start: 0.8687 (mt) cc_final: 0.8348 (tp) REVERT: B 811 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8306 (mmmt) REVERT: B 814 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7262 (mmtt) REVERT: B 815 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7125 (mtm-85) REVERT: B 823 PHE cc_start: 0.8161 (m-80) cc_final: 0.7640 (m-10) REVERT: B 867 ASP cc_start: 0.7976 (t0) cc_final: 0.7716 (t0) REVERT: B 869 MET cc_start: 0.8395 (mpp) cc_final: 0.7934 (ptp) REVERT: B 877 LEU cc_start: 0.8889 (mt) cc_final: 0.8672 (mt) REVERT: B 902 MET cc_start: 0.8240 (tpt) cc_final: 0.7705 (tpp) REVERT: B 917 TYR cc_start: 0.8129 (m-80) cc_final: 0.7458 (m-10) REVERT: B 921 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8401 (mtpp) REVERT: B 926 GLN cc_start: 0.8695 (mt0) cc_final: 0.8370 (tp40) REVERT: B 928 ASN cc_start: 0.8534 (m-40) cc_final: 0.8331 (m-40) REVERT: B 934 ILE cc_start: 0.8284 (mm) cc_final: 0.8062 (mm) REVERT: B 935 GLN cc_start: 0.8797 (tt0) cc_final: 0.8202 (tm-30) REVERT: B 954 GLN cc_start: 0.8177 (pp30) cc_final: 0.7871 (pp30) REVERT: B 955 ASN cc_start: 0.8818 (m110) cc_final: 0.8205 (m110) REVERT: B 965 GLN cc_start: 0.8648 (tp-100) cc_final: 0.7939 (tp40) REVERT: B 970 PHE cc_start: 0.7023 (m-10) cc_final: 0.5838 (m-10) REVERT: B 979 ASP cc_start: 0.8649 (t0) cc_final: 0.8241 (t0) REVERT: B 991 VAL cc_start: 0.9016 (m) cc_final: 0.8711 (t) REVERT: B 994 ASP cc_start: 0.8378 (t0) cc_final: 0.7934 (t0) REVERT: B 996 LEU cc_start: 0.9003 (mt) cc_final: 0.8774 (mt) REVERT: B 1001 LEU cc_start: 0.9116 (mt) cc_final: 0.8788 (mt) REVERT: B 1005 GLN cc_start: 0.8395 (pp30) cc_final: 0.8047 (pp30) REVERT: B 1028 LYS cc_start: 0.8526 (tppt) cc_final: 0.7587 (tppt) REVERT: B 1033 VAL cc_start: 0.7904 (t) cc_final: 0.7464 (t) REVERT: B 1092 GLU cc_start: 0.6802 (pm20) cc_final: 0.5683 (tp30) REVERT: B 1096 VAL cc_start: 0.8075 (p) cc_final: 0.7803 (m) REVERT: B 1105 THR cc_start: 0.7499 (m) cc_final: 0.6197 (m) REVERT: B 1109 PHE cc_start: 0.7163 (t80) cc_final: 0.6769 (t80) REVERT: B 1114 ILE cc_start: 0.8691 (mm) cc_final: 0.7988 (mm) REVERT: B 1115 ILE cc_start: 0.9030 (tp) cc_final: 0.8448 (tp) REVERT: C 65 PHE cc_start: 0.8478 (m-80) cc_final: 0.7671 (m-80) REVERT: C 66 HIS cc_start: 0.8092 (m170) cc_final: 0.7794 (m170) REVERT: C 135 PHE cc_start: 0.8521 (m-10) cc_final: 0.7531 (t80) REVERT: C 164 ASN cc_start: 0.8222 (t0) cc_final: 0.7964 (t0) REVERT: C 206 LYS cc_start: 0.7436 (mmpt) cc_final: 0.7102 (mmtt) REVERT: C 265 TYR cc_start: 0.7501 (p90) cc_final: 0.7044 (p90) REVERT: C 277 LEU cc_start: 0.8089 (mt) cc_final: 0.7798 (pp) REVERT: C 318 PHE cc_start: 0.7512 (t80) cc_final: 0.7223 (t80) REVERT: C 357 ARG cc_start: 0.5181 (mtt180) cc_final: 0.4900 (mtt180) REVERT: C 370 ASN cc_start: 0.8983 (m110) cc_final: 0.8530 (p0) REVERT: C 396 TYR cc_start: 0.7365 (m-80) cc_final: 0.6862 (m-10) REVERT: C 436 TRP cc_start: 0.7970 (p-90) cc_final: 0.7355 (p-90) REVERT: C 440 ASN cc_start: 0.8735 (m-40) cc_final: 0.8133 (p0) REVERT: C 533 LEU cc_start: 0.8922 (tp) cc_final: 0.8672 (tp) REVERT: C 557 LYS cc_start: 0.8971 (mppt) cc_final: 0.8609 (mppt) REVERT: C 576 VAL cc_start: 0.8430 (p) cc_final: 0.8169 (m) REVERT: C 657 ASN cc_start: 0.8597 (m-40) cc_final: 0.8284 (m-40) REVERT: C 712 ILE cc_start: 0.7928 (tp) cc_final: 0.7679 (tp) REVERT: C 723 THR cc_start: 0.8196 (t) cc_final: 0.7742 (p) REVERT: C 725 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7013 (tt0) REVERT: C 727 LEU cc_start: 0.8299 (mt) cc_final: 0.7913 (mt) REVERT: C 740 MET cc_start: 0.6627 (tpt) cc_final: 0.5970 (tpt) REVERT: C 759 PHE cc_start: 0.7889 (m-80) cc_final: 0.7603 (m-80) REVERT: C 772 VAL cc_start: 0.8795 (m) cc_final: 0.8555 (p) REVERT: C 774 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8285 (mm110) REVERT: C 776 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8902 (ttmt) REVERT: C 778 THR cc_start: 0.8848 (m) cc_final: 0.8604 (p) REVERT: C 790 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7918 (mmtm) REVERT: C 795 LYS cc_start: 0.8755 (mppt) cc_final: 0.8049 (mmtm) REVERT: C 796 ASP cc_start: 0.8522 (m-30) cc_final: 0.8148 (m-30) REVERT: C 808 ASP cc_start: 0.8321 (t70) cc_final: 0.8115 (t0) REVERT: C 859 THR cc_start: 0.8181 (t) cc_final: 0.7870 (p) REVERT: C 865 LEU cc_start: 0.8548 (mt) cc_final: 0.7881 (mt) REVERT: C 869 MET cc_start: 0.8345 (mtm) cc_final: 0.7724 (mtm) REVERT: C 901 GLN cc_start: 0.8748 (tt0) cc_final: 0.7950 (tm-30) REVERT: C 902 MET cc_start: 0.8535 (tmm) cc_final: 0.7899 (tmm) REVERT: C 905 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8199 (mtt-85) REVERT: C 909 ILE cc_start: 0.8962 (pt) cc_final: 0.8536 (mm) REVERT: C 913 GLN cc_start: 0.8440 (pm20) cc_final: 0.8175 (pm20) REVERT: C 925 ASN cc_start: 0.8748 (m-40) cc_final: 0.8526 (m-40) REVERT: C 926 GLN cc_start: 0.8632 (mt0) cc_final: 0.8346 (mt0) REVERT: C 936 ASP cc_start: 0.8514 (t0) cc_final: 0.8305 (t0) REVERT: C 947 LYS cc_start: 0.8676 (mttt) cc_final: 0.8397 (ptpp) REVERT: C 964 LYS cc_start: 0.8861 (tttt) cc_final: 0.8315 (ptmt) REVERT: C 965 GLN cc_start: 0.8861 (mt0) cc_final: 0.8184 (mm-40) REVERT: C 1013 ILE cc_start: 0.9000 (mt) cc_final: 0.8664 (mm) REVERT: C 1017 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 1023 ASN cc_start: 0.8782 (m110) cc_final: 0.8522 (m110) REVERT: C 1029 MET cc_start: 0.8693 (tpp) cc_final: 0.8401 (tpp) REVERT: C 1067 TYR cc_start: 0.8158 (t80) cc_final: 0.7841 (t80) REVERT: C 1081 ILE cc_start: 0.7900 (mt) cc_final: 0.7614 (mm) REVERT: C 1088 HIS cc_start: 0.7363 (m90) cc_final: 0.6866 (m-70) REVERT: C 1103 PHE cc_start: 0.7751 (m-80) cc_final: 0.7323 (m-80) REVERT: C 1110 TYR cc_start: 0.8299 (t80) cc_final: 0.8073 (t80) outliers start: 3 outliers final: 1 residues processed: 735 average time/residue: 0.1929 time to fit residues: 222.2841 Evaluate side-chains 691 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 690 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 93 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 95 optimal weight: 0.6980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 207 HIS ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.160579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120313 restraints weight = 55689.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125160 restraints weight = 35223.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.128660 restraints weight = 24795.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.131228 restraints weight = 18795.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133096 restraints weight = 15075.663| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26624 Z= 0.192 Angle : 0.773 19.204 36353 Z= 0.377 Chirality : 0.051 0.643 4208 Planarity : 0.005 0.073 4627 Dihedral : 9.060 99.713 4458 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3207 helix: 0.98 (0.20), residues: 673 sheet: -0.15 (0.20), residues: 651 loop : -1.24 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 158 TYR 0.042 0.002 TYR B 873 PHE 0.021 0.002 PHE B1103 TRP 0.033 0.003 TRP C1102 HIS 0.011 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00385 (26536) covalent geometry : angle 0.71702 (36139) SS BOND : bond 0.00436 ( 41) SS BOND : angle 2.12763 ( 82) hydrogen bonds : bond 0.04782 ( 873) hydrogen bonds : angle 5.97239 ( 2436) Misc. bond : bond 0.00733 ( 3) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 1.77016 ( 30) link_NAG-ASN : bond 0.01025 ( 34) link_NAG-ASN : angle 5.12817 ( 102) *********************** 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 743 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 1.003 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 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: 0.7386 (t70) cc_final: 0.7061 (t-90) REVERT: A 53 ASP cc_start: 0.8049 (t0) cc_final: 0.7419 (t0) REVERT: A 56 LEU cc_start: 0.8279 (mt) cc_final: 0.7834 (mt) REVERT: A 57 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: A 80 ASP cc_start: 0.8249 (t0) cc_final: 0.7729 (t0) REVERT: A 91 TYR cc_start: 0.6296 (t80) cc_final: 0.5910 (t80) REVERT: A 104 TRP cc_start: 0.6932 (m-90) cc_final: 0.6603 (m-90) REVERT: A 221 SER cc_start: 0.8316 (m) cc_final: 0.7564 (t) REVERT: A 224 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8275 (pm20) REVERT: A 240 THR cc_start: 0.8340 (t) cc_final: 0.7556 (t) REVERT: A 269 TYR cc_start: 0.7563 (m-80) cc_final: 0.6591 (m-80) REVERT: A 271 GLN cc_start: 0.8123 (mp10) cc_final: 0.7899 (mp10) REVERT: A 273 ARG cc_start: 0.8641 (mmt180) cc_final: 0.8334 (mmt180) REVERT: A 287 ASP cc_start: 0.8482 (t0) cc_final: 0.8206 (t70) REVERT: A 298 GLU cc_start: 0.8236 (tt0) cc_final: 0.7897 (tt0) REVERT: A 303 LEU cc_start: 0.8924 (tp) cc_final: 0.8653 (tp) REVERT: A 319 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7549 (mtm110) REVERT: A 342 PHE cc_start: 0.9085 (m-10) cc_final: 0.8753 (m-10) REVERT: A 357 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7467 (ptp-170) REVERT: A 393 THR cc_start: 0.6786 (m) cc_final: 0.6583 (p) REVERT: A 532 ASN cc_start: 0.7931 (t0) cc_final: 0.7616 (t0) REVERT: A 533 LEU cc_start: 0.8702 (tp) cc_final: 0.8405 (tp) REVERT: A 562 PHE cc_start: 0.7918 (p90) cc_final: 0.7679 (p90) REVERT: A 571 ASP cc_start: 0.7057 (t0) cc_final: 0.6704 (t0) REVERT: A 578 ASP cc_start: 0.8003 (t70) cc_final: 0.7713 (t0) REVERT: A 583 GLU cc_start: 0.7825 (mp0) cc_final: 0.7608 (mp0) REVERT: A 643 PHE cc_start: 0.7913 (t80) cc_final: 0.7701 (t80) REVERT: A 658 ASN cc_start: 0.7655 (t0) cc_final: 0.7190 (t0) REVERT: A 702 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7840 (tp30) REVERT: A 737 ASP cc_start: 0.8134 (t0) cc_final: 0.7899 (t70) REVERT: A 751 ASN cc_start: 0.8386 (m110) cc_final: 0.8038 (m110) REVERT: A 762 GLN cc_start: 0.8906 (mt0) cc_final: 0.8613 (mt0) REVERT: A 763 LEU cc_start: 0.8833 (mt) cc_final: 0.8525 (mt) REVERT: A 775 ASP cc_start: 0.8131 (t0) cc_final: 0.7887 (t0) REVERT: A 776 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8011 (mmmm) REVERT: A 777 ASN cc_start: 0.8885 (m-40) cc_final: 0.8636 (m-40) REVERT: A 787 GLN cc_start: 0.7910 (pm20) cc_final: 0.7108 (pp30) REVERT: A 788 ILE cc_start: 0.8167 (mm) cc_final: 0.7865 (mm) REVERT: A 818 ILE cc_start: 0.9221 (mt) cc_final: 0.8982 (mt) REVERT: A 823 PHE cc_start: 0.8463 (t80) cc_final: 0.8229 (t80) REVERT: A 858 LEU cc_start: 0.8479 (mt) cc_final: 0.8245 (mt) REVERT: A 866 THR cc_start: 0.8043 (p) cc_final: 0.7319 (m) REVERT: A 870 ILE cc_start: 0.8933 (mt) cc_final: 0.8693 (mt) REVERT: A 873 TYR cc_start: 0.8728 (m-10) cc_final: 0.8268 (m-80) REVERT: A 878 LEU cc_start: 0.8955 (tp) cc_final: 0.8693 (tp) REVERT: A 902 MET cc_start: 0.8608 (ttm) cc_final: 0.7932 (ttm) REVERT: A 911 VAL cc_start: 0.7087 (t) cc_final: 0.6844 (m) REVERT: A 914 ASN cc_start: 0.8635 (p0) cc_final: 0.8156 (p0) REVERT: A 918 GLU cc_start: 0.8263 (pt0) cc_final: 0.8036 (pt0) REVERT: A 919 ASN cc_start: 0.8642 (m110) cc_final: 0.8237 (m110) REVERT: A 921 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8191 (tptp) REVERT: A 926 GLN cc_start: 0.9051 (mt0) cc_final: 0.8561 (mt0) REVERT: A 928 ASN cc_start: 0.8535 (m-40) cc_final: 0.8237 (m-40) REVERT: A 933 LYS cc_start: 0.9014 (mttm) cc_final: 0.8346 (mmmm) REVERT: A 949 GLN cc_start: 0.8593 (pp30) cc_final: 0.8220 (pp30) REVERT: A 957 GLN cc_start: 0.9048 (tt0) cc_final: 0.8327 (tm-30) REVERT: A 964 LYS cc_start: 0.8893 (mttt) cc_final: 0.8364 (tptp) REVERT: A 965 GLN cc_start: 0.8930 (mt0) cc_final: 0.8683 (mt0) REVERT: A 973 ILE cc_start: 0.8686 (mt) cc_final: 0.8009 (tp) REVERT: A 991 VAL cc_start: 0.8212 (p) cc_final: 0.7693 (t) REVERT: A 993 ILE cc_start: 0.9175 (mm) cc_final: 0.8965 (mm) REVERT: A 995 ARG cc_start: 0.8863 (ttm170) cc_final: 0.8466 (tpp80) REVERT: A 1005 GLN cc_start: 0.8722 (tp40) cc_final: 0.8063 (tm-30) REVERT: A 1009 THR cc_start: 0.8866 (m) cc_final: 0.8219 (p) REVERT: A 1014 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8695 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8873 (tt0) cc_final: 0.8663 (tt0) REVERT: A 1023 ASN cc_start: 0.8538 (t0) cc_final: 0.8299 (t0) REVERT: A 1045 LYS cc_start: 0.8525 (mppt) cc_final: 0.8107 (mmtm) REVERT: A 1049 LEU cc_start: 0.8863 (mt) cc_final: 0.8657 (mt) REVERT: A 1081 ILE cc_start: 0.8994 (mm) cc_final: 0.8491 (mp) REVERT: A 1088 HIS cc_start: 0.7783 (m-70) cc_final: 0.7386 (m-70) REVERT: A 1091 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7190 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8723 (m90) cc_final: 0.8417 (m-70) REVERT: A 1109 PHE cc_start: 0.7907 (t80) cc_final: 0.7394 (t80) REVERT: A 1121 PHE cc_start: 0.7483 (p90) cc_final: 0.7101 (p90) REVERT: B 44 ARG cc_start: 0.8029 (mtt90) cc_final: 0.6930 (mtm-85) REVERT: B 52 GLN cc_start: 0.8231 (mp10) cc_final: 0.7927 (mp10) REVERT: B 53 ASP cc_start: 0.7214 (t0) cc_final: 0.6544 (t0) REVERT: B 54 LEU cc_start: 0.8175 (mp) cc_final: 0.7344 (tt) REVERT: B 65 PHE cc_start: 0.8200 (m-80) cc_final: 0.7350 (m-80) REVERT: B 92 PHE cc_start: 0.7724 (t80) cc_final: 0.7488 (t80) REVERT: B 97 LYS cc_start: 0.8052 (tptp) cc_final: 0.7722 (tppt) REVERT: B 99 ASN cc_start: 0.8771 (t0) cc_final: 0.8093 (t0) REVERT: B 187 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8057 (ptmt) REVERT: B 207 HIS cc_start: 0.8448 (m-70) cc_final: 0.7979 (m-70) REVERT: B 233 ILE cc_start: 0.6528 (pt) cc_final: 0.5517 (tp) REVERT: B 294 ASP cc_start: 0.8115 (m-30) cc_final: 0.7859 (m-30) REVERT: B 313 TYR cc_start: 0.8211 (m-80) cc_final: 0.7859 (m-80) REVERT: B 357 ARG cc_start: 0.6814 (tpp-160) cc_final: 0.6591 (tpp-160) REVERT: B 380 TYR cc_start: 0.8133 (m-80) cc_final: 0.7730 (m-80) REVERT: B 395 VAL cc_start: 0.7763 (t) cc_final: 0.7245 (m) REVERT: B 398 ASP cc_start: 0.6790 (m-30) cc_final: 0.6206 (m-30) REVERT: B 409 GLN cc_start: 0.8962 (mt0) cc_final: 0.8302 (tt0) REVERT: B 436 TRP cc_start: 0.8373 (p-90) cc_final: 0.7985 (p-90) REVERT: B 454 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7824 (ttp-170) REVERT: B 509 ARG cc_start: 0.6409 (mmt180) cc_final: 0.5682 (mmt180) REVERT: B 535 LYS cc_start: 0.8538 (tppp) cc_final: 0.7930 (tppt) REVERT: B 557 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7394 (mtmm) REVERT: B 619 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7874 (mp0) REVERT: B 712 ILE cc_start: 0.7910 (tt) cc_final: 0.7422 (tp) REVERT: B 740 MET cc_start: 0.9284 (tpp) cc_final: 0.8934 (tpt) REVERT: B 741 TYR cc_start: 0.8717 (t80) cc_final: 0.8227 (t80) REVERT: B 756 TYR cc_start: 0.8371 (m-80) cc_final: 0.7900 (m-80) REVERT: B 770 ILE cc_start: 0.8931 (mt) cc_final: 0.8668 (mt) REVERT: B 773 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 776 LYS cc_start: 0.8817 (tptp) cc_final: 0.8286 (tptp) REVERT: B 779 GLN cc_start: 0.8485 (tp40) cc_final: 0.7670 (tm-30) REVERT: B 780 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7450 (tp30) REVERT: B 786 LYS cc_start: 0.8115 (mppt) cc_final: 0.7832 (mppt) REVERT: B 811 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8345 (mmmt) REVERT: B 814 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7328 (mmtt) REVERT: B 823 PHE cc_start: 0.8136 (m-80) cc_final: 0.7722 (m-10) REVERT: B 902 MET cc_start: 0.8232 (tpt) cc_final: 0.7705 (tpp) REVERT: B 917 TYR cc_start: 0.8150 (m-10) cc_final: 0.7392 (m-10) REVERT: B 921 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8392 (mtpp) REVERT: B 926 GLN cc_start: 0.8726 (mt0) cc_final: 0.8363 (tp40) REVERT: B 934 ILE cc_start: 0.8285 (mm) cc_final: 0.8023 (mm) REVERT: B 954 GLN cc_start: 0.8235 (pp30) cc_final: 0.7918 (pp30) REVERT: B 955 ASN cc_start: 0.8882 (m110) cc_final: 0.8210 (m110) REVERT: B 957 GLN cc_start: 0.9040 (tt0) cc_final: 0.8425 (tp40) REVERT: B 964 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8491 (ttmm) REVERT: B 965 GLN cc_start: 0.8611 (tp-100) cc_final: 0.7907 (tp40) REVERT: B 970 PHE cc_start: 0.6966 (m-10) cc_final: 0.5766 (m-10) REVERT: B 979 ASP cc_start: 0.8659 (t0) cc_final: 0.8431 (t0) REVERT: B 991 VAL cc_start: 0.9039 (m) cc_final: 0.8765 (t) REVERT: B 996 LEU cc_start: 0.8995 (mt) cc_final: 0.8747 (mt) REVERT: B 1005 GLN cc_start: 0.8438 (pp30) cc_final: 0.8070 (pp30) REVERT: B 1028 LYS cc_start: 0.8422 (tppt) cc_final: 0.7647 (tppt) REVERT: B 1031 GLU cc_start: 0.7702 (tt0) cc_final: 0.6771 (tt0) REVERT: B 1033 VAL cc_start: 0.7813 (t) cc_final: 0.6978 (t) REVERT: B 1034 LEU cc_start: 0.7967 (mt) cc_final: 0.7701 (mt) REVERT: B 1038 LYS cc_start: 0.9131 (tptt) cc_final: 0.8705 (tptt) REVERT: B 1045 LYS cc_start: 0.8103 (pptt) cc_final: 0.7615 (pptt) REVERT: C 64 TRP cc_start: 0.7572 (t-100) cc_final: 0.7349 (t-100) REVERT: C 65 PHE cc_start: 0.8409 (m-80) cc_final: 0.7555 (m-80) REVERT: C 66 HIS cc_start: 0.8078 (m170) cc_final: 0.7867 (m170) REVERT: C 104 TRP cc_start: 0.5527 (m-90) cc_final: 0.4876 (m-90) REVERT: C 164 ASN cc_start: 0.8273 (t0) cc_final: 0.8056 (t0) REVERT: C 190 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7958 (mtt180) REVERT: C 265 TYR cc_start: 0.7438 (p90) cc_final: 0.7075 (p90) REVERT: C 267 VAL cc_start: 0.7512 (t) cc_final: 0.6312 (t) REVERT: C 318 PHE cc_start: 0.7673 (t80) cc_final: 0.7308 (t80) REVERT: C 370 ASN cc_start: 0.9012 (m110) cc_final: 0.8605 (p0) REVERT: C 436 TRP cc_start: 0.7901 (p-90) cc_final: 0.7276 (p-90) REVERT: C 440 ASN cc_start: 0.8732 (m-40) cc_final: 0.8092 (p0) REVERT: C 556 ASN cc_start: 0.8852 (p0) cc_final: 0.8632 (p0) REVERT: C 564 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7927 (mm-40) REVERT: C 576 VAL cc_start: 0.8479 (p) cc_final: 0.8276 (m) REVERT: C 712 ILE cc_start: 0.7926 (tp) cc_final: 0.7676 (tp) REVERT: C 725 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7254 (tt0) REVERT: C 727 LEU cc_start: 0.8305 (mt) cc_final: 0.7937 (mt) REVERT: C 751 ASN cc_start: 0.8333 (p0) cc_final: 0.8049 (p0) REVERT: C 755 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8531 (mm-40) REVERT: C 756 TYR cc_start: 0.7767 (m-80) cc_final: 0.7528 (m-80) REVERT: C 759 PHE cc_start: 0.7935 (m-80) cc_final: 0.7619 (m-80) REVERT: C 767 LEU cc_start: 0.9130 (mm) cc_final: 0.8703 (pp) REVERT: C 776 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8922 (ttmt) REVERT: C 778 THR cc_start: 0.8826 (m) cc_final: 0.8587 (p) REVERT: C 790 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7907 (mmtm) REVERT: C 796 ASP cc_start: 0.8513 (m-30) cc_final: 0.7769 (t0) REVERT: C 808 ASP cc_start: 0.8311 (t70) cc_final: 0.8074 (t0) REVERT: C 859 THR cc_start: 0.8411 (t) cc_final: 0.8147 (p) REVERT: C 869 MET cc_start: 0.8945 (mtm) cc_final: 0.8002 (mtm) REVERT: C 901 GLN cc_start: 0.8693 (tt0) cc_final: 0.7920 (tm-30) REVERT: C 902 MET cc_start: 0.8463 (tmm) cc_final: 0.8054 (tmm) REVERT: C 905 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8166 (mtt-85) REVERT: C 909 ILE cc_start: 0.8834 (pt) cc_final: 0.8365 (mm) REVERT: C 925 ASN cc_start: 0.8764 (m-40) cc_final: 0.8539 (m-40) REVERT: C 926 GLN cc_start: 0.8663 (mt0) cc_final: 0.8356 (mt0) REVERT: C 937 SER cc_start: 0.9249 (t) cc_final: 0.8973 (p) REVERT: C 947 LYS cc_start: 0.8857 (mttt) cc_final: 0.8492 (ptpp) REVERT: C 964 LYS cc_start: 0.8930 (tttt) cc_final: 0.8417 (ptpt) REVERT: C 965 GLN cc_start: 0.8943 (mt0) cc_final: 0.8606 (mm-40) REVERT: C 1013 ILE cc_start: 0.9002 (mt) cc_final: 0.8588 (mm) REVERT: C 1017 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8134 (mt-10) REVERT: C 1023 ASN cc_start: 0.8795 (m110) cc_final: 0.8526 (m110) REVERT: C 1028 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8813 (tptt) REVERT: C 1029 MET cc_start: 0.8648 (tpp) cc_final: 0.8407 (tpp) REVERT: C 1054 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7436 (tp40) REVERT: C 1081 ILE cc_start: 0.7906 (mt) cc_final: 0.7702 (mm) REVERT: C 1088 HIS cc_start: 0.7431 (m90) cc_final: 0.6800 (m-70) REVERT: C 1089 PHE cc_start: 0.6224 (m-80) cc_final: 0.6001 (m-80) REVERT: C 1103 PHE cc_start: 0.7699 (m-80) cc_final: 0.7218 (m-80) REVERT: C 1110 TYR cc_start: 0.8318 (t80) cc_final: 0.8078 (t80) REVERT: C 1111 GLU cc_start: 0.7848 (pm20) cc_final: 0.7408 (pm20) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.1868 time to fit residues: 216.5894 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 : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 92 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 286 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 266 optimal weight: 0.0040 chunk 132 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 935 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123771 restraints weight = 55322.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128741 restraints weight = 34808.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132308 restraints weight = 24298.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.134923 restraints weight = 18268.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136833 restraints weight = 14555.009| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26624 Z= 0.137 Angle : 0.738 17.767 36353 Z= 0.354 Chirality : 0.050 0.651 4208 Planarity : 0.004 0.069 4627 Dihedral : 8.777 97.754 4458 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 1.43 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3207 helix: 1.13 (0.20), residues: 677 sheet: -0.21 (0.19), residues: 681 loop : -1.27 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.057 0.001 TYR B 873 PHE 0.025 0.001 PHE A 906 TRP 0.042 0.002 TRP A1102 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (26536) covalent geometry : angle 0.68570 (36139) SS BOND : bond 0.00256 ( 41) SS BOND : angle 2.03181 ( 82) hydrogen bonds : bond 0.04372 ( 873) hydrogen bonds : angle 5.77344 ( 2436) Misc. bond : bond 0.00052 ( 3) link_BETA1-4 : bond 0.00281 ( 10) link_BETA1-4 : angle 1.62552 ( 30) link_NAG-ASN : bond 0.00801 ( 34) link_NAG-ASN : angle 4.85134 ( 102) *********************** 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 706 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 704 time to evaluate : 1.005 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 49 HIS cc_start: 0.7347 (t70) cc_final: 0.7025 (t-90) REVERT: A 53 ASP cc_start: 0.8038 (t0) cc_final: 0.7430 (t0) REVERT: A 56 LEU cc_start: 0.8280 (mt) cc_final: 0.7632 (mt) REVERT: A 80 ASP cc_start: 0.8250 (t0) cc_final: 0.7733 (t0) REVERT: A 91 TYR cc_start: 0.6155 (t80) cc_final: 0.5806 (t80) REVERT: A 221 SER cc_start: 0.8270 (m) cc_final: 0.7539 (t) REVERT: A 224 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8275 (pm20) REVERT: A 269 TYR cc_start: 0.7495 (m-80) cc_final: 0.6425 (m-80) REVERT: A 273 ARG cc_start: 0.8535 (mmt180) cc_final: 0.8242 (mmt180) REVERT: A 287 ASP cc_start: 0.8396 (t0) cc_final: 0.8145 (t70) REVERT: A 298 GLU cc_start: 0.8187 (tt0) cc_final: 0.7822 (tt0) REVERT: A 303 LEU cc_start: 0.8914 (tp) cc_final: 0.8625 (tp) REVERT: A 342 PHE cc_start: 0.9072 (m-10) cc_final: 0.8686 (m-10) REVERT: A 357 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.6798 (mtp180) REVERT: A 436 TRP cc_start: 0.7574 (m-10) cc_final: 0.7340 (m100) REVERT: A 532 ASN cc_start: 0.7808 (t0) cc_final: 0.7467 (t0) REVERT: A 533 LEU cc_start: 0.8565 (tp) cc_final: 0.8298 (tp) REVERT: A 578 ASP cc_start: 0.7824 (t70) cc_final: 0.7613 (t0) REVERT: A 658 ASN cc_start: 0.7947 (t0) cc_final: 0.7231 (t0) REVERT: A 751 ASN cc_start: 0.8343 (m110) cc_final: 0.8002 (m110) REVERT: A 762 GLN cc_start: 0.8834 (mt0) cc_final: 0.8574 (mt0) REVERT: A 763 LEU cc_start: 0.8809 (mt) cc_final: 0.8563 (mt) REVERT: A 776 LYS cc_start: 0.8760 (mmmm) cc_final: 0.7936 (mmmm) REVERT: A 787 GLN cc_start: 0.7832 (pm20) cc_final: 0.7026 (pp30) REVERT: A 797 PHE cc_start: 0.8980 (m-80) cc_final: 0.8537 (m-80) REVERT: A 818 ILE cc_start: 0.9195 (mt) cc_final: 0.8949 (pt) REVERT: A 823 PHE cc_start: 0.8420 (t80) cc_final: 0.8164 (t80) REVERT: A 869 MET cc_start: 0.8944 (mtm) cc_final: 0.7798 (mtm) REVERT: A 873 TYR cc_start: 0.8648 (m-10) cc_final: 0.8187 (m-80) REVERT: A 878 LEU cc_start: 0.8945 (tp) cc_final: 0.8660 (tp) REVERT: A 902 MET cc_start: 0.8562 (ttm) cc_final: 0.7906 (ttm) REVERT: A 911 VAL cc_start: 0.7123 (t) cc_final: 0.6861 (m) REVERT: A 914 ASN cc_start: 0.8605 (p0) cc_final: 0.8131 (p0) REVERT: A 919 ASN cc_start: 0.8584 (m110) cc_final: 0.8173 (m110) REVERT: A 921 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8299 (tptt) REVERT: A 926 GLN cc_start: 0.8977 (mt0) cc_final: 0.8475 (mt0) REVERT: A 928 ASN cc_start: 0.8433 (m-40) cc_final: 0.8142 (m-40) REVERT: A 933 LYS cc_start: 0.8974 (mttm) cc_final: 0.8289 (mmmm) REVERT: A 949 GLN cc_start: 0.8579 (pp30) cc_final: 0.8225 (pp30) REVERT: A 957 GLN cc_start: 0.9018 (tt0) cc_final: 0.8302 (tm-30) REVERT: A 965 GLN cc_start: 0.8903 (mt0) cc_final: 0.8567 (mt0) REVERT: A 991 VAL cc_start: 0.8169 (p) cc_final: 0.7620 (t) REVERT: A 995 ARG cc_start: 0.8810 (ttm170) cc_final: 0.8471 (tpp80) REVERT: A 1005 GLN cc_start: 0.8672 (tp40) cc_final: 0.8153 (tp40) REVERT: A 1009 THR cc_start: 0.8890 (m) cc_final: 0.8489 (p) REVERT: A 1014 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8692 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8787 (tt0) cc_final: 0.8548 (tt0) REVERT: A 1023 ASN cc_start: 0.8453 (t0) cc_final: 0.8236 (t0) REVERT: A 1045 LYS cc_start: 0.8531 (mppt) cc_final: 0.8145 (mmtm) REVERT: A 1060 VAL cc_start: 0.8837 (t) cc_final: 0.8471 (m) REVERT: A 1081 ILE cc_start: 0.8743 (mm) cc_final: 0.8458 (mp) REVERT: A 1088 HIS cc_start: 0.7692 (m-70) cc_final: 0.7336 (m-70) REVERT: A 1101 HIS cc_start: 0.8591 (m90) cc_final: 0.8258 (m-70) REVERT: A 1102 TRP cc_start: 0.7787 (m100) cc_final: 0.7533 (m100) REVERT: A 1109 PHE cc_start: 0.7757 (t80) cc_final: 0.7284 (t80) REVERT: A 1114 ILE cc_start: 0.9039 (mp) cc_final: 0.8681 (tp) REVERT: B 52 GLN cc_start: 0.8208 (mp10) cc_final: 0.7919 (mp10) REVERT: B 53 ASP cc_start: 0.7280 (t0) cc_final: 0.6576 (t0) REVERT: B 54 LEU cc_start: 0.8177 (mp) cc_final: 0.7332 (tt) REVERT: B 65 PHE cc_start: 0.8147 (m-80) cc_final: 0.7295 (m-80) REVERT: B 97 LYS cc_start: 0.8115 (tptp) cc_final: 0.7867 (tppt) REVERT: B 99 ASN cc_start: 0.8786 (t0) cc_final: 0.8129 (t0) REVERT: B 135 PHE cc_start: 0.8566 (m-80) cc_final: 0.8362 (m-80) REVERT: B 187 LYS cc_start: 0.8418 (tmtt) cc_final: 0.8097 (tptp) REVERT: B 207 HIS cc_start: 0.8411 (m-70) cc_final: 0.7938 (m-70) REVERT: B 233 ILE cc_start: 0.6432 (pt) cc_final: 0.5492 (tp) REVERT: B 293 LEU cc_start: 0.7945 (tt) cc_final: 0.7657 (tt) REVERT: B 296 LEU cc_start: 0.8884 (tp) cc_final: 0.8531 (tp) REVERT: B 300 LYS cc_start: 0.8574 (mttt) cc_final: 0.8043 (mttm) REVERT: B 309 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 313 TYR cc_start: 0.8180 (m-80) cc_final: 0.7861 (m-80) REVERT: B 380 TYR cc_start: 0.8158 (m-80) cc_final: 0.7614 (m-80) REVERT: B 395 VAL cc_start: 0.7715 (t) cc_final: 0.7204 (m) REVERT: B 398 ASP cc_start: 0.6556 (m-30) cc_final: 0.6217 (m-30) REVERT: B 409 GLN cc_start: 0.8930 (mt0) cc_final: 0.8330 (tt0) REVERT: B 509 ARG cc_start: 0.6400 (mmt180) cc_final: 0.5570 (mmt180) REVERT: B 535 LYS cc_start: 0.8540 (tppp) cc_final: 0.7895 (tppt) REVERT: B 557 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7297 (mtmm) REVERT: B 619 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7851 (mp0) REVERT: B 712 ILE cc_start: 0.7810 (tt) cc_final: 0.7408 (tp) REVERT: B 740 MET cc_start: 0.9232 (tpp) cc_final: 0.8793 (tpt) REVERT: B 741 TYR cc_start: 0.8685 (t80) cc_final: 0.8424 (t80) REVERT: B 758 SER cc_start: 0.8753 (m) cc_final: 0.8526 (t) REVERT: B 770 ILE cc_start: 0.8892 (mt) cc_final: 0.8652 (mt) REVERT: B 773 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 776 LYS cc_start: 0.8745 (tptp) cc_final: 0.8191 (tptp) REVERT: B 779 GLN cc_start: 0.8443 (tp40) cc_final: 0.7596 (tm-30) REVERT: B 780 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7317 (tp30) REVERT: B 786 LYS cc_start: 0.8164 (mppt) cc_final: 0.7862 (mppt) REVERT: B 818 ILE cc_start: 0.8617 (mm) cc_final: 0.8406 (mp) REVERT: B 823 PHE cc_start: 0.8030 (m-80) cc_final: 0.7766 (m-10) REVERT: B 877 LEU cc_start: 0.8892 (mt) cc_final: 0.8673 (mt) REVERT: B 894 LEU cc_start: 0.8003 (mm) cc_final: 0.7797 (mm) REVERT: B 902 MET cc_start: 0.8214 (tpt) cc_final: 0.7672 (tpp) REVERT: B 917 TYR cc_start: 0.8147 (m-10) cc_final: 0.7362 (m-10) REVERT: B 921 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8330 (mtpp) REVERT: B 926 GLN cc_start: 0.8644 (mt0) cc_final: 0.8272 (tp40) REVERT: B 934 ILE cc_start: 0.8166 (mm) cc_final: 0.7899 (mm) REVERT: B 935 GLN cc_start: 0.8892 (tt0) cc_final: 0.8233 (tm-30) REVERT: B 939 SER cc_start: 0.7021 (p) cc_final: 0.6778 (p) REVERT: B 954 GLN cc_start: 0.8156 (pp30) cc_final: 0.7809 (pp30) REVERT: B 955 ASN cc_start: 0.8893 (m110) cc_final: 0.8208 (m110) REVERT: B 957 GLN cc_start: 0.9001 (tt0) cc_final: 0.8341 (tp40) REVERT: B 964 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8302 (mmtm) REVERT: B 965 GLN cc_start: 0.8498 (tp-100) cc_final: 0.7784 (tp40) REVERT: B 970 PHE cc_start: 0.6955 (m-10) cc_final: 0.5681 (m-10) REVERT: B 979 ASP cc_start: 0.8604 (t0) cc_final: 0.8249 (t0) REVERT: B 991 VAL cc_start: 0.8903 (m) cc_final: 0.8587 (t) REVERT: B 994 ASP cc_start: 0.8083 (t0) cc_final: 0.7808 (t0) REVERT: B 996 LEU cc_start: 0.8930 (mt) cc_final: 0.8728 (mt) REVERT: B 1001 LEU cc_start: 0.9036 (mt) cc_final: 0.8797 (mt) REVERT: B 1005 GLN cc_start: 0.8333 (pp30) cc_final: 0.7946 (pp30) REVERT: B 1028 LYS cc_start: 0.8324 (tppt) cc_final: 0.7446 (tppt) REVERT: B 1031 GLU cc_start: 0.7630 (tt0) cc_final: 0.6738 (tt0) REVERT: B 1033 VAL cc_start: 0.7599 (t) cc_final: 0.7299 (t) REVERT: B 1038 LYS cc_start: 0.9083 (tptt) cc_final: 0.8650 (tptt) REVERT: B 1045 LYS cc_start: 0.8099 (pptt) cc_final: 0.7570 (pptt) REVERT: B 1062 PHE cc_start: 0.7057 (m-80) cc_final: 0.6836 (m-80) REVERT: B 1114 ILE cc_start: 0.8752 (mm) cc_final: 0.8526 (mm) REVERT: C 37 TYR cc_start: 0.7067 (p90) cc_final: 0.6830 (p90) REVERT: C 64 TRP cc_start: 0.7463 (t-100) cc_final: 0.7082 (t-100) REVERT: C 65 PHE cc_start: 0.8357 (m-80) cc_final: 0.7466 (m-80) REVERT: C 104 TRP cc_start: 0.5354 (m-90) cc_final: 0.4813 (m-90) REVERT: C 190 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7922 (mtt180) REVERT: C 238 PHE cc_start: 0.7621 (p90) cc_final: 0.6871 (p90) REVERT: C 265 TYR cc_start: 0.7319 (p90) cc_final: 0.7078 (p90) REVERT: C 267 VAL cc_start: 0.7493 (t) cc_final: 0.6430 (t) REVERT: C 277 LEU cc_start: 0.8177 (mt) cc_final: 0.7933 (mt) REVERT: C 318 PHE cc_start: 0.7589 (t80) cc_final: 0.7142 (t80) REVERT: C 370 ASN cc_start: 0.8960 (m110) cc_final: 0.8538 (p0) REVERT: C 377 PHE cc_start: 0.7939 (t80) cc_final: 0.7719 (t80) REVERT: C 396 TYR cc_start: 0.7814 (m-80) cc_final: 0.7449 (m-10) REVERT: C 436 TRP cc_start: 0.7824 (p-90) cc_final: 0.7241 (p-90) REVERT: C 440 ASN cc_start: 0.8723 (m-40) cc_final: 0.8086 (p0) REVERT: C 451 TYR cc_start: 0.6466 (m-80) cc_final: 0.3783 (m-80) REVERT: C 535 LYS cc_start: 0.8296 (mppt) cc_final: 0.7847 (ttmm) REVERT: C 557 LYS cc_start: 0.9000 (mppt) cc_final: 0.8762 (mmmt) REVERT: C 576 VAL cc_start: 0.8373 (p) cc_final: 0.8152 (m) REVERT: C 577 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7616 (ttm110) REVERT: C 725 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6963 (tt0) REVERT: C 727 LEU cc_start: 0.8301 (mt) cc_final: 0.7833 (mt) REVERT: C 731 MET cc_start: 0.8612 (ptt) cc_final: 0.7992 (ptt) REVERT: C 751 ASN cc_start: 0.8290 (p0) cc_final: 0.7888 (p0) REVERT: C 755 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8461 (mm-40) REVERT: C 756 TYR cc_start: 0.7648 (m-80) cc_final: 0.7416 (m-80) REVERT: C 759 PHE cc_start: 0.7921 (m-80) cc_final: 0.7587 (m-80) REVERT: C 774 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8225 (mm-40) REVERT: C 776 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8859 (ttmt) REVERT: C 778 THR cc_start: 0.8815 (m) cc_final: 0.8593 (p) REVERT: C 790 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7918 (mmtm) REVERT: C 796 ASP cc_start: 0.8695 (m-30) cc_final: 0.7241 (t0) REVERT: C 808 ASP cc_start: 0.8340 (t70) cc_final: 0.8107 (t0) REVERT: C 859 THR cc_start: 0.8344 (t) cc_final: 0.8059 (p) REVERT: C 865 LEU cc_start: 0.8449 (mt) cc_final: 0.7915 (mt) REVERT: C 869 MET cc_start: 0.8914 (mtm) cc_final: 0.7927 (mtm) REVERT: C 902 MET cc_start: 0.8388 (tmm) cc_final: 0.7908 (tmm) REVERT: C 905 ARG cc_start: 0.8856 (mtt-85) cc_final: 0.8148 (tpp80) REVERT: C 909 ILE cc_start: 0.8872 (pt) cc_final: 0.8357 (mm) REVERT: C 925 ASN cc_start: 0.8731 (m-40) cc_final: 0.8497 (m-40) REVERT: C 926 GLN cc_start: 0.8596 (mt0) cc_final: 0.8342 (mt0) REVERT: C 947 LYS cc_start: 0.8907 (mttt) cc_final: 0.8539 (ptpp) REVERT: C 949 GLN cc_start: 0.8368 (tp40) cc_final: 0.7908 (mt0) REVERT: C 964 LYS cc_start: 0.8923 (tttt) cc_final: 0.8396 (ptpt) REVERT: C 965 GLN cc_start: 0.8900 (mt0) cc_final: 0.8547 (mm-40) REVERT: C 1013 ILE cc_start: 0.8962 (mt) cc_final: 0.8380 (tp) REVERT: C 1014 ARG cc_start: 0.8716 (mtt90) cc_final: 0.7668 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 1023 ASN cc_start: 0.8761 (m110) cc_final: 0.8457 (m110) REVERT: C 1029 MET cc_start: 0.8587 (tpp) cc_final: 0.8378 (tpp) REVERT: C 1033 VAL cc_start: 0.7960 (t) cc_final: 0.7550 (t) REVERT: C 1034 LEU cc_start: 0.8305 (mt) cc_final: 0.8086 (mt) REVERT: C 1054 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7401 (tp40) REVERT: C 1081 ILE cc_start: 0.7893 (mt) cc_final: 0.7245 (mp) REVERT: C 1088 HIS cc_start: 0.7406 (m90) cc_final: 0.6917 (m-70) REVERT: C 1089 PHE cc_start: 0.6258 (m-80) cc_final: 0.5954 (m-80) REVERT: C 1103 PHE cc_start: 0.7816 (m-80) cc_final: 0.7421 (m-80) REVERT: C 1104 VAL cc_start: 0.8847 (t) cc_final: 0.8627 (m) outliers start: 2 outliers final: 0 residues processed: 704 average time/residue: 0.1866 time to fit residues: 206.4769 Evaluate side-chains 652 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 302 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 237 optimal weight: 0.4980 chunk 196 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 644 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 437 ASN B 703 ASN B 953 ASN B1088 HIS C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** 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 = 0.4334 r_free = 0.4334 target = 0.162738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122973 restraints weight = 55202.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127935 restraints weight = 34744.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.131524 restraints weight = 24326.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134190 restraints weight = 18334.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.136100 restraints weight = 14608.492| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26624 Z= 0.144 Angle : 0.739 17.536 36353 Z= 0.357 Chirality : 0.050 0.639 4208 Planarity : 0.005 0.074 4627 Dihedral : 8.627 94.893 4458 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3207 helix: 1.09 (0.20), residues: 676 sheet: -0.21 (0.19), residues: 712 loop : -1.27 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 905 TYR 0.027 0.001 TYR B 873 PHE 0.020 0.001 PHE A 906 TRP 0.022 0.002 TRP A1102 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00303 (26536) covalent geometry : angle 0.68820 (36139) SS BOND : bond 0.00291 ( 41) SS BOND : angle 1.91540 ( 82) hydrogen bonds : bond 0.04314 ( 873) hydrogen bonds : angle 5.65774 ( 2436) Misc. bond : bond 0.00058 ( 3) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.61161 ( 30) link_NAG-ASN : bond 0.00840 ( 34) link_NAG-ASN : angle 4.82119 ( 102) *********************** 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 712 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 710 time to evaluate : 0.986 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 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: 0.7369 (t70) cc_final: 0.6932 (t-90) REVERT: A 53 ASP cc_start: 0.8145 (t0) cc_final: 0.7545 (t0) REVERT: A 56 LEU cc_start: 0.8301 (mt) cc_final: 0.7624 (mt) REVERT: A 80 ASP cc_start: 0.8218 (t0) cc_final: 0.7710 (t0) REVERT: A 91 TYR cc_start: 0.6165 (t80) cc_final: 0.5774 (t80) REVERT: A 216 LEU cc_start: 0.6323 (mt) cc_final: 0.5927 (mp) REVERT: A 221 SER cc_start: 0.8312 (m) cc_final: 0.7595 (t) REVERT: A 224 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8289 (pm20) REVERT: A 269 TYR cc_start: 0.7584 (m-80) cc_final: 0.6496 (m-80) REVERT: A 273 ARG cc_start: 0.8552 (mmt180) cc_final: 0.8257 (mmt180) REVERT: A 287 ASP cc_start: 0.8422 (t0) cc_final: 0.8200 (t70) REVERT: A 298 GLU cc_start: 0.8147 (tt0) cc_final: 0.7794 (tt0) REVERT: A 303 LEU cc_start: 0.8938 (tp) cc_final: 0.8628 (tp) REVERT: A 319 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7487 (mtm110) REVERT: A 342 PHE cc_start: 0.9084 (m-10) cc_final: 0.8708 (m-10) REVERT: A 357 ARG cc_start: 0.7458 (ptp-170) cc_final: 0.6914 (mtp180) REVERT: A 436 TRP cc_start: 0.7569 (m-10) cc_final: 0.7209 (m100) REVERT: A 532 ASN cc_start: 0.7766 (t0) cc_final: 0.7454 (t0) REVERT: A 533 LEU cc_start: 0.8570 (tp) cc_final: 0.8291 (tp) REVERT: A 658 ASN cc_start: 0.7901 (t0) cc_final: 0.7328 (t0) REVERT: A 745 ASP cc_start: 0.8041 (p0) cc_final: 0.7733 (p0) REVERT: A 751 ASN cc_start: 0.8335 (m110) cc_final: 0.7982 (m110) REVERT: A 762 GLN cc_start: 0.8850 (mt0) cc_final: 0.8575 (mt0) REVERT: A 763 LEU cc_start: 0.8886 (mt) cc_final: 0.8648 (mt) REVERT: A 776 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8119 (mmmm) REVERT: A 788 ILE cc_start: 0.8008 (mm) cc_final: 0.7697 (tp) REVERT: A 797 PHE cc_start: 0.8931 (m-80) cc_final: 0.8485 (m-80) REVERT: A 818 ILE cc_start: 0.9213 (mt) cc_final: 0.8966 (pt) REVERT: A 823 PHE cc_start: 0.8413 (t80) cc_final: 0.8165 (t80) REVERT: A 858 LEU cc_start: 0.8453 (mt) cc_final: 0.8240 (mt) REVERT: A 869 MET cc_start: 0.8884 (mtm) cc_final: 0.7849 (mtm) REVERT: A 873 TYR cc_start: 0.8601 (m-10) cc_final: 0.8111 (m-80) REVERT: A 878 LEU cc_start: 0.8946 (tp) cc_final: 0.8674 (tp) REVERT: A 902 MET cc_start: 0.8552 (ttm) cc_final: 0.7903 (ttm) REVERT: A 911 VAL cc_start: 0.7068 (t) cc_final: 0.6796 (m) REVERT: A 914 ASN cc_start: 0.8593 (p0) cc_final: 0.8209 (p0) REVERT: A 919 ASN cc_start: 0.8593 (m110) cc_final: 0.8191 (m110) REVERT: A 921 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8351 (tptt) REVERT: A 926 GLN cc_start: 0.8979 (mt0) cc_final: 0.8469 (mt0) REVERT: A 928 ASN cc_start: 0.8446 (m-40) cc_final: 0.8142 (m-40) REVERT: A 933 LYS cc_start: 0.8979 (mttm) cc_final: 0.8277 (mmmm) REVERT: A 949 GLN cc_start: 0.8588 (pp30) cc_final: 0.8292 (pp30) REVERT: A 957 GLN cc_start: 0.9014 (tt0) cc_final: 0.8409 (tm-30) REVERT: A 962 LEU cc_start: 0.8914 (tp) cc_final: 0.8697 (tt) REVERT: A 964 LYS cc_start: 0.8812 (mttt) cc_final: 0.8326 (tptp) REVERT: A 965 GLN cc_start: 0.8813 (mt0) cc_final: 0.8531 (mt0) REVERT: A 991 VAL cc_start: 0.8222 (p) cc_final: 0.7674 (t) REVERT: A 995 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8481 (tpp80) REVERT: A 1005 GLN cc_start: 0.8712 (tp40) cc_final: 0.8176 (tp40) REVERT: A 1009 THR cc_start: 0.8919 (m) cc_final: 0.8473 (p) REVERT: A 1014 ARG cc_start: 0.8967 (mtt-85) cc_final: 0.8730 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8763 (tt0) cc_final: 0.8518 (tt0) REVERT: A 1045 LYS cc_start: 0.8565 (mppt) cc_final: 0.8156 (mmtm) REVERT: A 1081 ILE cc_start: 0.8771 (mm) cc_final: 0.8440 (mp) REVERT: A 1083 HIS cc_start: 0.7920 (t-90) cc_final: 0.7532 (t-90) REVERT: A 1088 HIS cc_start: 0.7723 (m-70) cc_final: 0.7338 (m-70) REVERT: A 1091 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7082 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8606 (m90) cc_final: 0.8290 (m-70) REVERT: A 1102 TRP cc_start: 0.7891 (m100) cc_final: 0.7658 (m100) REVERT: A 1105 THR cc_start: 0.7267 (t) cc_final: 0.7016 (m) REVERT: A 1109 PHE cc_start: 0.7799 (t80) cc_final: 0.7331 (t80) REVERT: A 1114 ILE cc_start: 0.9050 (mp) cc_final: 0.8681 (tp) REVERT: B 52 GLN cc_start: 0.8194 (mp10) cc_final: 0.7980 (mp10) REVERT: B 53 ASP cc_start: 0.7359 (t0) cc_final: 0.6803 (t0) REVERT: B 65 PHE cc_start: 0.8230 (m-80) cc_final: 0.7374 (m-80) REVERT: B 92 PHE cc_start: 0.7706 (t80) cc_final: 0.7433 (t80) REVERT: B 97 LYS cc_start: 0.8176 (tptp) cc_final: 0.7862 (tppt) REVERT: B 99 ASN cc_start: 0.8807 (t0) cc_final: 0.8214 (t0) REVERT: B 187 LYS cc_start: 0.8518 (tmtt) cc_final: 0.8149 (ptmt) REVERT: B 207 HIS cc_start: 0.8367 (m-70) cc_final: 0.7881 (m-70) REVERT: B 233 ILE cc_start: 0.6639 (pt) cc_final: 0.5847 (tp) REVERT: B 240 THR cc_start: 0.8707 (m) cc_final: 0.8440 (t) REVERT: B 293 LEU cc_start: 0.7937 (tt) cc_final: 0.7600 (tt) REVERT: B 296 LEU cc_start: 0.8874 (tp) cc_final: 0.8521 (tp) REVERT: B 300 LYS cc_start: 0.8586 (mttt) cc_final: 0.8046 (mttm) REVERT: B 309 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 313 TYR cc_start: 0.8204 (m-80) cc_final: 0.7905 (m-80) REVERT: B 409 GLN cc_start: 0.8956 (mt0) cc_final: 0.8369 (tt0) REVERT: B 454 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7825 (ttp-170) REVERT: B 509 ARG cc_start: 0.6619 (mmt180) cc_final: 0.5971 (mmt180) REVERT: B 535 LYS cc_start: 0.8591 (tppp) cc_final: 0.7941 (tppt) REVERT: B 557 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7307 (mtmm) REVERT: B 619 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7821 (mp0) REVERT: B 712 ILE cc_start: 0.7768 (tt) cc_final: 0.7414 (tp) REVERT: B 722 VAL cc_start: 0.8012 (t) cc_final: 0.7742 (t) REVERT: B 725 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6109 (tm-30) REVERT: B 740 MET cc_start: 0.9252 (tpp) cc_final: 0.8665 (tpt) REVERT: B 758 SER cc_start: 0.8805 (m) cc_final: 0.8498 (t) REVERT: B 759 PHE cc_start: 0.8326 (m-80) cc_final: 0.7961 (m-80) REVERT: B 764 ASN cc_start: 0.8464 (m110) cc_final: 0.8254 (m110) REVERT: B 770 ILE cc_start: 0.8881 (mt) cc_final: 0.8635 (mt) REVERT: B 773 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 776 LYS cc_start: 0.8704 (tptp) cc_final: 0.8085 (tptp) REVERT: B 778 THR cc_start: 0.8777 (m) cc_final: 0.8425 (p) REVERT: B 779 GLN cc_start: 0.8484 (tp40) cc_final: 0.7638 (tm-30) REVERT: B 786 LYS cc_start: 0.8176 (mppt) cc_final: 0.7860 (mppt) REVERT: B 823 PHE cc_start: 0.8102 (m-80) cc_final: 0.7794 (m-10) REVERT: B 877 LEU cc_start: 0.8941 (mt) cc_final: 0.8736 (mt) REVERT: B 882 ILE cc_start: 0.8569 (mm) cc_final: 0.8360 (tp) REVERT: B 894 LEU cc_start: 0.8014 (mm) cc_final: 0.7808 (mm) REVERT: B 902 MET cc_start: 0.8225 (tpt) cc_final: 0.7664 (tpp) REVERT: B 907 ASN cc_start: 0.8315 (t0) cc_final: 0.8070 (t0) REVERT: B 917 TYR cc_start: 0.8138 (m-10) cc_final: 0.7363 (m-10) REVERT: B 921 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8387 (mtpp) REVERT: B 926 GLN cc_start: 0.8638 (mt0) cc_final: 0.8291 (tp40) REVERT: B 934 ILE cc_start: 0.8162 (mm) cc_final: 0.7928 (mm) REVERT: B 935 GLN cc_start: 0.8917 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 954 GLN cc_start: 0.8203 (pp30) cc_final: 0.7884 (pp30) REVERT: B 955 ASN cc_start: 0.8893 (m110) cc_final: 0.8195 (m110) REVERT: B 964 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8415 (mmtt) REVERT: B 965 GLN cc_start: 0.8517 (tp-100) cc_final: 0.7739 (tp40) REVERT: B 970 PHE cc_start: 0.6988 (m-10) cc_final: 0.5743 (m-10) REVERT: B 991 VAL cc_start: 0.8913 (m) cc_final: 0.8577 (t) REVERT: B 994 ASP cc_start: 0.8367 (t0) cc_final: 0.7965 (t0) REVERT: B 996 LEU cc_start: 0.8916 (mt) cc_final: 0.8711 (mt) REVERT: B 1001 LEU cc_start: 0.9090 (mt) cc_final: 0.8811 (mt) REVERT: B 1005 GLN cc_start: 0.8356 (pp30) cc_final: 0.7973 (pp30) REVERT: B 1008 VAL cc_start: 0.9024 (m) cc_final: 0.8747 (m) REVERT: B 1028 LYS cc_start: 0.8342 (tppt) cc_final: 0.7519 (tppt) REVERT: B 1031 GLU cc_start: 0.7653 (tt0) cc_final: 0.6812 (tt0) REVERT: B 1033 VAL cc_start: 0.7640 (t) cc_final: 0.7355 (t) REVERT: B 1038 LYS cc_start: 0.9097 (tptt) cc_final: 0.8669 (tptt) REVERT: B 1045 LYS cc_start: 0.8154 (pptt) cc_final: 0.7633 (pptt) REVERT: C 58 PHE cc_start: 0.8619 (m-80) cc_final: 0.8275 (m-80) REVERT: C 64 TRP cc_start: 0.7495 (t-100) cc_final: 0.7217 (t-100) REVERT: C 65 PHE cc_start: 0.8366 (m-80) cc_final: 0.7426 (m-80) REVERT: C 66 HIS cc_start: 0.7937 (m170) cc_final: 0.7515 (m170) REVERT: C 104 TRP cc_start: 0.5383 (m-90) cc_final: 0.4844 (m-90) REVERT: C 206 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6869 (mttt) REVERT: C 265 TYR cc_start: 0.7300 (p90) cc_final: 0.7015 (p90) REVERT: C 267 VAL cc_start: 0.7565 (t) cc_final: 0.6341 (t) REVERT: C 271 GLN cc_start: 0.8075 (mp10) cc_final: 0.7634 (tm-30) REVERT: C 277 LEU cc_start: 0.8157 (mt) cc_final: 0.7850 (mt) REVERT: C 290 ASP cc_start: 0.5953 (t0) cc_final: 0.5704 (t0) REVERT: C 318 PHE cc_start: 0.7666 (t80) cc_final: 0.7201 (t80) REVERT: C 370 ASN cc_start: 0.9007 (m110) cc_final: 0.8569 (p0) REVERT: C 436 TRP cc_start: 0.7813 (p-90) cc_final: 0.7243 (p-90) REVERT: C 440 ASN cc_start: 0.8721 (m-40) cc_final: 0.8065 (p0) REVERT: C 533 LEU cc_start: 0.8907 (tp) cc_final: 0.8666 (tp) REVERT: C 576 VAL cc_start: 0.8397 (p) cc_final: 0.8183 (m) REVERT: C 577 ARG cc_start: 0.8312 (ttm170) cc_final: 0.7648 (ttm110) REVERT: C 583 GLU cc_start: 0.8489 (mp0) cc_final: 0.8163 (mp0) REVERT: C 727 LEU cc_start: 0.8336 (mt) cc_final: 0.8008 (mt) REVERT: C 731 MET cc_start: 0.8648 (ptt) cc_final: 0.8390 (ptt) REVERT: C 756 TYR cc_start: 0.7651 (m-80) cc_final: 0.7408 (m-80) REVERT: C 759 PHE cc_start: 0.7895 (m-80) cc_final: 0.7610 (m-80) REVERT: C 761 THR cc_start: 0.8562 (p) cc_final: 0.8279 (t) REVERT: C 776 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8850 (ttmt) REVERT: C 778 THR cc_start: 0.8800 (m) cc_final: 0.8527 (p) REVERT: C 790 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7914 (mmtm) REVERT: C 796 ASP cc_start: 0.8425 (m-30) cc_final: 0.7411 (t0) REVERT: C 808 ASP cc_start: 0.8279 (t70) cc_final: 0.8045 (t0) REVERT: C 820 ASP cc_start: 0.7029 (m-30) cc_final: 0.6801 (m-30) REVERT: C 859 THR cc_start: 0.8300 (t) cc_final: 0.8023 (p) REVERT: C 869 MET cc_start: 0.8926 (mtm) cc_final: 0.8000 (mtm) REVERT: C 902 MET cc_start: 0.8473 (tmm) cc_final: 0.7980 (tmm) REVERT: C 905 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8164 (tpp80) REVERT: C 909 ILE cc_start: 0.8879 (pt) cc_final: 0.8328 (mm) REVERT: C 925 ASN cc_start: 0.8738 (m-40) cc_final: 0.8490 (m-40) REVERT: C 926 GLN cc_start: 0.8609 (mt0) cc_final: 0.8353 (mt0) REVERT: C 947 LYS cc_start: 0.8958 (mttt) cc_final: 0.8479 (mtmm) REVERT: C 964 LYS cc_start: 0.8936 (tttt) cc_final: 0.8389 (ptmt) REVERT: C 965 GLN cc_start: 0.8877 (mt0) cc_final: 0.8531 (mm-40) REVERT: C 1013 ILE cc_start: 0.8997 (mt) cc_final: 0.8392 (tp) REVERT: C 1014 ARG cc_start: 0.8870 (mtt90) cc_final: 0.7738 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8057 (mt-10) REVERT: C 1023 ASN cc_start: 0.8745 (m110) cc_final: 0.8457 (m110) REVERT: C 1028 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8915 (tptt) REVERT: C 1029 MET cc_start: 0.8590 (tpp) cc_final: 0.8380 (tpp) REVERT: C 1033 VAL cc_start: 0.7972 (t) cc_final: 0.7530 (t) REVERT: C 1034 LEU cc_start: 0.8375 (mt) cc_final: 0.8142 (mt) REVERT: C 1054 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7501 (tp40) REVERT: C 1072 GLU cc_start: 0.8349 (pm20) cc_final: 0.7834 (pm20) REVERT: C 1081 ILE cc_start: 0.7915 (mt) cc_final: 0.7290 (mp) REVERT: C 1088 HIS cc_start: 0.7388 (m90) cc_final: 0.7014 (m-70) REVERT: C 1103 PHE cc_start: 0.7839 (m-80) cc_final: 0.7439 (m-80) outliers start: 2 outliers final: 0 residues processed: 710 average time/residue: 0.1957 time to fit residues: 216.3668 Evaluate side-chains 657 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 139 optimal weight: 0.0010 chunk 215 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** 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** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 450 ASN B 957 GLN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.160728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121398 restraints weight = 55267.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126239 restraints weight = 34741.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129790 restraints weight = 24354.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.132369 restraints weight = 18330.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134255 restraints weight = 14641.320| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26624 Z= 0.161 Angle : 0.747 17.233 36353 Z= 0.362 Chirality : 0.050 0.643 4208 Planarity : 0.005 0.060 4627 Dihedral : 8.513 92.132 4458 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.14), residues: 3207 helix: 1.02 (0.20), residues: 673 sheet: -0.18 (0.20), residues: 691 loop : -1.29 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 905 TYR 0.024 0.001 TYR B 365 PHE 0.030 0.002 PHE C 906 TRP 0.018 0.002 TRP C1102 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00340 (26536) covalent geometry : angle 0.69991 (36139) SS BOND : bond 0.00324 ( 41) SS BOND : angle 1.92387 ( 82) hydrogen bonds : bond 0.04339 ( 873) hydrogen bonds : angle 5.66847 ( 2436) Misc. bond : bond 0.00059 ( 3) link_BETA1-4 : bond 0.00304 ( 10) link_BETA1-4 : angle 1.58861 ( 30) link_NAG-ASN : bond 0.00811 ( 34) link_NAG-ASN : angle 4.62402 ( 102) *********************** 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 707 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.002 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 41 LYS cc_start: 0.8800 (mmpt) cc_final: 0.7676 (mmmm) REVERT: A 49 HIS cc_start: 0.7339 (t70) cc_final: 0.6931 (t-90) REVERT: A 53 ASP cc_start: 0.8247 (t0) cc_final: 0.7684 (t0) REVERT: A 56 LEU cc_start: 0.8329 (mt) cc_final: 0.7890 (mt) REVERT: A 80 ASP cc_start: 0.8326 (t0) cc_final: 0.7774 (t0) REVERT: A 91 TYR cc_start: 0.6219 (t80) cc_final: 0.5916 (t80) REVERT: A 216 LEU cc_start: 0.6317 (mt) cc_final: 0.5912 (mp) REVERT: A 221 SER cc_start: 0.8362 (m) cc_final: 0.7669 (t) REVERT: A 224 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8280 (pm20) REVERT: A 269 TYR cc_start: 0.7654 (m-80) cc_final: 0.6569 (m-80) REVERT: A 273 ARG cc_start: 0.8604 (mmt180) cc_final: 0.8312 (mmt180) REVERT: A 287 ASP cc_start: 0.8415 (t0) cc_final: 0.8202 (t70) REVERT: A 298 GLU cc_start: 0.8170 (tt0) cc_final: 0.7834 (tt0) REVERT: A 303 LEU cc_start: 0.8956 (tp) cc_final: 0.8660 (tp) REVERT: A 319 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7531 (mtm110) REVERT: A 342 PHE cc_start: 0.9096 (m-10) cc_final: 0.8727 (m-10) REVERT: A 436 TRP cc_start: 0.7558 (m-10) cc_final: 0.7227 (m100) REVERT: A 533 LEU cc_start: 0.8544 (tp) cc_final: 0.8343 (tp) REVERT: A 643 PHE cc_start: 0.8037 (t80) cc_final: 0.7810 (t80) REVERT: A 658 ASN cc_start: 0.7992 (t0) cc_final: 0.7463 (t0) REVERT: A 737 ASP cc_start: 0.8008 (t70) cc_final: 0.7678 (t70) REVERT: A 745 ASP cc_start: 0.8075 (p0) cc_final: 0.7759 (p0) REVERT: A 751 ASN cc_start: 0.8340 (m110) cc_final: 0.7990 (m110) REVERT: A 762 GLN cc_start: 0.8850 (mt0) cc_final: 0.8568 (mt0) REVERT: A 763 LEU cc_start: 0.8924 (mt) cc_final: 0.8681 (mt) REVERT: A 770 ILE cc_start: 0.9049 (mt) cc_final: 0.8544 (mt) REVERT: A 774 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8229 (mm-40) REVERT: A 776 LYS cc_start: 0.8639 (mmmm) cc_final: 0.7936 (mmmm) REVERT: A 788 ILE cc_start: 0.7939 (mm) cc_final: 0.7693 (tp) REVERT: A 797 PHE cc_start: 0.8919 (m-80) cc_final: 0.8453 (m-80) REVERT: A 818 ILE cc_start: 0.9242 (mt) cc_final: 0.9004 (pt) REVERT: A 823 PHE cc_start: 0.8443 (t80) cc_final: 0.8188 (t80) REVERT: A 869 MET cc_start: 0.8946 (mtm) cc_final: 0.7935 (mtm) REVERT: A 873 TYR cc_start: 0.8615 (m-10) cc_final: 0.8110 (m-80) REVERT: A 878 LEU cc_start: 0.8918 (tp) cc_final: 0.8565 (tt) REVERT: A 902 MET cc_start: 0.8648 (ttm) cc_final: 0.7312 (tmm) REVERT: A 911 VAL cc_start: 0.7093 (t) cc_final: 0.6792 (m) REVERT: A 914 ASN cc_start: 0.8586 (p0) cc_final: 0.8202 (p0) REVERT: A 919 ASN cc_start: 0.8588 (m110) cc_final: 0.8207 (m110) REVERT: A 921 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8306 (tptp) REVERT: A 926 GLN cc_start: 0.9011 (mt0) cc_final: 0.8564 (mt0) REVERT: A 933 LYS cc_start: 0.9006 (mttm) cc_final: 0.8317 (mmmm) REVERT: A 949 GLN cc_start: 0.8574 (pp30) cc_final: 0.8229 (pp30) REVERT: A 957 GLN cc_start: 0.9032 (tt0) cc_final: 0.8319 (tm-30) REVERT: A 962 LEU cc_start: 0.8945 (tp) cc_final: 0.8664 (tt) REVERT: A 964 LYS cc_start: 0.8866 (mttt) cc_final: 0.8411 (tptp) REVERT: A 965 GLN cc_start: 0.8797 (mt0) cc_final: 0.8521 (mt0) REVERT: A 991 VAL cc_start: 0.8323 (p) cc_final: 0.7820 (t) REVERT: A 995 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8510 (tpp80) REVERT: A 1005 GLN cc_start: 0.8728 (tp40) cc_final: 0.8197 (tp40) REVERT: A 1009 THR cc_start: 0.8917 (m) cc_final: 0.8413 (p) REVERT: A 1017 GLU cc_start: 0.8768 (tt0) cc_final: 0.8495 (tt0) REVERT: A 1045 LYS cc_start: 0.8526 (mppt) cc_final: 0.8121 (mmtm) REVERT: A 1054 GLN cc_start: 0.6824 (mp10) cc_final: 0.6508 (mp10) REVERT: A 1081 ILE cc_start: 0.8728 (mm) cc_final: 0.8457 (mp) REVERT: A 1088 HIS cc_start: 0.7757 (m-70) cc_final: 0.7371 (m-70) REVERT: A 1091 ARG cc_start: 0.7438 (mtt180) cc_final: 0.7154 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8625 (m90) cc_final: 0.8332 (m-70) REVERT: A 1102 TRP cc_start: 0.7913 (m100) cc_final: 0.7621 (m100) REVERT: A 1109 PHE cc_start: 0.7822 (t80) cc_final: 0.7316 (t80) REVERT: A 1114 ILE cc_start: 0.9047 (mp) cc_final: 0.8698 (tp) REVERT: A 1121 PHE cc_start: 0.7435 (p90) cc_final: 0.7134 (p90) REVERT: B 44 ARG cc_start: 0.7856 (mtt90) cc_final: 0.6995 (mtm-85) REVERT: B 52 GLN cc_start: 0.8185 (mp10) cc_final: 0.7960 (mp10) REVERT: B 53 ASP cc_start: 0.7394 (t0) cc_final: 0.6761 (t0) REVERT: B 54 LEU cc_start: 0.8224 (mp) cc_final: 0.7929 (mp) REVERT: B 65 PHE cc_start: 0.8271 (m-80) cc_final: 0.7441 (m-80) REVERT: B 92 PHE cc_start: 0.7718 (t80) cc_final: 0.7437 (t80) REVERT: B 99 ASN cc_start: 0.8856 (t0) cc_final: 0.8277 (t0) REVERT: B 207 HIS cc_start: 0.8338 (m-70) cc_final: 0.7874 (m-70) REVERT: B 233 ILE cc_start: 0.6510 (pt) cc_final: 0.5626 (tp) REVERT: B 240 THR cc_start: 0.8734 (m) cc_final: 0.8506 (t) REVERT: B 293 LEU cc_start: 0.7997 (tt) cc_final: 0.7613 (tt) REVERT: B 294 ASP cc_start: 0.7962 (m-30) cc_final: 0.7683 (m-30) REVERT: B 296 LEU cc_start: 0.8829 (tp) cc_final: 0.8524 (tp) REVERT: B 300 LYS cc_start: 0.8631 (mttt) cc_final: 0.8100 (mttm) REVERT: B 309 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8357 (mm-30) REVERT: B 313 TYR cc_start: 0.8247 (m-80) cc_final: 0.7882 (m-80) REVERT: B 355 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7213 (ttp80) REVERT: B 398 ASP cc_start: 0.6309 (m-30) cc_final: 0.6062 (m-30) REVERT: B 409 GLN cc_start: 0.8940 (mt0) cc_final: 0.8368 (tt0) REVERT: B 454 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7838 (ttp-170) REVERT: B 509 ARG cc_start: 0.6608 (mmt180) cc_final: 0.5587 (mmm160) REVERT: B 535 LYS cc_start: 0.8659 (tppp) cc_final: 0.8009 (tppt) REVERT: B 557 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7308 (mtmm) REVERT: B 619 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7804 (mp0) REVERT: B 662 CYS cc_start: 0.4664 (p) cc_final: 0.4064 (p) REVERT: B 702 GLU cc_start: 0.8407 (mp0) cc_final: 0.7990 (mp0) REVERT: B 712 ILE cc_start: 0.7827 (tt) cc_final: 0.7467 (tp) REVERT: B 722 VAL cc_start: 0.8048 (t) cc_final: 0.7775 (t) REVERT: B 725 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6798 (tm-30) REVERT: B 734 THR cc_start: 0.8882 (m) cc_final: 0.8537 (p) REVERT: B 740 MET cc_start: 0.9339 (tpp) cc_final: 0.8691 (tpt) REVERT: B 758 SER cc_start: 0.8859 (m) cc_final: 0.8561 (t) REVERT: B 759 PHE cc_start: 0.8332 (m-80) cc_final: 0.8005 (m-80) REVERT: B 776 LYS cc_start: 0.8721 (tptp) cc_final: 0.8095 (tptp) REVERT: B 778 THR cc_start: 0.8835 (m) cc_final: 0.8481 (p) REVERT: B 779 GLN cc_start: 0.8556 (tp40) cc_final: 0.7703 (tm-30) REVERT: B 786 LYS cc_start: 0.8194 (mppt) cc_final: 0.7842 (mppt) REVERT: B 823 PHE cc_start: 0.8132 (m-80) cc_final: 0.7813 (m-10) REVERT: B 864 LEU cc_start: 0.8471 (tp) cc_final: 0.8022 (mm) REVERT: B 870 ILE cc_start: 0.8637 (tt) cc_final: 0.8292 (tp) REVERT: B 877 LEU cc_start: 0.8936 (mt) cc_final: 0.8704 (mt) REVERT: B 894 LEU cc_start: 0.8107 (mm) cc_final: 0.7901 (mm) REVERT: B 902 MET cc_start: 0.8265 (tpt) cc_final: 0.7633 (tpp) REVERT: B 905 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: B 907 ASN cc_start: 0.8305 (t0) cc_final: 0.8071 (t0) REVERT: B 917 TYR cc_start: 0.8161 (m-10) cc_final: 0.7348 (m-10) REVERT: B 921 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8380 (mtpp) REVERT: B 926 GLN cc_start: 0.8499 (mt0) cc_final: 0.8072 (tp40) REVERT: B 934 ILE cc_start: 0.8121 (mm) cc_final: 0.7873 (mm) REVERT: B 935 GLN cc_start: 0.8949 (tt0) cc_final: 0.8315 (tm-30) REVERT: B 954 GLN cc_start: 0.8260 (pp30) cc_final: 0.7942 (pp30) REVERT: B 955 ASN cc_start: 0.8919 (m110) cc_final: 0.8156 (m110) REVERT: B 957 GLN cc_start: 0.9095 (tt0) cc_final: 0.8411 (tp40) REVERT: B 964 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8448 (mmtt) REVERT: B 965 GLN cc_start: 0.8545 (tp-100) cc_final: 0.7799 (tp40) REVERT: B 970 PHE cc_start: 0.6990 (m-10) cc_final: 0.5852 (m-10) REVERT: B 991 VAL cc_start: 0.8946 (m) cc_final: 0.8653 (t) REVERT: B 994 ASP cc_start: 0.8358 (t0) cc_final: 0.7967 (t0) REVERT: B 996 LEU cc_start: 0.8929 (mt) cc_final: 0.8702 (mt) REVERT: B 1005 GLN cc_start: 0.8370 (pp30) cc_final: 0.7996 (pp30) REVERT: B 1008 VAL cc_start: 0.9057 (m) cc_final: 0.8786 (m) REVERT: B 1028 LYS cc_start: 0.8393 (tppt) cc_final: 0.7565 (tppt) REVERT: B 1031 GLU cc_start: 0.7637 (tt0) cc_final: 0.6763 (tt0) REVERT: B 1033 VAL cc_start: 0.7729 (t) cc_final: 0.7441 (t) REVERT: B 1038 LYS cc_start: 0.9122 (tptt) cc_final: 0.8700 (tptt) REVERT: B 1045 LYS cc_start: 0.8100 (pptt) cc_final: 0.7603 (pptt) REVERT: B 1073 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7157 (mtpp) REVERT: B 1074 ASN cc_start: 0.7209 (m-40) cc_final: 0.6988 (m-40) REVERT: C 58 PHE cc_start: 0.8640 (m-80) cc_final: 0.8218 (m-80) REVERT: C 64 TRP cc_start: 0.7508 (t-100) cc_final: 0.7104 (t-100) REVERT: C 66 HIS cc_start: 0.7983 (m170) cc_final: 0.7544 (m170) REVERT: C 99 ASN cc_start: 0.8795 (m-40) cc_final: 0.8474 (m-40) REVERT: C 104 TRP cc_start: 0.5555 (m-90) cc_final: 0.4955 (m-90) REVERT: C 206 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7067 (mtpp) REVERT: C 265 TYR cc_start: 0.7331 (p90) cc_final: 0.7084 (p90) REVERT: C 267 VAL cc_start: 0.7602 (t) cc_final: 0.6608 (t) REVERT: C 277 LEU cc_start: 0.8219 (mt) cc_final: 0.7935 (mt) REVERT: C 290 ASP cc_start: 0.5915 (t0) cc_final: 0.5693 (t0) REVERT: C 370 ASN cc_start: 0.9024 (m110) cc_final: 0.8625 (p0) REVERT: C 436 TRP cc_start: 0.7844 (p-90) cc_final: 0.7196 (p-90) REVERT: C 440 ASN cc_start: 0.8674 (m-40) cc_final: 0.8028 (p0) REVERT: C 557 LYS cc_start: 0.9015 (mppt) cc_final: 0.8594 (mmtm) REVERT: C 577 ARG cc_start: 0.8383 (ttm170) cc_final: 0.7630 (ttm110) REVERT: C 693 ILE cc_start: 0.8312 (tt) cc_final: 0.8112 (tt) REVERT: C 727 LEU cc_start: 0.8377 (mt) cc_final: 0.8078 (mt) REVERT: C 731 MET cc_start: 0.8651 (ptt) cc_final: 0.8388 (ptt) REVERT: C 756 TYR cc_start: 0.7755 (m-80) cc_final: 0.7375 (m-80) REVERT: C 759 PHE cc_start: 0.7956 (m-80) cc_final: 0.7594 (m-80) REVERT: C 776 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8840 (ttmt) REVERT: C 778 THR cc_start: 0.8806 (m) cc_final: 0.8529 (p) REVERT: C 790 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7874 (mmtm) REVERT: C 796 ASP cc_start: 0.8387 (m-30) cc_final: 0.7878 (t0) REVERT: C 808 ASP cc_start: 0.8262 (t70) cc_final: 0.8018 (t0) REVERT: C 859 THR cc_start: 0.8310 (t) cc_final: 0.8061 (p) REVERT: C 869 MET cc_start: 0.8925 (mtm) cc_final: 0.8001 (mtm) REVERT: C 902 MET cc_start: 0.8395 (tmm) cc_final: 0.7947 (tmm) REVERT: C 905 ARG cc_start: 0.8911 (mtt-85) cc_final: 0.8273 (tpp80) REVERT: C 909 ILE cc_start: 0.8819 (pt) cc_final: 0.8316 (mm) REVERT: C 925 ASN cc_start: 0.8759 (m-40) cc_final: 0.8515 (m-40) REVERT: C 926 GLN cc_start: 0.8637 (mt0) cc_final: 0.8354 (mt0) REVERT: C 936 ASP cc_start: 0.8438 (t0) cc_final: 0.8222 (t0) REVERT: C 947 LYS cc_start: 0.9017 (mttt) cc_final: 0.8528 (mtmm) REVERT: C 964 LYS cc_start: 0.8976 (tttt) cc_final: 0.8435 (ptpt) REVERT: C 965 GLN cc_start: 0.8899 (mt0) cc_final: 0.8597 (mm-40) REVERT: C 980 ILE cc_start: 0.8558 (pt) cc_final: 0.7890 (mt) REVERT: C 988 GLU cc_start: 0.8275 (mp0) cc_final: 0.7967 (mp0) REVERT: C 1013 ILE cc_start: 0.9026 (mt) cc_final: 0.8423 (tp) REVERT: C 1014 ARG cc_start: 0.8886 (mtt90) cc_final: 0.7751 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 1019 ARG cc_start: 0.8750 (ttt90) cc_final: 0.8211 (tpp80) REVERT: C 1023 ASN cc_start: 0.8763 (m110) cc_final: 0.8440 (m110) REVERT: C 1028 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8794 (tptt) REVERT: C 1029 MET cc_start: 0.8605 (tpp) cc_final: 0.8390 (tpp) REVERT: C 1033 VAL cc_start: 0.8028 (t) cc_final: 0.7573 (t) REVERT: C 1034 LEU cc_start: 0.8392 (mt) cc_final: 0.8141 (mt) REVERT: C 1054 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7562 (tp40) REVERT: C 1072 GLU cc_start: 0.8386 (pm20) cc_final: 0.7950 (pm20) REVERT: C 1081 ILE cc_start: 0.7882 (mt) cc_final: 0.7259 (mp) REVERT: C 1088 HIS cc_start: 0.7375 (m90) cc_final: 0.6840 (m-70) REVERT: C 1089 PHE cc_start: 0.6217 (m-10) cc_final: 0.5925 (m-80) REVERT: C 1103 PHE cc_start: 0.7898 (m-80) cc_final: 0.7464 (m-80) outliers start: 1 outliers final: 0 residues processed: 706 average time/residue: 0.1900 time to fit residues: 209.2536 Evaluate side-chains 660 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 215 optimal weight: 0.0370 chunk 163 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 957 GLN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.159316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.118580 restraints weight = 56307.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123615 restraints weight = 35233.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127278 restraints weight = 24632.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129943 restraints weight = 18574.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.131895 restraints weight = 14832.011| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26624 Z= 0.179 Angle : 0.761 17.502 36353 Z= 0.373 Chirality : 0.051 0.655 4208 Planarity : 0.005 0.060 4627 Dihedral : 8.443 89.808 4458 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.14), residues: 3207 helix: 0.93 (0.20), residues: 679 sheet: -0.26 (0.20), residues: 665 loop : -1.31 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 905 TYR 0.033 0.002 TYR B 873 PHE 0.026 0.002 PHE C 906 TRP 0.052 0.003 TRP C1102 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00362 (26536) covalent geometry : angle 0.71560 (36139) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.86145 ( 82) hydrogen bonds : bond 0.04498 ( 873) hydrogen bonds : angle 5.71736 ( 2436) Misc. bond : bond 0.00056 ( 3) link_BETA1-4 : bond 0.00225 ( 10) link_BETA1-4 : angle 1.59038 ( 30) link_NAG-ASN : bond 0.00834 ( 34) link_NAG-ASN : angle 4.60092 ( 102) ********************** 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 722 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 721 time to evaluate : 0.654 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 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: symmetry clash REVERT: A 49 HIS cc_start: 0.7299 (t70) cc_final: 0.6949 (t70) REVERT: A 51 THR cc_start: 0.8468 (m) cc_final: 0.8076 (t) REVERT: A 80 ASP cc_start: 0.8427 (t0) cc_final: 0.7912 (t0) REVERT: A 91 TYR cc_start: 0.6214 (t80) cc_final: 0.5908 (t80) REVERT: A 216 LEU cc_start: 0.6317 (mt) cc_final: 0.6050 (mt) REVERT: A 221 SER cc_start: 0.8377 (m) cc_final: 0.7681 (t) REVERT: A 224 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8305 (pm20) REVERT: A 269 TYR cc_start: 0.7689 (m-80) cc_final: 0.6651 (m-80) REVERT: A 273 ARG cc_start: 0.8668 (mmt180) cc_final: 0.8390 (mmt180) REVERT: A 278 LYS cc_start: 0.7371 (tmmt) cc_final: 0.7116 (tptp) REVERT: A 287 ASP cc_start: 0.8450 (t0) cc_final: 0.8012 (p0) REVERT: A 298 GLU cc_start: 0.8160 (tt0) cc_final: 0.7816 (tt0) REVERT: A 303 LEU cc_start: 0.9001 (tp) cc_final: 0.8672 (tp) REVERT: A 315 THR cc_start: 0.7198 (t) cc_final: 0.6098 (t) REVERT: A 318 PHE cc_start: 0.7726 (t80) cc_final: 0.7508 (t80) REVERT: A 342 PHE cc_start: 0.9148 (m-10) cc_final: 0.8792 (m-10) REVERT: A 436 TRP cc_start: 0.7617 (m-10) cc_final: 0.7334 (m100) REVERT: A 532 ASN cc_start: 0.7760 (t0) cc_final: 0.7552 (t0) REVERT: A 533 LEU cc_start: 0.8550 (tp) cc_final: 0.8326 (tp) REVERT: A 658 ASN cc_start: 0.7974 (t0) cc_final: 0.7486 (t0) REVERT: A 674 TYR cc_start: 0.6874 (t80) cc_final: 0.6392 (t80) REVERT: A 702 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7618 (tp30) REVERT: A 737 ASP cc_start: 0.8032 (t70) cc_final: 0.7760 (t70) REVERT: A 745 ASP cc_start: 0.8128 (p0) cc_final: 0.7797 (p0) REVERT: A 751 ASN cc_start: 0.8324 (m110) cc_final: 0.7995 (m110) REVERT: A 763 LEU cc_start: 0.8918 (mt) cc_final: 0.8680 (mt) REVERT: A 770 ILE cc_start: 0.9087 (mt) cc_final: 0.8580 (mt) REVERT: A 776 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8044 (mmmm) REVERT: A 788 ILE cc_start: 0.7889 (mm) cc_final: 0.7648 (tp) REVERT: A 797 PHE cc_start: 0.8899 (m-80) cc_final: 0.8428 (m-80) REVERT: A 818 ILE cc_start: 0.9256 (mt) cc_final: 0.9026 (pt) REVERT: A 823 PHE cc_start: 0.8446 (t80) cc_final: 0.8216 (t80) REVERT: A 858 LEU cc_start: 0.8438 (mt) cc_final: 0.8233 (mt) REVERT: A 873 TYR cc_start: 0.8602 (m-10) cc_final: 0.8145 (m-80) REVERT: A 878 LEU cc_start: 0.8974 (tp) cc_final: 0.8621 (tt) REVERT: A 902 MET cc_start: 0.8646 (ttm) cc_final: 0.7372 (tmm) REVERT: A 911 VAL cc_start: 0.7094 (t) cc_final: 0.6812 (m) REVERT: A 914 ASN cc_start: 0.8606 (p0) cc_final: 0.8214 (p0) REVERT: A 919 ASN cc_start: 0.8619 (m110) cc_final: 0.8248 (m110) REVERT: A 921 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8335 (tptp) REVERT: A 926 GLN cc_start: 0.9067 (mt0) cc_final: 0.8629 (mt0) REVERT: A 933 LYS cc_start: 0.9047 (mttm) cc_final: 0.8370 (mmmm) REVERT: A 949 GLN cc_start: 0.8610 (pp30) cc_final: 0.8288 (pp30) REVERT: A 957 GLN cc_start: 0.9048 (tt0) cc_final: 0.8461 (tm-30) REVERT: A 962 LEU cc_start: 0.8937 (tp) cc_final: 0.8622 (tt) REVERT: A 964 LYS cc_start: 0.8912 (mttt) cc_final: 0.8439 (tptp) REVERT: A 965 GLN cc_start: 0.8835 (mt0) cc_final: 0.8530 (mt0) REVERT: A 977 LEU cc_start: 0.8989 (tp) cc_final: 0.8740 (tt) REVERT: A 988 GLU cc_start: 0.7790 (mp0) cc_final: 0.7382 (pm20) REVERT: A 991 VAL cc_start: 0.8428 (p) cc_final: 0.7915 (t) REVERT: A 995 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8524 (tpp80) REVERT: A 1005 GLN cc_start: 0.8731 (tp40) cc_final: 0.8012 (tm-30) REVERT: A 1009 THR cc_start: 0.8962 (m) cc_final: 0.8203 (p) REVERT: A 1012 LEU cc_start: 0.9297 (mt) cc_final: 0.9003 (mm) REVERT: A 1017 GLU cc_start: 0.8776 (tt0) cc_final: 0.8501 (tt0) REVERT: A 1041 ASP cc_start: 0.7666 (t0) cc_final: 0.7277 (t0) REVERT: A 1045 LYS cc_start: 0.8523 (mppt) cc_final: 0.8075 (mmtm) REVERT: A 1054 GLN cc_start: 0.6947 (mp10) cc_final: 0.6613 (mp10) REVERT: A 1088 HIS cc_start: 0.7829 (m-70) cc_final: 0.7332 (m-70) REVERT: A 1091 ARG cc_start: 0.7422 (mtt180) cc_final: 0.7172 (mtt-85) REVERT: A 1101 HIS cc_start: 0.8676 (m90) cc_final: 0.8333 (m-70) REVERT: A 1102 TRP cc_start: 0.8011 (m100) cc_final: 0.7765 (m100) REVERT: A 1109 PHE cc_start: 0.7920 (t80) cc_final: 0.7371 (t80) REVERT: A 1114 ILE cc_start: 0.9030 (mp) cc_final: 0.8682 (tp) REVERT: A 1121 PHE cc_start: 0.7400 (p90) cc_final: 0.7150 (p90) REVERT: B 44 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7369 (mtm-85) REVERT: B 54 LEU cc_start: 0.8246 (mp) cc_final: 0.7444 (tt) REVERT: B 65 PHE cc_start: 0.8368 (m-80) cc_final: 0.7690 (m-80) REVERT: B 99 ASN cc_start: 0.8888 (t0) cc_final: 0.8223 (t0) REVERT: B 135 PHE cc_start: 0.8641 (m-80) cc_final: 0.8425 (m-80) REVERT: B 187 LYS cc_start: 0.8376 (pttm) cc_final: 0.8050 (pttm) REVERT: B 190 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7734 (mmt180) REVERT: B 233 ILE cc_start: 0.6592 (pt) cc_final: 0.5682 (tp) REVERT: B 277 LEU cc_start: 0.7594 (mm) cc_final: 0.7314 (mm) REVERT: B 285 ILE cc_start: 0.8539 (mt) cc_final: 0.8292 (mt) REVERT: B 293 LEU cc_start: 0.8029 (tt) cc_final: 0.7630 (tt) REVERT: B 298 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 309 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 313 TYR cc_start: 0.8265 (m-80) cc_final: 0.7819 (m-80) REVERT: B 374 PHE cc_start: 0.8162 (m-80) cc_final: 0.7857 (m-80) REVERT: B 380 TYR cc_start: 0.8222 (m-80) cc_final: 0.7861 (m-80) REVERT: B 395 VAL cc_start: 0.7940 (t) cc_final: 0.7556 (m) REVERT: B 409 GLN cc_start: 0.8960 (mt0) cc_final: 0.8406 (tt0) REVERT: B 535 LYS cc_start: 0.8706 (tppp) cc_final: 0.8069 (tppt) REVERT: B 541 PHE cc_start: 0.7601 (p90) cc_final: 0.7319 (p90) REVERT: B 557 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7430 (mtmm) REVERT: B 577 ARG cc_start: 0.7521 (tmt170) cc_final: 0.6996 (tmt170) REVERT: B 619 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7809 (mp0) REVERT: B 702 GLU cc_start: 0.8361 (mp0) cc_final: 0.7995 (mp0) REVERT: B 712 ILE cc_start: 0.7885 (tt) cc_final: 0.7448 (tp) REVERT: B 722 VAL cc_start: 0.8025 (t) cc_final: 0.7760 (t) REVERT: B 734 THR cc_start: 0.8869 (m) cc_final: 0.8546 (p) REVERT: B 740 MET cc_start: 0.9262 (tpp) cc_final: 0.8738 (tpt) REVERT: B 756 TYR cc_start: 0.8297 (m-80) cc_final: 0.7911 (m-80) REVERT: B 758 SER cc_start: 0.8886 (m) cc_final: 0.8605 (t) REVERT: B 759 PHE cc_start: 0.8358 (m-80) cc_final: 0.8086 (m-80) REVERT: B 763 LEU cc_start: 0.8894 (mm) cc_final: 0.8640 (mm) REVERT: B 764 ASN cc_start: 0.8629 (m110) cc_final: 0.8402 (m-40) REVERT: B 770 ILE cc_start: 0.8852 (mt) cc_final: 0.8617 (mt) REVERT: B 773 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7970 (mt-10) REVERT: B 776 LYS cc_start: 0.8748 (tptp) cc_final: 0.8116 (tptp) REVERT: B 778 THR cc_start: 0.8822 (m) cc_final: 0.8499 (p) REVERT: B 779 GLN cc_start: 0.8613 (tp40) cc_final: 0.7753 (tm-30) REVERT: B 786 LYS cc_start: 0.8274 (mppt) cc_final: 0.7897 (mppt) REVERT: B 800 PHE cc_start: 0.8215 (m-80) cc_final: 0.7721 (m-80) REVERT: B 823 PHE cc_start: 0.8157 (m-80) cc_final: 0.7779 (m-10) REVERT: B 864 LEU cc_start: 0.8488 (tp) cc_final: 0.7996 (mm) REVERT: B 894 LEU cc_start: 0.8147 (mm) cc_final: 0.7946 (mm) REVERT: B 902 MET cc_start: 0.8289 (tpt) cc_final: 0.7468 (mmm) REVERT: B 907 ASN cc_start: 0.8339 (t0) cc_final: 0.8112 (t0) REVERT: B 917 TYR cc_start: 0.8228 (m-10) cc_final: 0.7504 (m-10) REVERT: B 921 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8403 (mtpp) REVERT: B 926 GLN cc_start: 0.8521 (mt0) cc_final: 0.8119 (tp40) REVERT: B 934 ILE cc_start: 0.8167 (mm) cc_final: 0.7925 (mm) REVERT: B 935 GLN cc_start: 0.8964 (tt0) cc_final: 0.8290 (tm-30) REVERT: B 954 GLN cc_start: 0.8293 (pp30) cc_final: 0.7990 (pp30) REVERT: B 955 ASN cc_start: 0.8904 (m110) cc_final: 0.8101 (m110) REVERT: B 957 GLN cc_start: 0.9173 (tt0) cc_final: 0.8426 (tp40) REVERT: B 964 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8495 (ttmm) REVERT: B 965 GLN cc_start: 0.8558 (tp-100) cc_final: 0.7913 (tp-100) REVERT: B 970 PHE cc_start: 0.7084 (m-10) cc_final: 0.5733 (m-10) REVERT: B 991 VAL cc_start: 0.8966 (m) cc_final: 0.8695 (t) REVERT: B 994 ASP cc_start: 0.8374 (t0) cc_final: 0.7916 (t0) REVERT: B 996 LEU cc_start: 0.8973 (mt) cc_final: 0.8766 (mt) REVERT: B 1008 VAL cc_start: 0.9075 (m) cc_final: 0.8861 (m) REVERT: B 1028 LYS cc_start: 0.8423 (tppt) cc_final: 0.7606 (tppt) REVERT: B 1031 GLU cc_start: 0.7685 (tt0) cc_final: 0.6809 (tt0) REVERT: B 1038 LYS cc_start: 0.9133 (tptt) cc_final: 0.8720 (tptt) REVERT: B 1045 LYS cc_start: 0.8084 (pptt) cc_final: 0.7581 (pptt) REVERT: B 1073 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7186 (mtpp) REVERT: B 1074 ASN cc_start: 0.7167 (m-40) cc_final: 0.6949 (m-40) REVERT: B 1077 THR cc_start: 0.7338 (t) cc_final: 0.7104 (t) REVERT: B 1109 PHE cc_start: 0.7448 (t80) cc_final: 0.7136 (t80) REVERT: C 58 PHE cc_start: 0.8623 (m-80) cc_final: 0.8283 (m-80) REVERT: C 64 TRP cc_start: 0.7520 (t-100) cc_final: 0.7136 (t-100) REVERT: C 66 HIS cc_start: 0.7936 (m170) cc_final: 0.7282 (m170) REVERT: C 104 TRP cc_start: 0.5732 (m-90) cc_final: 0.5047 (m-90) REVERT: C 206 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7106 (mtpp) REVERT: C 265 TYR cc_start: 0.7387 (p90) cc_final: 0.7155 (p90) REVERT: C 267 VAL cc_start: 0.7669 (t) cc_final: 0.6698 (t) REVERT: C 277 LEU cc_start: 0.8253 (mt) cc_final: 0.7974 (mt) REVERT: C 290 ASP cc_start: 0.5922 (t0) cc_final: 0.5703 (t0) REVERT: C 370 ASN cc_start: 0.9047 (m110) cc_final: 0.8670 (p0) REVERT: C 440 ASN cc_start: 0.8695 (m-40) cc_final: 0.8029 (p0) REVERT: C 533 LEU cc_start: 0.9079 (tp) cc_final: 0.8796 (tp) REVERT: C 576 VAL cc_start: 0.8435 (p) cc_final: 0.8193 (m) REVERT: C 618 THR cc_start: 0.8286 (t) cc_final: 0.8083 (p) REVERT: C 727 LEU cc_start: 0.8376 (mt) cc_final: 0.8102 (mt) REVERT: C 756 TYR cc_start: 0.7842 (m-80) cc_final: 0.7537 (m-80) REVERT: C 759 PHE cc_start: 0.7979 (m-80) cc_final: 0.7574 (m-80) REVERT: C 761 THR cc_start: 0.8503 (p) cc_final: 0.8216 (t) REVERT: C 776 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8839 (ttmt) REVERT: C 778 THR cc_start: 0.8790 (m) cc_final: 0.8524 (p) REVERT: C 790 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7864 (mmtm) REVERT: C 796 ASP cc_start: 0.8666 (m-30) cc_final: 0.7860 (t0) REVERT: C 808 ASP cc_start: 0.8184 (t70) cc_final: 0.7921 (t0) REVERT: C 859 THR cc_start: 0.8352 (t) cc_final: 0.8062 (p) REVERT: C 869 MET cc_start: 0.8938 (mtm) cc_final: 0.8023 (mtm) REVERT: C 902 MET cc_start: 0.8417 (tmm) cc_final: 0.7983 (tmm) REVERT: C 905 ARG cc_start: 0.8892 (mtt-85) cc_final: 0.8550 (tpp80) REVERT: C 909 ILE cc_start: 0.8835 (pt) cc_final: 0.8251 (mm) REVERT: C 925 ASN cc_start: 0.8792 (m-40) cc_final: 0.8552 (m-40) REVERT: C 926 GLN cc_start: 0.8677 (mt0) cc_final: 0.8419 (mt0) REVERT: C 936 ASP cc_start: 0.8453 (t0) cc_final: 0.8241 (t0) REVERT: C 947 LYS cc_start: 0.9068 (mttt) cc_final: 0.8533 (mtmm) REVERT: C 964 LYS cc_start: 0.9045 (tttt) cc_final: 0.8511 (ptpt) REVERT: C 965 GLN cc_start: 0.8898 (mt0) cc_final: 0.8629 (mm-40) REVERT: C 980 ILE cc_start: 0.8603 (pt) cc_final: 0.8032 (mt) REVERT: C 1013 ILE cc_start: 0.9056 (mt) cc_final: 0.8449 (tp) REVERT: C 1014 ARG cc_start: 0.8932 (mtt90) cc_final: 0.7876 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 1023 ASN cc_start: 0.8809 (m110) cc_final: 0.8539 (m110) REVERT: C 1028 LYS cc_start: 0.9176 (mmtp) cc_final: 0.8869 (tptt) REVERT: C 1029 MET cc_start: 0.8584 (tpp) cc_final: 0.8359 (tpp) REVERT: C 1033 VAL cc_start: 0.8072 (t) cc_final: 0.7606 (t) REVERT: C 1034 LEU cc_start: 0.8391 (mt) cc_final: 0.8144 (mt) REVERT: C 1050 MET cc_start: 0.5872 (ppp) cc_final: 0.5453 (ppp) REVERT: C 1072 GLU cc_start: 0.8405 (pm20) cc_final: 0.7988 (pm20) REVERT: C 1081 ILE cc_start: 0.7913 (mt) cc_final: 0.7265 (mp) REVERT: C 1088 HIS cc_start: 0.7347 (m90) cc_final: 0.6858 (m-70) REVERT: C 1089 PHE cc_start: 0.6251 (m-10) cc_final: 0.5960 (m-80) REVERT: C 1103 PHE cc_start: 0.7911 (m-80) cc_final: 0.7456 (m-80) outliers start: 1 outliers final: 0 residues processed: 721 average time/residue: 0.1727 time to fit residues: 193.8332 Evaluate side-chains 688 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 104 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 288 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.159926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119821 restraints weight = 55945.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124682 restraints weight = 35703.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128255 restraints weight = 25236.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130849 restraints weight = 19125.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132678 restraints weight = 15345.663| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26624 Z= 0.153 Angle : 0.752 17.319 36353 Z= 0.366 Chirality : 0.050 0.677 4208 Planarity : 0.005 0.151 4627 Dihedral : 8.365 88.604 4458 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3207 helix: 0.97 (0.20), residues: 679 sheet: -0.18 (0.20), residues: 657 loop : -1.37 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG B 328 TYR 0.032 0.002 TYR B 873 PHE 0.022 0.002 PHE C 906 TRP 0.022 0.002 TRP B 436 HIS 0.014 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (26536) covalent geometry : angle 0.70785 (36139) SS BOND : bond 0.00279 ( 41) SS BOND : angle 2.06710 ( 82) hydrogen bonds : bond 0.04293 ( 873) hydrogen bonds : angle 5.65310 ( 2436) Misc. bond : bond 0.00350 ( 3) link_BETA1-4 : bond 0.00272 ( 10) link_BETA1-4 : angle 1.57499 ( 30) link_NAG-ASN : bond 0.00798 ( 34) link_NAG-ASN : angle 4.47369 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.12 seconds wall clock time: 108 minutes 1.84 seconds (6481.84 seconds total)