Starting phenix.real_space_refine on Sat Mar 7 09:42:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7s_12755/03_2026/7o7s_12755.cif" } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 26326 2.51 5 N 6891 2.21 5 O 8072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41466 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9958 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 66, 'TRANS': 1209} Chain breaks: 1 Chain: "B" Number of atoms: 9958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 9958 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 66, 'TRANS': 1209} Chain breaks: 1 Chain: "C" Number of atoms: 9967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 9967 Classifications: {'peptide': 1277} Link IDs: {'PTRANS': 66, 'TRANS': 1210} Chain breaks: 1 Chain: "D" Number of atoms: 10985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 10985 Classifications: {'peptide': 1407} Link IDs: {'PTRANS': 73, 'TRANS': 1333} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.16, per 1000 atoms: 0.27 Number of scatterers: 41466 At special positions: 0 Unit cell: (214.608, 150.436, 189.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 8072 8.00 N 6891 7.00 C 26326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.04 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.02 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.05 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.02 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.04 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.04 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.04 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.04 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.04 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.04 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.04 Simple disulfide: pdb=" SG CYS D1352 " - pdb=" SG CYS D1467 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA L 3 " - " MAN L 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 869 " " NAG D2004 " - " ASN D 991 " " NAG D2005 " - " ASN D1424 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 247 " " NAG L 1 " - " ASN D 396 " " NAG M 1 " - " ASN D 410 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9826 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 16.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 6.708A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 3.816A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 7.448A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.797A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 removed outlier: 4.440A pdb=" N ASN B1123 " --> pdb=" O PRO B1119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1124 " --> pdb=" O VAL B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 6.224A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 4.012A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 removed outlier: 4.875A pdb=" N MET D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 962 removed outlier: 7.617A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 958 through 962' Processing helix chain 'D' and resid 973 through 993 removed outlier: 4.929A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 978 " --> pdb=" O GLU D 974 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 4.366A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 989 " --> pdb=" O TYR D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.769A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 4.757A pdb=" N LYS D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR D1048 " --> pdb=" O PHE D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 4.086A pdb=" N ALA D1066 " --> pdb=" O HIS D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 removed outlier: 3.577A pdb=" N THR D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 5.409A pdb=" N ALA D1151 " --> pdb=" O LYS D1147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 4.115A pdb=" N LYS D1168 " --> pdb=" O LYS D1164 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1217 removed outlier: 3.546A pdb=" N LEU D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.031A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 5.887A pdb=" N VAL D1255 " --> pdb=" O THR D1251 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D1256 " --> pdb=" O GLN D1252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU D1261 " --> pdb=" O ALA D1257 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA D1266 " --> pdb=" O SER D1262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA D1267 " --> pdb=" O LYS D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' Processing helix chain 'D' and resid 1393 through 1400 517 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12883 1.34 - 1.47: 10310 1.47 - 1.60: 18921 1.60 - 1.73: 0 1.73 - 1.86: 260 Bond restraints: 42374 Sorted by residual: bond pdb=" C LEU D 468 " pdb=" N PRO D 469 " ideal model delta sigma weight residual 1.335 1.375 -0.040 8.70e-03 1.32e+04 2.07e+01 bond pdb=" C PRO B 936 " pdb=" N PRO B 937 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.05e+01 bond pdb=" C LEU D 987 " pdb=" O LEU D 987 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.22e-02 6.72e+03 1.75e+01 bond pdb=" N PRO B 969 " pdb=" CA PRO B 969 " ideal model delta sigma weight residual 1.470 1.518 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ALA C 599 " pdb=" N VAL C 600 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.39e-02 5.18e+03 1.38e+01 ... (remaining 42369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 55148 2.90 - 5.80: 2221 5.80 - 8.70: 173 8.70 - 11.60: 21 11.60 - 14.50: 9 Bond angle restraints: 57572 Sorted by residual: angle pdb=" N PRO D 454 " pdb=" CA PRO D 454 " pdb=" C PRO D 454 " ideal model delta sigma weight residual 114.27 100.39 13.88 1.35e+00 5.49e-01 1.06e+02 angle pdb=" C TYR D 989 " pdb=" CA TYR D 989 " pdb=" CB TYR D 989 " ideal model delta sigma weight residual 110.88 96.52 14.36 1.57e+00 4.06e-01 8.36e+01 angle pdb=" N ALA B 391 " pdb=" CA ALA B 391 " pdb=" C ALA B 391 " ideal model delta sigma weight residual 113.28 102.31 10.97 1.22e+00 6.72e-01 8.08e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" C PRO C 609 " ideal model delta sigma weight residual 110.80 99.52 11.28 1.51e+00 4.39e-01 5.58e+01 angle pdb=" N VAL D1116 " pdb=" CA VAL D1116 " pdb=" C VAL D1116 " ideal model delta sigma weight residual 111.81 105.73 6.08 8.60e-01 1.35e+00 5.00e+01 ... (remaining 57567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 23472 21.48 - 42.96: 2275 42.96 - 64.44: 333 64.44 - 85.93: 101 85.93 - 107.41: 28 Dihedral angle restraints: 26209 sinusoidal: 10953 harmonic: 15256 Sorted by residual: dihedral pdb=" C ASN A 55 " pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" CB ASN A 55 " ideal model delta harmonic sigma weight residual -122.60 -142.52 19.92 0 2.50e+00 1.60e-01 6.35e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 158.59 -65.59 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" C TYR D 989 " pdb=" N TYR D 989 " pdb=" CA TYR D 989 " pdb=" CB TYR D 989 " ideal model delta harmonic sigma weight residual -122.60 -103.94 -18.66 0 2.50e+00 1.60e-01 5.57e+01 ... (remaining 26206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 6674 0.392 - 0.783: 10 0.783 - 1.175: 1 1.175 - 1.566: 0 1.566 - 1.958: 1 Chirality restraints: 6686 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" CB VAL B1120 " pdb=" CA VAL B1120 " pdb=" CG1 VAL B1120 " pdb=" CG2 VAL B1120 " both_signs ideal model delta sigma weight residual False -2.63 -0.67 -1.96 2.00e-01 2.50e+01 9.58e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.96e+01 ... (remaining 6683 not shown) Planarity restraints: 7387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D2003 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG D2003 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D2003 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D2003 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG D2003 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2004 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG A2004 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A2004 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A2004 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A2004 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C2004 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C2004 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C2004 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C2004 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG C2004 " 0.146 2.00e-02 2.50e+03 ... (remaining 7384 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 579 2.47 - 3.07: 32362 3.07 - 3.68: 69201 3.68 - 4.29: 94035 4.29 - 4.90: 144446 Nonbonded interactions: 340623 Sorted by model distance: nonbonded pdb=" SG CYS D 972 " pdb=" CD GLN D 975 " model vdw 1.857 3.630 nonbonded pdb=" O TYR C 394 " pdb=" O6 NAG C2004 " model vdw 1.968 3.040 nonbonded pdb=" OG SER D 457 " pdb=" OD1 ASN D 483 " model vdw 2.010 3.040 nonbonded pdb=" O ALA C 590 " pdb=" OG SER C 593 " model vdw 2.012 3.040 nonbonded pdb=" OE2 GLU A 926 " pdb=" OG SER A 928 " model vdw 2.027 3.040 ... (remaining 340618 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 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 2005)) selection = (chain 'B' and (resid 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 2005)) selection = (chain 'C' and (resid 29 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2001 through 2005)) selection = (chain 'D' and (resid 29 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2005)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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=1.00 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 37.130 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 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 : 0.009 0.095 42463 Z= 0.447 Angle : 1.290 14.498 57794 Z= 0.719 Chirality : 0.074 1.958 6686 Planarity : 0.021 0.306 7358 Dihedral : 17.306 107.408 16248 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.69 % Allowed : 20.13 % Favored : 79.18 % Rotamer: Outliers : 1.09 % Allowed : 10.64 % Favored : 88.27 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.96 (0.09), residues: 5220 helix: -3.07 (0.14), residues: 771 sheet: -3.71 (0.13), residues: 1127 loop : -4.56 (0.08), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 598 TYR 0.043 0.003 TYR C1152 PHE 0.051 0.004 PHE D1049 TRP 0.025 0.004 TRP A 739 HIS 0.014 0.002 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00902 (42374) covalent geometry : angle 1.28156 (57572) SS BOND : bond 0.00665 ( 45) SS BOND : angle 1.96681 ( 90) hydrogen bonds : bond 0.10685 ( 517) hydrogen bonds : angle 7.70536 ( 1551) link_ALPHA1-6 : bond 0.00082 ( 1) link_ALPHA1-6 : angle 0.63283 ( 3) link_BETA1-4 : bond 0.00661 ( 14) link_BETA1-4 : angle 2.48570 ( 42) link_NAG-ASN : bond 0.00443 ( 29) link_NAG-ASN : angle 3.40551 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 632 time to evaluate : 1.364 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 45 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 121 MET cc_start: 0.8955 (ttt) cc_final: 0.8734 (ttt) REVERT: A 229 PHE cc_start: 0.7332 (p90) cc_final: 0.6716 (p90) REVERT: A 310 GLN cc_start: 0.7999 (mp-120) cc_final: 0.7464 (mp10) REVERT: A 411 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6529 (p) REVERT: A 440 GLU cc_start: 0.6369 (tt0) cc_final: 0.5269 (mm-30) REVERT: A 464 MET cc_start: 0.8752 (ttt) cc_final: 0.8519 (ttt) REVERT: A 561 GLU cc_start: 0.7733 (tp30) cc_final: 0.7408 (tp30) REVERT: A 586 ARG cc_start: 0.7653 (ttt90) cc_final: 0.7224 (mmm-85) REVERT: A 959 MET cc_start: 0.5759 (mtt) cc_final: 0.5278 (ptt) REVERT: A 1122 ARG cc_start: 0.8892 (mtp180) cc_final: 0.8272 (mmm160) REVERT: A 1133 LYS cc_start: 0.9046 (tttt) cc_final: 0.8662 (tptt) REVERT: A 1216 TYR cc_start: 0.8193 (m-80) cc_final: 0.7974 (m-80) REVERT: B 142 GLN cc_start: 0.8273 (mt0) cc_final: 0.7847 (mt0) REVERT: B 226 LEU cc_start: 0.8252 (mp) cc_final: 0.7620 (pt) REVERT: B 256 TYR cc_start: 0.8474 (t80) cc_final: 0.8270 (t80) REVERT: B 325 GLN cc_start: 0.9151 (tt0) cc_final: 0.8918 (tm-30) REVERT: B 354 LYS cc_start: 0.8977 (tttp) cc_final: 0.8763 (tttt) REVERT: B 409 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8001 (tp) REVERT: B 462 GLU cc_start: 0.8609 (pt0) cc_final: 0.8329 (pm20) REVERT: B 531 LYS cc_start: 0.7870 (pttm) cc_final: 0.7533 (tttt) REVERT: B 619 TYR cc_start: 0.7512 (m-10) cc_final: 0.7288 (m-80) REVERT: B 636 ASP cc_start: 0.6712 (p0) cc_final: 0.6466 (p0) REVERT: B 789 PHE cc_start: 0.6326 (t80) cc_final: 0.6076 (t80) REVERT: B 1040 TRP cc_start: 0.6068 (t60) cc_final: 0.5813 (t60) REVERT: B 1207 GLU cc_start: 0.6644 (pp20) cc_final: 0.6222 (pt0) REVERT: B 1274 LYS cc_start: 0.8938 (pttt) cc_final: 0.8718 (ptmt) REVERT: B 1296 ASN cc_start: 0.8750 (t0) cc_final: 0.8514 (t0) REVERT: C 209 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7409 (tmtt) REVERT: C 335 LEU cc_start: 0.8854 (tt) cc_final: 0.8293 (pt) REVERT: C 356 ASP cc_start: 0.9109 (t0) cc_final: 0.8890 (t0) REVERT: C 363 ILE cc_start: 0.8465 (tp) cc_final: 0.8237 (tp) REVERT: C 373 ASP cc_start: 0.7854 (t70) cc_final: 0.7363 (m-30) REVERT: C 449 TYR cc_start: 0.7217 (m-80) cc_final: 0.6915 (m-80) REVERT: C 464 MET cc_start: 0.7714 (ttm) cc_final: 0.7474 (mtm) REVERT: C 528 ILE cc_start: 0.7097 (pt) cc_final: 0.6851 (pt) REVERT: C 569 ASP cc_start: 0.8390 (t0) cc_final: 0.8188 (t0) REVERT: C 945 ARG cc_start: 0.7458 (tmt170) cc_final: 0.7047 (ttt180) REVERT: C 1005 ILE cc_start: 0.5185 (mt) cc_final: 0.4801 (mt) REVERT: C 1104 TYR cc_start: 0.5543 (t80) cc_final: 0.3845 (t80) REVERT: C 1126 PHE cc_start: 0.8990 (m-80) cc_final: 0.8620 (m-80) REVERT: C 1136 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8557 (tm-30) REVERT: C 1325 GLN cc_start: 0.9257 (tt0) cc_final: 0.8339 (tt0) REVERT: D 48 CYS cc_start: 0.3556 (OUTLIER) cc_final: 0.3015 (p) REVERT: D 130 PHE cc_start: 0.9092 (p90) cc_final: 0.8776 (p90) REVERT: D 149 VAL cc_start: 0.6346 (t) cc_final: 0.5573 (t) REVERT: D 286 PHE cc_start: 0.8066 (m-80) cc_final: 0.7810 (m-80) REVERT: D 387 ARG cc_start: 0.9138 (mmp-170) cc_final: 0.8762 (mmp80) REVERT: D 406 GLN cc_start: 0.9271 (tm-30) cc_final: 0.9001 (tm-30) REVERT: D 446 HIS cc_start: 0.5968 (t70) cc_final: 0.5603 (t70) REVERT: D 550 ASP cc_start: 0.7866 (t0) cc_final: 0.7531 (t0) REVERT: D 567 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8819 (tptp) REVERT: D 569 ASP cc_start: 0.9613 (t0) cc_final: 0.9397 (t70) REVERT: D 968 MET cc_start: -0.1215 (tpt) cc_final: -0.1741 (ttt) REVERT: D 988 ASP cc_start: 0.0042 (OUTLIER) cc_final: -0.0333 (p0) REVERT: D 1012 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7968 (p90) REVERT: D 1173 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7796 (mm-30) REVERT: D 1378 MET cc_start: 0.7736 (mmt) cc_final: 0.5964 (tpt) outliers start: 50 outliers final: 12 residues processed: 677 average time/residue: 0.2366 time to fit residues: 264.4934 Evaluate side-chains 456 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 439 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 189 GLN A 200 GLN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 479 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 562 ASN A 584 HIS A 967 GLN A1035 ASN B 81 ASN B 106 GLN B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 HIS B 511 HIS B 566 ASN B 584 HIS B 880 GLN B 983 ASN B1013 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1243 ASN C 97 ASN C 173 ASN C 177 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 HIS C1009 ASN C1035 ASN C1074 GLN D 132 GLN D 177 GLN D 182 GLN D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 HIS D 938 ASN D1051 GLN D1062 HIS D1159 ASN D1259 HIS D1331 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.154729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.126968 restraints weight = 199382.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.130483 restraints weight = 138869.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.132997 restraints weight = 103596.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.134826 restraints weight = 81644.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.136359 restraints weight = 67079.840| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 42463 Z= 0.207 Angle : 1.001 15.545 57794 Z= 0.499 Chirality : 0.056 0.506 6686 Planarity : 0.007 0.086 7358 Dihedral : 11.042 66.225 6502 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.92 % Favored : 84.81 % Rotamer: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.09), residues: 5220 helix: -2.28 (0.15), residues: 797 sheet: -3.22 (0.13), residues: 1167 loop : -4.12 (0.08), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1073 TYR 0.027 0.003 TYR D1007 PHE 0.044 0.003 PHE A 980 TRP 0.027 0.003 TRP A1132 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00455 (42374) covalent geometry : angle 0.98212 (57572) SS BOND : bond 0.00662 ( 45) SS BOND : angle 2.11113 ( 90) hydrogen bonds : bond 0.06876 ( 517) hydrogen bonds : angle 6.79673 ( 1551) link_ALPHA1-6 : bond 0.01030 ( 1) link_ALPHA1-6 : angle 1.69345 ( 3) link_BETA1-4 : bond 0.01165 ( 14) link_BETA1-4 : angle 3.63009 ( 42) link_NAG-ASN : bond 0.00900 ( 29) link_NAG-ASN : angle 4.03497 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 598 time to evaluate : 1.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: A 82 ASP cc_start: 0.9368 (m-30) cc_final: 0.8989 (m-30) REVERT: A 121 MET cc_start: 0.8652 (ttt) cc_final: 0.8442 (ttt) REVERT: A 215 THR cc_start: 0.8652 (t) cc_final: 0.8281 (p) REVERT: A 229 PHE cc_start: 0.7134 (p90) cc_final: 0.6587 (p90) REVERT: A 399 THR cc_start: 0.7745 (p) cc_final: 0.7327 (t) REVERT: A 415 MET cc_start: 0.3413 (ttt) cc_final: 0.3104 (ttt) REVERT: A 436 TRP cc_start: 0.6811 (m100) cc_final: 0.5867 (t-100) REVERT: A 440 GLU cc_start: 0.5822 (tt0) cc_final: 0.4958 (mp0) REVERT: A 464 MET cc_start: 0.8748 (ttt) cc_final: 0.8318 (ttt) REVERT: A 481 ILE cc_start: 0.8854 (mp) cc_final: 0.8582 (mp) REVERT: A 530 VAL cc_start: 0.7914 (t) cc_final: 0.7569 (t) REVERT: A 561 GLU cc_start: 0.6938 (tp30) cc_final: 0.6634 (tp30) REVERT: A 567 LYS cc_start: 0.8743 (tttt) cc_final: 0.8235 (mptt) REVERT: A 586 ARG cc_start: 0.7561 (ttt90) cc_final: 0.6882 (mmm-85) REVERT: A 673 MET cc_start: 0.8492 (tpt) cc_final: 0.8026 (tpp) REVERT: A 959 MET cc_start: 0.5982 (mtt) cc_final: 0.5306 (ptt) REVERT: A 1040 TRP cc_start: 0.5448 (t60) cc_final: 0.3780 (t60) REVERT: A 1064 THR cc_start: 0.7763 (m) cc_final: 0.7530 (p) REVERT: A 1136 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 1154 PHE cc_start: 0.5247 (m-80) cc_final: 0.4939 (m-80) REVERT: B 293 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7882 (pp30) REVERT: B 309 PHE cc_start: 0.7309 (m-80) cc_final: 0.6759 (m-80) REVERT: B 325 GLN cc_start: 0.9127 (tt0) cc_final: 0.8767 (tm-30) REVERT: B 461 LEU cc_start: 0.7721 (mp) cc_final: 0.6710 (tp) REVERT: B 479 HIS cc_start: 0.8098 (m170) cc_final: 0.7803 (m-70) REVERT: B 520 MET cc_start: 0.9161 (pmm) cc_final: 0.8699 (ppp) REVERT: B 531 LYS cc_start: 0.7921 (pttm) cc_final: 0.7660 (tttt) REVERT: B 550 ASP cc_start: 0.8647 (t70) cc_final: 0.8328 (m-30) REVERT: B 619 TYR cc_start: 0.6776 (m-10) cc_final: 0.6553 (m-80) REVERT: B 789 PHE cc_start: 0.6222 (t80) cc_final: 0.5872 (t80) REVERT: B 1022 ASP cc_start: 0.8855 (p0) cc_final: 0.8641 (p0) REVERT: B 1258 LEU cc_start: 0.8556 (mt) cc_final: 0.8348 (tp) REVERT: B 1296 ASN cc_start: 0.8701 (t0) cc_final: 0.8465 (t0) REVERT: C 151 MET cc_start: 0.2698 (mmm) cc_final: 0.0870 (mmm) REVERT: C 161 LEU cc_start: 0.5237 (pt) cc_final: 0.4943 (mm) REVERT: C 177 GLN cc_start: 0.7363 (tt0) cc_final: 0.6849 (tm-30) REVERT: C 189 GLN cc_start: 0.7912 (pm20) cc_final: 0.7624 (tm-30) REVERT: C 363 ILE cc_start: 0.8367 (tp) cc_final: 0.8051 (tp) REVERT: C 373 ASP cc_start: 0.7707 (t70) cc_final: 0.7403 (m-30) REVERT: C 418 SER cc_start: 0.9343 (m) cc_final: 0.8949 (p) REVERT: C 464 MET cc_start: 0.7715 (ttm) cc_final: 0.7379 (mtm) REVERT: C 558 TYR cc_start: 0.7084 (m-80) cc_final: 0.6249 (m-80) REVERT: C 569 ASP cc_start: 0.8028 (t0) cc_final: 0.7740 (t70) REVERT: C 1005 ILE cc_start: 0.4938 (mt) cc_final: 0.4591 (mt) REVERT: C 1104 TYR cc_start: 0.5051 (t80) cc_final: 0.3574 (t80) REVERT: C 1126 PHE cc_start: 0.8689 (m-80) cc_final: 0.8382 (m-80) REVERT: C 1136 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8387 (tm-30) REVERT: C 1325 GLN cc_start: 0.9073 (tt0) cc_final: 0.8753 (tt0) REVERT: C 1328 LEU cc_start: 0.7878 (tp) cc_final: 0.7466 (tp) REVERT: D 117 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6920 (ptt180) REVERT: D 130 PHE cc_start: 0.9154 (p90) cc_final: 0.8833 (p90) REVERT: D 149 VAL cc_start: 0.5850 (t) cc_final: 0.5273 (t) REVERT: D 181 PHE cc_start: 0.6330 (p90) cc_final: 0.5869 (p90) REVERT: D 286 PHE cc_start: 0.8136 (m-80) cc_final: 0.7697 (m-80) REVERT: D 446 HIS cc_start: 0.5814 (t70) cc_final: 0.5555 (t-90) REVERT: D 449 TYR cc_start: 0.6617 (m-80) cc_final: 0.5872 (m-80) REVERT: D 491 LYS cc_start: 0.9315 (ptpp) cc_final: 0.8866 (ttmm) REVERT: D 554 ASP cc_start: 0.8490 (p0) cc_final: 0.8000 (p0) REVERT: D 567 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8902 (tptp) REVERT: D 853 ARG cc_start: 0.9183 (tmm160) cc_final: 0.8980 (mmt-90) REVERT: D 968 MET cc_start: -0.1463 (tpt) cc_final: -0.2002 (ttt) REVERT: D 1007 TYR cc_start: 0.6699 (m-80) cc_final: 0.5866 (t80) REVERT: D 1173 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7589 (mm-30) REVERT: D 1378 MET cc_start: 0.7653 (mmt) cc_final: 0.6113 (tpt) outliers start: 22 outliers final: 5 residues processed: 620 average time/residue: 0.2324 time to fit residues: 240.1793 Evaluate side-chains 439 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 432 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 301 optimal weight: 0.0870 chunk 152 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 502 optimal weight: 9.9990 chunk 465 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 413 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 290 optimal weight: 7.9990 overall best weight: 3.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 694 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 HIS ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1242 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 413 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 HIS C1074 GLN ** C1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN C1243 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN D 635 ASN D 647 ASN D 747 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.152195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.124048 restraints weight = 199928.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.128050 restraints weight = 150942.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.130113 restraints weight = 108170.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.131765 restraints weight = 83802.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.132446 restraints weight = 71607.120| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 42463 Z= 0.222 Angle : 0.957 11.836 57794 Z= 0.481 Chirality : 0.055 0.449 6686 Planarity : 0.007 0.080 7358 Dihedral : 9.803 59.664 6502 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.73 % Favored : 84.08 % Rotamer: Outliers : 0.22 % Allowed : 8.19 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.10), residues: 5220 helix: -1.89 (0.15), residues: 796 sheet: -2.95 (0.13), residues: 1271 loop : -3.95 (0.09), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B1163 TYR 0.034 0.003 TYR D 619 PHE 0.049 0.003 PHE D1049 TRP 0.030 0.003 TRP B1183 HIS 0.012 0.002 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00486 (42374) covalent geometry : angle 0.94056 (57572) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.84913 ( 90) hydrogen bonds : bond 0.06795 ( 517) hydrogen bonds : angle 6.73694 ( 1551) link_ALPHA1-6 : bond 0.00635 ( 1) link_ALPHA1-6 : angle 1.43088 ( 3) link_BETA1-4 : bond 0.00881 ( 14) link_BETA1-4 : angle 2.96586 ( 42) link_NAG-ASN : bond 0.00832 ( 29) link_NAG-ASN : angle 3.85244 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 553 time to evaluate : 1.541 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 82 ASP cc_start: 0.9507 (m-30) cc_final: 0.8848 (m-30) REVERT: A 121 MET cc_start: 0.8951 (ttt) cc_final: 0.8634 (ttt) REVERT: A 209 LYS cc_start: 0.7625 (mttt) cc_final: 0.7177 (mttt) REVERT: A 215 THR cc_start: 0.8719 (t) cc_final: 0.8332 (p) REVERT: A 229 PHE cc_start: 0.7240 (p90) cc_final: 0.6669 (p90) REVERT: A 237 LYS cc_start: 0.8894 (tppt) cc_final: 0.8331 (tppt) REVERT: A 436 TRP cc_start: 0.6821 (m100) cc_final: 0.5729 (t-100) REVERT: A 440 GLU cc_start: 0.5679 (tt0) cc_final: 0.4531 (mp0) REVERT: A 464 MET cc_start: 0.8729 (ttt) cc_final: 0.8362 (ttt) REVERT: A 520 MET cc_start: 0.6615 (mmt) cc_final: 0.6163 (mmt) REVERT: A 530 VAL cc_start: 0.8219 (t) cc_final: 0.7864 (t) REVERT: A 567 LYS cc_start: 0.8834 (tttt) cc_final: 0.8481 (mptt) REVERT: A 586 ARG cc_start: 0.7900 (ttt90) cc_final: 0.6941 (mmm-85) REVERT: A 597 LEU cc_start: 0.6193 (mp) cc_final: 0.5845 (mp) REVERT: A 959 MET cc_start: 0.6075 (mtt) cc_final: 0.5649 (ptt) REVERT: A 1112 ILE cc_start: 0.7706 (mt) cc_final: 0.7486 (mt) REVERT: A 1133 LYS cc_start: 0.9012 (tptt) cc_final: 0.8787 (tptp) REVERT: A 1136 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 1154 PHE cc_start: 0.5339 (m-80) cc_final: 0.5052 (m-80) REVERT: A 1259 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.4723 (m90) REVERT: A 1263 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8426 (mmmt) REVERT: B 256 TYR cc_start: 0.8569 (t80) cc_final: 0.8146 (t80) REVERT: B 409 ILE cc_start: 0.7700 (mp) cc_final: 0.7055 (tp) REVERT: B 461 LEU cc_start: 0.7938 (mp) cc_final: 0.7229 (tp) REVERT: B 500 MET cc_start: 0.6492 (tmm) cc_final: 0.5968 (ttt) REVERT: B 531 LYS cc_start: 0.8072 (pttm) cc_final: 0.7791 (tttt) REVERT: B 550 ASP cc_start: 0.8876 (t70) cc_final: 0.8436 (m-30) REVERT: B 619 TYR cc_start: 0.7192 (m-10) cc_final: 0.6572 (m-80) REVERT: B 627 LEU cc_start: 0.7865 (tp) cc_final: 0.7643 (mt) REVERT: B 666 MET cc_start: 0.6816 (ttp) cc_final: 0.6522 (ptm) REVERT: B 789 PHE cc_start: 0.6414 (t80) cc_final: 0.6113 (t80) REVERT: B 977 MET cc_start: 0.8948 (mmp) cc_final: 0.8706 (mmp) REVERT: B 1328 LEU cc_start: 0.9526 (tp) cc_final: 0.8972 (tp) REVERT: C 101 MET cc_start: 0.7600 (mpp) cc_final: 0.7275 (mpp) REVERT: C 189 GLN cc_start: 0.8041 (pm20) cc_final: 0.7700 (tm-30) REVERT: C 363 ILE cc_start: 0.8526 (tp) cc_final: 0.8186 (tp) REVERT: C 373 ASP cc_start: 0.7727 (t70) cc_final: 0.7372 (m-30) REVERT: C 418 SER cc_start: 0.9327 (m) cc_final: 0.9003 (p) REVERT: C 569 ASP cc_start: 0.8280 (t0) cc_final: 0.8007 (t70) REVERT: C 666 MET cc_start: 0.8458 (tpp) cc_final: 0.7732 (tpt) REVERT: C 667 TYR cc_start: 0.8824 (t80) cc_final: 0.8421 (t80) REVERT: C 1042 THR cc_start: 0.2510 (p) cc_final: 0.2134 (t) REVERT: C 1104 TYR cc_start: 0.5298 (t80) cc_final: 0.3772 (t80) REVERT: C 1126 PHE cc_start: 0.8799 (m-80) cc_final: 0.8466 (m-80) REVERT: C 1325 GLN cc_start: 0.9172 (tt0) cc_final: 0.8841 (tt0) REVERT: D 121 MET cc_start: 0.9045 (tmm) cc_final: 0.8719 (tmm) REVERT: D 181 PHE cc_start: 0.6279 (p90) cc_final: 0.5672 (p90) REVERT: D 214 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7598 (ttt90) REVERT: D 286 PHE cc_start: 0.8446 (m-80) cc_final: 0.8210 (m-80) REVERT: D 358 HIS cc_start: 0.7300 (p-80) cc_final: 0.6963 (p-80) REVERT: D 385 PHE cc_start: 0.8302 (m-10) cc_final: 0.7836 (m-10) REVERT: D 387 ARG cc_start: 0.9218 (mmp80) cc_final: 0.8978 (mmp80) REVERT: D 446 HIS cc_start: 0.6213 (t70) cc_final: 0.5991 (t-90) REVERT: D 449 TYR cc_start: 0.6825 (m-80) cc_final: 0.6082 (m-80) REVERT: D 546 LEU cc_start: 0.6858 (tp) cc_final: 0.6470 (tp) REVERT: D 550 ASP cc_start: 0.8076 (t0) cc_final: 0.7641 (t0) REVERT: D 567 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8890 (tptp) REVERT: D 662 ASN cc_start: 0.9265 (p0) cc_final: 0.8918 (p0) REVERT: D 968 MET cc_start: -0.1621 (tpt) cc_final: -0.2216 (ttt) REVERT: D 1007 TYR cc_start: 0.6872 (m-80) cc_final: 0.5979 (t80) REVERT: D 1173 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7539 (mm-30) REVERT: D 1378 MET cc_start: 0.7668 (mmt) cc_final: 0.5912 (tpt) outliers start: 10 outliers final: 2 residues processed: 561 average time/residue: 0.2387 time to fit residues: 221.4527 Evaluate side-chains 436 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 433 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 396 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 412 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 chunk 479 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 365 optimal weight: 0.4980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 ASN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 ASN C1241 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.148178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.116686 restraints weight = 197944.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.119871 restraints weight = 145577.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.121543 restraints weight = 118469.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.123805 restraints weight = 91828.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.124672 restraints weight = 75003.561| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 42463 Z= 0.228 Angle : 0.960 13.552 57794 Z= 0.483 Chirality : 0.055 0.411 6686 Planarity : 0.007 0.136 7358 Dihedral : 9.288 59.822 6502 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.69 % Favored : 84.12 % Rotamer: Outliers : 0.13 % Allowed : 7.41 % Favored : 92.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.10), residues: 5220 helix: -1.86 (0.16), residues: 805 sheet: -2.84 (0.14), residues: 1252 loop : -3.79 (0.09), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 117 TYR 0.032 0.003 TYR A 619 PHE 0.055 0.003 PHE D1049 TRP 0.030 0.003 TRP C1132 HIS 0.012 0.002 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00497 (42374) covalent geometry : angle 0.94565 (57572) SS BOND : bond 0.00604 ( 45) SS BOND : angle 1.95451 ( 90) hydrogen bonds : bond 0.06623 ( 517) hydrogen bonds : angle 6.68890 ( 1551) link_ALPHA1-6 : bond 0.00644 ( 1) link_ALPHA1-6 : angle 1.72452 ( 3) link_BETA1-4 : bond 0.00549 ( 14) link_BETA1-4 : angle 2.62536 ( 42) link_NAG-ASN : bond 0.00745 ( 29) link_NAG-ASN : angle 3.55291 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 532 time to evaluate : 1.574 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 63 SER cc_start: 0.7272 (t) cc_final: 0.6974 (p) REVERT: A 215 THR cc_start: 0.8974 (t) cc_final: 0.8734 (t) REVERT: A 229 PHE cc_start: 0.7398 (p90) cc_final: 0.6366 (p90) REVERT: A 237 LYS cc_start: 0.8886 (tppt) cc_final: 0.8354 (tppt) REVERT: A 310 GLN cc_start: 0.8680 (tp40) cc_final: 0.8462 (tp-100) REVERT: A 415 MET cc_start: 0.4267 (ttt) cc_final: 0.3803 (ttt) REVERT: A 436 TRP cc_start: 0.7119 (m100) cc_final: 0.6874 (m100) REVERT: A 464 MET cc_start: 0.8709 (ttt) cc_final: 0.8324 (ttt) REVERT: A 481 ILE cc_start: 0.8984 (mp) cc_final: 0.8554 (mp) REVERT: A 519 ASP cc_start: 0.8910 (t0) cc_final: 0.8600 (t70) REVERT: A 520 MET cc_start: 0.7259 (mmt) cc_final: 0.6608 (mmt) REVERT: A 567 LYS cc_start: 0.8916 (tttt) cc_final: 0.8663 (mptt) REVERT: A 597 LEU cc_start: 0.6768 (mp) cc_final: 0.6324 (mp) REVERT: A 931 LEU cc_start: 0.8669 (tp) cc_final: 0.7829 (tp) REVERT: A 959 MET cc_start: 0.6463 (mtt) cc_final: 0.5994 (ptt) REVERT: A 1122 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8451 (mmm160) REVERT: A 1133 LYS cc_start: 0.9032 (tptt) cc_final: 0.8699 (tptp) REVERT: A 1263 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8337 (mmmt) REVERT: A 1299 LEU cc_start: 0.8954 (mp) cc_final: 0.8279 (mp) REVERT: B 30 GLN cc_start: 0.6897 (mp10) cc_final: 0.6142 (mp10) REVERT: B 256 TYR cc_start: 0.8470 (t80) cc_final: 0.8057 (t80) REVERT: B 385 PHE cc_start: 0.7715 (m-80) cc_final: 0.7378 (m-80) REVERT: B 415 MET cc_start: 0.0419 (ttp) cc_final: -0.0247 (tpt) REVERT: B 461 LEU cc_start: 0.8173 (mp) cc_final: 0.7581 (tp) REVERT: B 500 MET cc_start: 0.6744 (tmm) cc_final: 0.6178 (ttt) REVERT: B 531 LYS cc_start: 0.8146 (pttm) cc_final: 0.7815 (tttt) REVERT: B 550 ASP cc_start: 0.9078 (t70) cc_final: 0.8561 (m-30) REVERT: B 571 SER cc_start: 0.7997 (t) cc_final: 0.7395 (t) REVERT: B 586 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6387 (mtp85) REVERT: B 619 TYR cc_start: 0.7365 (m-10) cc_final: 0.6659 (m-80) REVERT: B 977 MET cc_start: 0.9036 (mmp) cc_final: 0.8745 (mmp) REVERT: B 1184 GLU cc_start: 0.6533 (pt0) cc_final: 0.6152 (pt0) REVERT: B 1328 LEU cc_start: 0.9603 (tp) cc_final: 0.9179 (tp) REVERT: C 203 TYR cc_start: 0.7811 (m-80) cc_final: 0.7515 (m-80) REVERT: C 363 ILE cc_start: 0.8562 (tp) cc_final: 0.8307 (tp) REVERT: C 373 ASP cc_start: 0.7767 (t70) cc_final: 0.7467 (m-30) REVERT: C 569 ASP cc_start: 0.8378 (t0) cc_final: 0.8133 (t70) REVERT: C 787 ARG cc_start: 0.6346 (mtp180) cc_final: 0.5733 (ttm170) REVERT: C 977 MET cc_start: 0.5766 (ptt) cc_final: 0.5485 (ptt) REVERT: C 1005 ILE cc_start: 0.4586 (mt) cc_final: 0.4362 (mt) REVERT: C 1042 THR cc_start: 0.3007 (p) cc_final: 0.2586 (t) REVERT: C 1104 TYR cc_start: 0.5453 (t80) cc_final: 0.3894 (t80) REVERT: C 1123 ASN cc_start: 0.8395 (m-40) cc_final: 0.8038 (m110) REVERT: C 1126 PHE cc_start: 0.8963 (m-80) cc_final: 0.8601 (m-80) REVERT: C 1325 GLN cc_start: 0.9259 (tt0) cc_final: 0.9003 (tt0) REVERT: D 181 PHE cc_start: 0.6369 (p90) cc_final: 0.5843 (p90) REVERT: D 214 ARG cc_start: 0.8449 (mtp-110) cc_final: 0.7941 (ttt90) REVERT: D 321 HIS cc_start: 0.9584 (p90) cc_final: 0.9097 (p-80) REVERT: D 358 HIS cc_start: 0.7617 (p-80) cc_final: 0.7246 (p-80) REVERT: D 359 PHE cc_start: 0.7750 (p90) cc_final: 0.7539 (p90) REVERT: D 446 HIS cc_start: 0.6328 (t70) cc_final: 0.6127 (t70) REVERT: D 449 TYR cc_start: 0.7254 (m-80) cc_final: 0.6705 (m-80) REVERT: D 546 LEU cc_start: 0.7058 (tp) cc_final: 0.6674 (tp) REVERT: D 567 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8848 (tptp) REVERT: D 662 ASN cc_start: 0.9338 (p0) cc_final: 0.8919 (p0) REVERT: D 959 MET cc_start: 0.7884 (ppp) cc_final: 0.7558 (ppp) REVERT: D 961 ASN cc_start: 0.7481 (t0) cc_final: 0.7063 (m-40) REVERT: D 968 MET cc_start: -0.1908 (tpt) cc_final: -0.2368 (ttt) REVERT: D 1007 TYR cc_start: 0.6983 (m-80) cc_final: 0.6029 (t80) REVERT: D 1378 MET cc_start: 0.7820 (mmt) cc_final: 0.6027 (tpp) outliers start: 6 outliers final: 2 residues processed: 538 average time/residue: 0.2385 time to fit residues: 211.8094 Evaluate side-chains 413 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 411 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 372 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 389 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 513 optimal weight: 40.0000 chunk 369 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN C 483 ASN C 592 GLN ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 747 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1277 GLN D1358 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.128290 restraints weight = 196708.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.131720 restraints weight = 132470.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.134071 restraints weight = 96785.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.136001 restraints weight = 75106.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.137219 restraints weight = 60747.472| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 42463 Z= 0.160 Angle : 0.862 16.756 57794 Z= 0.428 Chirality : 0.051 0.456 6686 Planarity : 0.006 0.145 7358 Dihedral : 8.725 59.467 6502 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.03 % Favored : 86.82 % Rotamer: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.10), residues: 5220 helix: -1.31 (0.17), residues: 807 sheet: -2.64 (0.14), residues: 1311 loop : -3.62 (0.09), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 684 TYR 0.044 0.002 TYR C1152 PHE 0.063 0.002 PHE B1049 TRP 0.020 0.002 TRP C1132 HIS 0.011 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00352 (42374) covalent geometry : angle 0.84504 (57572) SS BOND : bond 0.00403 ( 45) SS BOND : angle 2.24243 ( 90) hydrogen bonds : bond 0.06018 ( 517) hydrogen bonds : angle 6.23829 ( 1551) link_ALPHA1-6 : bond 0.00467 ( 1) link_ALPHA1-6 : angle 1.53871 ( 3) link_BETA1-4 : bond 0.00542 ( 14) link_BETA1-4 : angle 2.59775 ( 42) link_NAG-ASN : bond 0.00700 ( 29) link_NAG-ASN : angle 3.47589 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 577 time to evaluate : 1.403 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.7231 (t) cc_final: 0.6897 (p) REVERT: A 121 MET cc_start: 0.8916 (ttt) cc_final: 0.8527 (tmm) REVERT: A 215 THR cc_start: 0.8851 (t) cc_final: 0.8410 (p) REVERT: A 229 PHE cc_start: 0.7214 (p90) cc_final: 0.6333 (p90) REVERT: A 237 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8461 (tppt) REVERT: A 384 ILE cc_start: 0.9379 (pt) cc_final: 0.8961 (mm) REVERT: A 436 TRP cc_start: 0.6475 (m100) cc_final: 0.5529 (t-100) REVERT: A 464 MET cc_start: 0.8683 (ttt) cc_final: 0.8385 (ttt) REVERT: A 481 ILE cc_start: 0.8964 (mp) cc_final: 0.8587 (mp) REVERT: A 530 VAL cc_start: 0.7839 (t) cc_final: 0.7567 (t) REVERT: A 567 LYS cc_start: 0.8834 (tttt) cc_final: 0.8538 (mptt) REVERT: A 914 THR cc_start: 0.9059 (m) cc_final: 0.8844 (m) REVERT: A 916 PHE cc_start: 0.8846 (t80) cc_final: 0.8201 (t80) REVERT: A 931 LEU cc_start: 0.8007 (tp) cc_final: 0.7769 (tp) REVERT: A 959 MET cc_start: 0.6175 (mtt) cc_final: 0.5694 (ptt) REVERT: A 1112 ILE cc_start: 0.7798 (mt) cc_final: 0.7568 (mt) REVERT: A 1122 ARG cc_start: 0.8741 (mtp180) cc_final: 0.8406 (mmm160) REVERT: A 1133 LYS cc_start: 0.9109 (tptt) cc_final: 0.8622 (tptp) REVERT: A 1263 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8337 (mmmt) REVERT: A 1280 ILE cc_start: 0.8214 (mp) cc_final: 0.7735 (mp) REVERT: A 1305 LEU cc_start: 0.6870 (mp) cc_final: 0.6622 (tp) REVERT: A 1314 MET cc_start: 0.8358 (mpp) cc_final: 0.7743 (mpp) REVERT: B 256 TYR cc_start: 0.8289 (t80) cc_final: 0.7846 (t80) REVERT: B 385 PHE cc_start: 0.7679 (m-80) cc_final: 0.7302 (m-80) REVERT: B 415 MET cc_start: 0.0421 (ttp) cc_final: -0.0425 (tpt) REVERT: B 461 LEU cc_start: 0.8128 (mp) cc_final: 0.7359 (tp) REVERT: B 464 MET cc_start: 0.8712 (tmm) cc_final: 0.8448 (tmm) REVERT: B 531 LYS cc_start: 0.8047 (pttm) cc_final: 0.7746 (tttt) REVERT: B 550 ASP cc_start: 0.8666 (t70) cc_final: 0.8419 (t70) REVERT: B 586 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6279 (mtp85) REVERT: B 619 TYR cc_start: 0.7085 (m-10) cc_final: 0.6436 (m-80) REVERT: B 739 TRP cc_start: 0.8101 (t60) cc_final: 0.6519 (t60) REVERT: B 1012 TYR cc_start: 0.7628 (t80) cc_final: 0.7427 (t80) REVERT: B 1040 TRP cc_start: 0.6549 (t60) cc_final: 0.6235 (t60) REVERT: B 1041 LEU cc_start: 0.9399 (tp) cc_final: 0.9153 (tp) REVERT: B 1172 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 1184 GLU cc_start: 0.6230 (pt0) cc_final: 0.5790 (pt0) REVERT: C 101 MET cc_start: 0.7545 (mpp) cc_final: 0.7280 (mpp) REVERT: C 363 ILE cc_start: 0.8244 (tp) cc_final: 0.8027 (tp) REVERT: C 945 ARG cc_start: 0.7738 (tmt170) cc_final: 0.7175 (ttt180) REVERT: C 1042 THR cc_start: 0.1598 (p) cc_final: 0.0942 (t) REVERT: C 1104 TYR cc_start: 0.5176 (t80) cc_final: 0.3837 (t80) REVERT: C 1126 PHE cc_start: 0.8849 (m-80) cc_final: 0.8484 (m-80) REVERT: D 151 MET cc_start: 0.5394 (ttm) cc_final: 0.4872 (tpp) REVERT: D 181 PHE cc_start: 0.6241 (p90) cc_final: 0.5691 (p90) REVERT: D 288 GLU cc_start: 0.8282 (mp0) cc_final: 0.8006 (mp0) REVERT: D 358 HIS cc_start: 0.7484 (p-80) cc_final: 0.7198 (p-80) REVERT: D 385 PHE cc_start: 0.8180 (m-80) cc_final: 0.7530 (m-80) REVERT: D 387 ARG cc_start: 0.9316 (mmp80) cc_final: 0.8987 (mmp80) REVERT: D 415 MET cc_start: 0.6233 (mmp) cc_final: 0.5643 (mmp) REVERT: D 449 TYR cc_start: 0.6585 (m-80) cc_final: 0.6172 (m-80) REVERT: D 464 MET cc_start: 0.8001 (ptt) cc_final: 0.7791 (ptt) REVERT: D 491 LYS cc_start: 0.9243 (ptpp) cc_final: 0.8866 (ttmm) REVERT: D 531 LYS cc_start: 0.7360 (pttp) cc_final: 0.7028 (pttp) REVERT: D 546 LEU cc_start: 0.7505 (tp) cc_final: 0.7094 (tp) REVERT: D 550 ASP cc_start: 0.7583 (t0) cc_final: 0.7104 (t0) REVERT: D 567 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8682 (tptp) REVERT: D 662 ASN cc_start: 0.9239 (p0) cc_final: 0.8780 (p0) REVERT: D 968 MET cc_start: -0.1581 (tpt) cc_final: -0.2227 (ttt) REVERT: D 1007 TYR cc_start: 0.6743 (m-80) cc_final: 0.5914 (t80) REVERT: D 1378 MET cc_start: 0.7900 (mmt) cc_final: 0.6174 (tpp) REVERT: D 1398 MET cc_start: -0.3553 (ppp) cc_final: -0.3758 (ppp) outliers start: 3 outliers final: 0 residues processed: 579 average time/residue: 0.2375 time to fit residues: 228.1461 Evaluate side-chains 430 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 432 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 340 optimal weight: 0.0050 chunk 224 optimal weight: 2.9990 chunk 413 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 447 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 461 optimal weight: 50.0000 overall best weight: 1.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1242 GLN B1252 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 511 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 HIS ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1143 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.153280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.124936 restraints weight = 199309.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.128035 restraints weight = 143580.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.130306 restraints weight = 110948.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.132055 restraints weight = 89653.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.133321 restraints weight = 75116.636| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 42463 Z= 0.161 Angle : 0.848 14.794 57794 Z= 0.421 Chirality : 0.051 0.344 6686 Planarity : 0.006 0.133 7358 Dihedral : 8.427 59.817 6502 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.47 % Favored : 86.42 % Rotamer: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.10), residues: 5220 helix: -1.13 (0.17), residues: 820 sheet: -2.48 (0.14), residues: 1317 loop : -3.58 (0.09), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 684 TYR 0.062 0.002 TYR A1152 PHE 0.057 0.002 PHE A1196 TRP 0.029 0.002 TRP B 741 HIS 0.009 0.001 HIS B1118 Details of bonding type rmsd covalent geometry : bond 0.00355 (42374) covalent geometry : angle 0.83138 (57572) SS BOND : bond 0.00495 ( 45) SS BOND : angle 2.15776 ( 90) hydrogen bonds : bond 0.05817 ( 517) hydrogen bonds : angle 6.13183 ( 1551) link_ALPHA1-6 : bond 0.00467 ( 1) link_ALPHA1-6 : angle 1.48006 ( 3) link_BETA1-4 : bond 0.00579 ( 14) link_BETA1-4 : angle 2.44187 ( 42) link_NAG-ASN : bond 0.00672 ( 29) link_NAG-ASN : angle 3.48400 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 555 time to evaluate : 1.464 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: 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 63 SER cc_start: 0.7204 (t) cc_final: 0.6857 (p) REVERT: A 82 ASP cc_start: 0.9402 (m-30) cc_final: 0.9063 (m-30) REVERT: A 126 ASP cc_start: 0.7825 (p0) cc_final: 0.7544 (p0) REVERT: A 179 GLN cc_start: 0.6117 (tm-30) cc_final: 0.5701 (tm-30) REVERT: A 215 THR cc_start: 0.8863 (t) cc_final: 0.8487 (p) REVERT: A 229 PHE cc_start: 0.7644 (p90) cc_final: 0.7291 (p90) REVERT: A 237 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8605 (tppt) REVERT: A 384 ILE cc_start: 0.9424 (pt) cc_final: 0.8995 (mm) REVERT: A 399 THR cc_start: 0.8017 (p) cc_final: 0.7527 (t) REVERT: A 436 TRP cc_start: 0.6851 (m100) cc_final: 0.5595 (t-100) REVERT: A 464 MET cc_start: 0.8676 (ttt) cc_final: 0.8346 (ttt) REVERT: A 530 VAL cc_start: 0.8064 (t) cc_final: 0.7795 (t) REVERT: A 567 LYS cc_start: 0.8865 (tttt) cc_final: 0.8600 (mptt) REVERT: A 916 PHE cc_start: 0.8964 (t80) cc_final: 0.8298 (t80) REVERT: A 931 LEU cc_start: 0.8329 (tp) cc_final: 0.7926 (tp) REVERT: A 959 MET cc_start: 0.6327 (mtt) cc_final: 0.5769 (ptt) REVERT: A 1112 ILE cc_start: 0.7959 (mt) cc_final: 0.7734 (mt) REVERT: A 1122 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8516 (mmm160) REVERT: A 1133 LYS cc_start: 0.9169 (tptt) cc_final: 0.8668 (tppt) REVERT: A 1216 TYR cc_start: 0.8330 (m-80) cc_final: 0.8062 (m-80) REVERT: B 142 GLN cc_start: 0.8759 (pm20) cc_final: 0.8268 (pm20) REVERT: B 256 TYR cc_start: 0.8402 (t80) cc_final: 0.7877 (t80) REVERT: B 348 THR cc_start: 0.8203 (m) cc_final: 0.7548 (p) REVERT: B 385 PHE cc_start: 0.7776 (m-80) cc_final: 0.7411 (m-80) REVERT: B 415 MET cc_start: 0.0393 (ttp) cc_final: -0.0217 (tpt) REVERT: B 461 LEU cc_start: 0.8483 (mp) cc_final: 0.7905 (tp) REVERT: B 531 LYS cc_start: 0.8099 (pttm) cc_final: 0.7884 (tttt) REVERT: B 586 ARG cc_start: 0.7046 (mtp85) cc_final: 0.6372 (mtp85) REVERT: B 619 TYR cc_start: 0.7198 (m-10) cc_final: 0.6512 (m-80) REVERT: B 977 MET cc_start: 0.8875 (mmp) cc_final: 0.8627 (mmp) REVERT: B 1012 TYR cc_start: 0.7748 (t80) cc_final: 0.7403 (t80) REVERT: B 1132 TRP cc_start: 0.8474 (t60) cc_final: 0.7939 (t60) REVERT: B 1172 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8550 (tm-30) REVERT: B 1183 TRP cc_start: 0.7902 (m-90) cc_final: 0.7321 (m-90) REVERT: B 1184 GLU cc_start: 0.6404 (pt0) cc_final: 0.6171 (pt0) REVERT: B 1290 PHE cc_start: 0.8486 (m-10) cc_final: 0.8114 (m-10) REVERT: B 1328 LEU cc_start: 0.9552 (tp) cc_final: 0.8877 (tp) REVERT: C 207 VAL cc_start: 0.8417 (m) cc_final: 0.8087 (t) REVERT: C 319 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7406 (mmmt) REVERT: C 323 GLU cc_start: 0.8929 (mp0) cc_final: 0.8669 (mp0) REVERT: C 363 ILE cc_start: 0.8303 (tp) cc_final: 0.8100 (tp) REVERT: C 460 HIS cc_start: 0.8159 (t-90) cc_final: 0.7919 (t-90) REVERT: C 464 MET cc_start: 0.7994 (mtm) cc_final: 0.7196 (ttp) REVERT: C 539 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7761 (ttp80) REVERT: C 666 MET cc_start: 0.8419 (tpp) cc_final: 0.8112 (tpt) REVERT: C 945 ARG cc_start: 0.7865 (tmt170) cc_final: 0.7410 (ttt180) REVERT: C 968 MET cc_start: 0.5028 (mmt) cc_final: 0.4507 (mmt) REVERT: C 1042 THR cc_start: 0.2062 (p) cc_final: 0.1360 (t) REVERT: C 1104 TYR cc_start: 0.5290 (t80) cc_final: 0.3973 (t80) REVERT: C 1126 PHE cc_start: 0.8713 (m-80) cc_final: 0.8448 (m-80) REVERT: D 151 MET cc_start: 0.5310 (ttm) cc_final: 0.4850 (tpp) REVERT: D 181 PHE cc_start: 0.6336 (p90) cc_final: 0.5775 (p90) REVERT: D 214 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.7548 (ttt90) REVERT: D 246 MET cc_start: -0.0752 (ttm) cc_final: -0.1172 (mtt) REVERT: D 385 PHE cc_start: 0.8301 (m-80) cc_final: 0.7659 (m-80) REVERT: D 387 ARG cc_start: 0.9296 (mmp80) cc_final: 0.8966 (mmp80) REVERT: D 415 MET cc_start: 0.6286 (mmp) cc_final: 0.5609 (mmp) REVERT: D 449 TYR cc_start: 0.6773 (m-80) cc_final: 0.6295 (m-80) REVERT: D 491 LYS cc_start: 0.9295 (ptpp) cc_final: 0.8923 (ttmm) REVERT: D 500 MET cc_start: 0.2323 (mmm) cc_final: 0.1556 (mmm) REVERT: D 531 LYS cc_start: 0.7719 (pttp) cc_final: 0.7382 (pttp) REVERT: D 546 LEU cc_start: 0.7519 (tp) cc_final: 0.7112 (tp) REVERT: D 550 ASP cc_start: 0.7781 (t0) cc_final: 0.7175 (t0) REVERT: D 567 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8733 (tptp) REVERT: D 662 ASN cc_start: 0.9278 (p0) cc_final: 0.8852 (p0) REVERT: D 963 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 968 MET cc_start: -0.1833 (tpt) cc_final: -0.2434 (ttt) REVERT: D 1007 TYR cc_start: 0.6748 (m-80) cc_final: 0.5845 (t80) REVERT: D 1378 MET cc_start: 0.7906 (mmt) cc_final: 0.6347 (tpp) outliers start: 2 outliers final: 0 residues processed: 557 average time/residue: 0.2364 time to fit residues: 216.9294 Evaluate side-chains 421 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 263 optimal weight: 0.7980 chunk 447 optimal weight: 10.0000 chunk 412 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 chunk 466 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 441 optimal weight: 4.9990 chunk 480 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 HIS C 651 ASN ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 ASN C1302 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN D 680 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.152958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.124380 restraints weight = 196194.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.128474 restraints weight = 149934.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.130173 restraints weight = 108989.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.132112 restraints weight = 86273.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.133201 restraints weight = 71608.351| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 42463 Z= 0.161 Angle : 0.838 14.225 57794 Z= 0.416 Chirality : 0.051 0.433 6686 Planarity : 0.006 0.092 7358 Dihedral : 8.260 59.879 6502 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.97 % Favored : 86.92 % Rotamer: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.10), residues: 5220 helix: -1.04 (0.17), residues: 826 sheet: -2.37 (0.14), residues: 1326 loop : -3.48 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1122 TYR 0.042 0.002 TYR A1152 PHE 0.038 0.002 PHE B1126 TRP 0.017 0.002 TRP C1237 HIS 0.011 0.001 HIS A1259 Details of bonding type rmsd covalent geometry : bond 0.00356 (42374) covalent geometry : angle 0.82353 (57572) SS BOND : bond 0.00453 ( 45) SS BOND : angle 2.04765 ( 90) hydrogen bonds : bond 0.05743 ( 517) hydrogen bonds : angle 6.07320 ( 1551) link_ALPHA1-6 : bond 0.00447 ( 1) link_ALPHA1-6 : angle 1.46444 ( 3) link_BETA1-4 : bond 0.00582 ( 14) link_BETA1-4 : angle 2.40490 ( 42) link_NAG-ASN : bond 0.00633 ( 29) link_NAG-ASN : angle 3.30519 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 538 time to evaluate : 1.516 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.7228 (t) cc_final: 0.6925 (p) REVERT: A 82 ASP cc_start: 0.9366 (m-30) cc_final: 0.9006 (m-30) REVERT: A 215 THR cc_start: 0.8781 (t) cc_final: 0.8416 (p) REVERT: A 229 PHE cc_start: 0.7609 (p90) cc_final: 0.7285 (p90) REVERT: A 237 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8611 (tppt) REVERT: A 245 GLU cc_start: 0.8901 (mp0) cc_final: 0.8579 (mp0) REVERT: A 246 MET cc_start: -0.2854 (mmm) cc_final: -0.3123 (mmt) REVERT: A 316 TYR cc_start: 0.3877 (m-10) cc_final: 0.2559 (t80) REVERT: A 384 ILE cc_start: 0.9387 (pt) cc_final: 0.8993 (mm) REVERT: A 399 THR cc_start: 0.7930 (p) cc_final: 0.7449 (t) REVERT: A 415 MET cc_start: 0.2955 (ttt) cc_final: 0.2550 (ttt) REVERT: A 436 TRP cc_start: 0.6747 (m100) cc_final: 0.6424 (m100) REVERT: A 464 MET cc_start: 0.8690 (ttt) cc_final: 0.8334 (ttt) REVERT: A 530 VAL cc_start: 0.8115 (t) cc_final: 0.7848 (t) REVERT: A 567 LYS cc_start: 0.8853 (tttt) cc_final: 0.8552 (mptt) REVERT: A 916 PHE cc_start: 0.8977 (t80) cc_final: 0.8347 (t80) REVERT: A 931 LEU cc_start: 0.8440 (tp) cc_final: 0.8176 (tp) REVERT: A 959 MET cc_start: 0.6204 (mtt) cc_final: 0.5663 (ptt) REVERT: A 1112 ILE cc_start: 0.7883 (mt) cc_final: 0.7642 (mt) REVERT: A 1122 ARG cc_start: 0.8773 (mtp180) cc_final: 0.8495 (mmm160) REVERT: A 1133 LYS cc_start: 0.9174 (tptt) cc_final: 0.8856 (mmmt) REVERT: A 1154 PHE cc_start: 0.5703 (m-80) cc_final: 0.5401 (m-80) REVERT: A 1216 TYR cc_start: 0.8390 (m-80) cc_final: 0.8127 (m-10) REVERT: A 1280 ILE cc_start: 0.8342 (mp) cc_final: 0.7822 (mp) REVERT: A 1314 MET cc_start: 0.8352 (mpp) cc_final: 0.7809 (mpp) REVERT: B 142 GLN cc_start: 0.8763 (pm20) cc_final: 0.8283 (pm20) REVERT: B 255 THR cc_start: 0.9286 (p) cc_final: 0.9022 (p) REVERT: B 385 PHE cc_start: 0.7730 (m-80) cc_final: 0.7382 (m-80) REVERT: B 393 TYR cc_start: 0.8590 (t80) cc_final: 0.8143 (t80) REVERT: B 415 MET cc_start: 0.0442 (ttp) cc_final: -0.0127 (tpt) REVERT: B 461 LEU cc_start: 0.8544 (mp) cc_final: 0.7961 (tp) REVERT: B 557 LYS cc_start: 0.9287 (mppt) cc_final: 0.9033 (mmtm) REVERT: B 558 TYR cc_start: 0.8059 (m-80) cc_final: 0.7689 (m-80) REVERT: B 619 TYR cc_start: 0.7178 (m-10) cc_final: 0.6532 (m-80) REVERT: B 808 PHE cc_start: 0.8515 (p90) cc_final: 0.8189 (p90) REVERT: B 1012 TYR cc_start: 0.7836 (t80) cc_final: 0.7455 (t80) REVERT: B 1132 TRP cc_start: 0.8459 (t60) cc_final: 0.7967 (t60) REVERT: B 1183 TRP cc_start: 0.8228 (m-90) cc_final: 0.7532 (m-90) REVERT: B 1184 GLU cc_start: 0.6578 (pt0) cc_final: 0.6342 (pt0) REVERT: C 207 VAL cc_start: 0.8428 (m) cc_final: 0.8139 (t) REVERT: C 319 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7481 (mmmt) REVERT: C 323 GLU cc_start: 0.8937 (mp0) cc_final: 0.8655 (mp0) REVERT: C 363 ILE cc_start: 0.8302 (tp) cc_final: 0.8092 (tp) REVERT: C 460 HIS cc_start: 0.8209 (t-90) cc_final: 0.7933 (t-90) REVERT: C 464 MET cc_start: 0.7992 (mtm) cc_final: 0.7408 (tmm) REVERT: C 539 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7775 (ttp80) REVERT: C 666 MET cc_start: 0.8393 (tpp) cc_final: 0.7979 (tpt) REVERT: C 683 ILE cc_start: 0.7387 (tp) cc_final: 0.7030 (mp) REVERT: C 945 ARG cc_start: 0.7912 (tmt170) cc_final: 0.7518 (ttt180) REVERT: C 1042 THR cc_start: 0.2264 (p) cc_final: 0.1613 (t) REVERT: C 1104 TYR cc_start: 0.5296 (t80) cc_final: 0.3928 (t80) REVERT: C 1123 ASN cc_start: 0.8319 (m-40) cc_final: 0.8104 (m110) REVERT: C 1126 PHE cc_start: 0.8779 (m-80) cc_final: 0.8496 (m-80) REVERT: C 1136 GLN cc_start: 0.8625 (pp30) cc_final: 0.8229 (pp30) REVERT: C 1208 MET cc_start: 0.8145 (ppp) cc_final: 0.7801 (ppp) REVERT: D 151 MET cc_start: 0.5219 (ttm) cc_final: 0.4760 (tpp) REVERT: D 181 PHE cc_start: 0.6315 (p90) cc_final: 0.5775 (p90) REVERT: D 214 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.7579 (ttt90) REVERT: D 385 PHE cc_start: 0.8359 (m-80) cc_final: 0.7706 (m-80) REVERT: D 387 ARG cc_start: 0.9262 (mmp80) cc_final: 0.8927 (mmp80) REVERT: D 449 TYR cc_start: 0.6567 (m-80) cc_final: 0.6176 (m-80) REVERT: D 491 LYS cc_start: 0.9306 (ptpp) cc_final: 0.8938 (ttmm) REVERT: D 500 MET cc_start: 0.2563 (mmm) cc_final: 0.1914 (mmm) REVERT: D 531 LYS cc_start: 0.7884 (pttp) cc_final: 0.7537 (pttp) REVERT: D 546 LEU cc_start: 0.7554 (tp) cc_final: 0.7142 (tp) REVERT: D 550 ASP cc_start: 0.7999 (t0) cc_final: 0.7499 (t0) REVERT: D 567 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8679 (tptp) REVERT: D 662 ASN cc_start: 0.9212 (p0) cc_final: 0.8751 (p0) REVERT: D 916 PHE cc_start: 0.8444 (m-80) cc_final: 0.8218 (m-80) REVERT: D 963 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7285 (tt0) REVERT: D 968 MET cc_start: -0.2034 (tpt) cc_final: -0.2709 (ttt) REVERT: D 1007 TYR cc_start: 0.6636 (m-80) cc_final: 0.5760 (t80) REVERT: D 1378 MET cc_start: 0.7689 (mmt) cc_final: 0.6152 (tpp) outliers start: 2 outliers final: 0 residues processed: 540 average time/residue: 0.2369 time to fit residues: 211.6907 Evaluate side-chains 416 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 328 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 466 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN D 112 GLN D 132 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.149361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.116994 restraints weight = 192664.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.120249 restraints weight = 137157.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.122771 restraints weight = 105868.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.124616 restraints weight = 86385.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.125786 restraints weight = 73435.072| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 42463 Z= 0.181 Angle : 0.855 16.850 57794 Z= 0.424 Chirality : 0.051 0.368 6686 Planarity : 0.006 0.132 7358 Dihedral : 8.276 59.987 6502 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.79 % Favored : 86.11 % Rotamer: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.10), residues: 5220 helix: -1.10 (0.17), residues: 822 sheet: -2.42 (0.13), residues: 1357 loop : -3.47 (0.10), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1163 TYR 0.050 0.002 TYR A1152 PHE 0.034 0.002 PHE B1126 TRP 0.020 0.002 TRP A 765 HIS 0.013 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00401 (42374) covalent geometry : angle 0.84034 (57572) SS BOND : bond 0.00543 ( 45) SS BOND : angle 2.03456 ( 90) hydrogen bonds : bond 0.05797 ( 517) hydrogen bonds : angle 6.20999 ( 1551) link_ALPHA1-6 : bond 0.00437 ( 1) link_ALPHA1-6 : angle 1.47735 ( 3) link_BETA1-4 : bond 0.00593 ( 14) link_BETA1-4 : angle 2.41268 ( 42) link_NAG-ASN : bond 0.00664 ( 29) link_NAG-ASN : angle 3.28180 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 1.387 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.7242 (t) cc_final: 0.6965 (p) REVERT: A 82 ASP cc_start: 0.9363 (m-30) cc_final: 0.8965 (m-30) REVERT: A 215 THR cc_start: 0.8686 (t) cc_final: 0.8309 (p) REVERT: A 229 PHE cc_start: 0.7392 (p90) cc_final: 0.7162 (p90) REVERT: A 310 GLN cc_start: 0.9016 (tp40) cc_final: 0.8788 (tp40) REVERT: A 316 TYR cc_start: 0.3616 (m-10) cc_final: 0.1808 (t80) REVERT: A 436 TRP cc_start: 0.7006 (m100) cc_final: 0.6611 (m100) REVERT: A 464 MET cc_start: 0.8674 (ttt) cc_final: 0.8333 (ttt) REVERT: A 530 VAL cc_start: 0.8046 (t) cc_final: 0.7768 (t) REVERT: A 567 LYS cc_start: 0.8903 (tttt) cc_final: 0.8641 (mptt) REVERT: A 669 PHE cc_start: 0.8265 (m-80) cc_final: 0.8064 (m-80) REVERT: A 916 PHE cc_start: 0.8968 (t80) cc_final: 0.8345 (t80) REVERT: A 931 LEU cc_start: 0.8281 (tp) cc_final: 0.7918 (tp) REVERT: A 959 MET cc_start: 0.6264 (mtt) cc_final: 0.5666 (ptt) REVERT: A 1112 ILE cc_start: 0.7945 (mt) cc_final: 0.7704 (mt) REVERT: A 1133 LYS cc_start: 0.9181 (tptt) cc_final: 0.8579 (tppt) REVERT: A 1216 TYR cc_start: 0.8484 (m-80) cc_final: 0.8269 (m-10) REVERT: A 1314 MET cc_start: 0.8157 (mpp) cc_final: 0.7757 (mpp) REVERT: B 142 GLN cc_start: 0.8750 (pm20) cc_final: 0.8179 (pm20) REVERT: B 256 TYR cc_start: 0.8353 (t80) cc_final: 0.7990 (t80) REVERT: B 385 PHE cc_start: 0.7823 (m-80) cc_final: 0.7491 (m-80) REVERT: B 409 ILE cc_start: 0.7541 (mp) cc_final: 0.6665 (tp) REVERT: B 415 MET cc_start: 0.0753 (ttp) cc_final: 0.0131 (tpt) REVERT: B 461 LEU cc_start: 0.8629 (mp) cc_final: 0.8008 (tp) REVERT: B 500 MET cc_start: 0.6643 (tmm) cc_final: 0.5729 (ttt) REVERT: B 619 TYR cc_start: 0.7253 (m-10) cc_final: 0.6612 (m-80) REVERT: B 977 MET cc_start: 0.8879 (mmp) cc_final: 0.8670 (mmp) REVERT: B 1132 TRP cc_start: 0.8328 (t60) cc_final: 0.7826 (t60) REVERT: B 1183 TRP cc_start: 0.7896 (m-90) cc_final: 0.7318 (m-90) REVERT: B 1328 LEU cc_start: 0.9643 (tp) cc_final: 0.8952 (tp) REVERT: C 323 GLU cc_start: 0.8999 (mp0) cc_final: 0.8732 (mp0) REVERT: C 460 HIS cc_start: 0.8375 (t-90) cc_final: 0.8114 (t-90) REVERT: C 464 MET cc_start: 0.8157 (mtm) cc_final: 0.7455 (tmm) REVERT: C 539 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7719 (ttp80) REVERT: C 584 HIS cc_start: 0.8661 (t-90) cc_final: 0.8222 (t70) REVERT: C 945 ARG cc_start: 0.7990 (tmt170) cc_final: 0.6784 (ttt180) REVERT: C 1042 THR cc_start: 0.2578 (p) cc_final: 0.1929 (t) REVERT: C 1123 ASN cc_start: 0.8319 (m-40) cc_final: 0.8111 (m110) REVERT: C 1126 PHE cc_start: 0.8706 (m-80) cc_final: 0.8470 (m-80) REVERT: C 1136 GLN cc_start: 0.8606 (pp30) cc_final: 0.8143 (pp30) REVERT: C 1325 GLN cc_start: 0.9023 (tt0) cc_final: 0.8747 (tt0) REVERT: D 181 PHE cc_start: 0.6550 (p90) cc_final: 0.5976 (p90) REVERT: D 246 MET cc_start: -0.0982 (ttm) cc_final: -0.1551 (mtm) REVERT: D 359 PHE cc_start: 0.7651 (p90) cc_final: 0.7436 (p90) REVERT: D 385 PHE cc_start: 0.8293 (m-80) cc_final: 0.7609 (m-80) REVERT: D 387 ARG cc_start: 0.9250 (mmp80) cc_final: 0.8945 (mmp80) REVERT: D 415 MET cc_start: 0.6467 (mmp) cc_final: 0.5842 (mmp) REVERT: D 449 TYR cc_start: 0.6910 (m-80) cc_final: 0.6463 (m-80) REVERT: D 491 LYS cc_start: 0.9319 (ptpp) cc_final: 0.8948 (ttmm) REVERT: D 546 LEU cc_start: 0.7604 (tp) cc_final: 0.7181 (tp) REVERT: D 550 ASP cc_start: 0.7981 (t0) cc_final: 0.7338 (t0) REVERT: D 662 ASN cc_start: 0.9243 (p0) cc_final: 0.8840 (p0) REVERT: D 968 MET cc_start: -0.2217 (tpt) cc_final: -0.2881 (ttt) REVERT: D 1007 TYR cc_start: 0.6585 (m-80) cc_final: 0.5750 (t80) REVERT: D 1378 MET cc_start: 0.7805 (mmt) cc_final: 0.6795 (tpt) outliers start: 3 outliers final: 0 residues processed: 517 average time/residue: 0.2423 time to fit residues: 209.6707 Evaluate side-chains 410 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 168 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 447 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 119 optimal weight: 0.0000 chunk 49 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 189 GLN C 402 HIS C 483 ASN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 132 GLN D 321 HIS ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN ** D 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.119707 restraints weight = 190772.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.124048 restraints weight = 136977.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.127400 restraints weight = 96278.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.128199 restraints weight = 74644.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.128806 restraints weight = 64875.073| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 42463 Z= 0.156 Angle : 0.830 13.873 57794 Z= 0.411 Chirality : 0.050 0.365 6686 Planarity : 0.006 0.146 7358 Dihedral : 8.146 59.614 6502 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.89 % Favored : 86.99 % Rotamer: Outliers : 0.04 % Allowed : 1.22 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.10), residues: 5220 helix: -0.95 (0.17), residues: 819 sheet: -2.37 (0.13), residues: 1394 loop : -3.40 (0.10), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 117 TYR 0.055 0.002 TYR A1152 PHE 0.035 0.002 PHE B1126 TRP 0.037 0.002 TRP B1237 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00346 (42374) covalent geometry : angle 0.81567 (57572) SS BOND : bond 0.00342 ( 45) SS BOND : angle 2.02960 ( 90) hydrogen bonds : bond 0.05614 ( 517) hydrogen bonds : angle 6.05071 ( 1551) link_ALPHA1-6 : bond 0.00447 ( 1) link_ALPHA1-6 : angle 1.45784 ( 3) link_BETA1-4 : bond 0.00611 ( 14) link_BETA1-4 : angle 2.37695 ( 42) link_NAG-ASN : bond 0.00624 ( 29) link_NAG-ASN : angle 3.28833 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 519 time to evaluate : 1.497 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.7209 (t) cc_final: 0.6965 (p) REVERT: A 82 ASP cc_start: 0.9298 (m-30) cc_final: 0.8964 (m-30) REVERT: A 215 THR cc_start: 0.8717 (t) cc_final: 0.8404 (p) REVERT: A 229 PHE cc_start: 0.7559 (p90) cc_final: 0.7112 (p90) REVERT: A 245 GLU cc_start: 0.8947 (mp0) cc_final: 0.8617 (mp0) REVERT: A 316 TYR cc_start: 0.3631 (m-10) cc_final: 0.2240 (t80) REVERT: A 436 TRP cc_start: 0.6746 (m100) cc_final: 0.6381 (m100) REVERT: A 464 MET cc_start: 0.8667 (ttt) cc_final: 0.8320 (ttt) REVERT: A 491 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8641 (tppt) REVERT: A 530 VAL cc_start: 0.7974 (t) cc_final: 0.7683 (t) REVERT: A 567 LYS cc_start: 0.8857 (tttt) cc_final: 0.8614 (mptt) REVERT: A 669 PHE cc_start: 0.8122 (m-80) cc_final: 0.7904 (m-80) REVERT: A 900 ILE cc_start: 0.7642 (tt) cc_final: 0.7020 (tt) REVERT: A 901 LYS cc_start: 0.9384 (mppt) cc_final: 0.8799 (tptt) REVERT: A 916 PHE cc_start: 0.8875 (t80) cc_final: 0.8216 (t80) REVERT: A 931 LEU cc_start: 0.8249 (tp) cc_final: 0.7911 (tp) REVERT: A 959 MET cc_start: 0.6116 (mtt) cc_final: 0.5572 (ptt) REVERT: A 1112 ILE cc_start: 0.7894 (mt) cc_final: 0.7645 (mt) REVERT: A 1133 LYS cc_start: 0.8984 (tptt) cc_final: 0.8583 (tppt) REVERT: A 1216 TYR cc_start: 0.8437 (m-80) cc_final: 0.8222 (m-10) REVERT: A 1263 LYS cc_start: 0.8584 (mmmt) cc_final: 0.7662 (tttt) REVERT: A 1314 MET cc_start: 0.8100 (mpp) cc_final: 0.7651 (mpp) REVERT: B 142 GLN cc_start: 0.8647 (pm20) cc_final: 0.8090 (pm20) REVERT: B 164 LEU cc_start: 0.8037 (tp) cc_final: 0.7737 (tp) REVERT: B 363 ILE cc_start: 0.8739 (tp) cc_final: 0.7798 (tp) REVERT: B 385 PHE cc_start: 0.7759 (m-80) cc_final: 0.7445 (m-80) REVERT: B 393 TYR cc_start: 0.8591 (t80) cc_final: 0.8278 (t80) REVERT: B 409 ILE cc_start: 0.7506 (mp) cc_final: 0.6691 (tp) REVERT: B 415 MET cc_start: 0.0817 (ttp) cc_final: 0.0239 (tpt) REVERT: B 461 LEU cc_start: 0.8683 (mp) cc_final: 0.8127 (tp) REVERT: B 500 MET cc_start: 0.6519 (tmm) cc_final: 0.5673 (ttt) REVERT: B 619 TYR cc_start: 0.7162 (m-10) cc_final: 0.6282 (m-80) REVERT: B 1132 TRP cc_start: 0.8352 (t60) cc_final: 0.7929 (t60) REVERT: B 1183 TRP cc_start: 0.8065 (m-90) cc_final: 0.7483 (m-90) REVERT: C 323 GLU cc_start: 0.9062 (mp0) cc_final: 0.8799 (mp0) REVERT: C 460 HIS cc_start: 0.8347 (t-90) cc_final: 0.8075 (t-90) REVERT: C 464 MET cc_start: 0.8218 (mtm) cc_final: 0.7551 (tmm) REVERT: C 539 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7679 (ttp80) REVERT: C 584 HIS cc_start: 0.8677 (t-90) cc_final: 0.8243 (t70) REVERT: C 666 MET cc_start: 0.8429 (tpp) cc_final: 0.8077 (tpt) REVERT: C 683 ILE cc_start: 0.7543 (tp) cc_final: 0.7209 (mp) REVERT: C 945 ARG cc_start: 0.7944 (tmt170) cc_final: 0.6806 (ttt180) REVERT: C 1042 THR cc_start: 0.2050 (p) cc_final: 0.1336 (t) REVERT: C 1123 ASN cc_start: 0.8213 (m-40) cc_final: 0.8004 (m110) REVERT: C 1126 PHE cc_start: 0.8685 (m-80) cc_final: 0.8444 (m-80) REVERT: C 1136 GLN cc_start: 0.8570 (pp30) cc_final: 0.8124 (pp30) REVERT: C 1208 MET cc_start: 0.7977 (ppp) cc_final: 0.7627 (ppp) REVERT: D 181 PHE cc_start: 0.6556 (p90) cc_final: 0.5972 (p90) REVERT: D 320 LEU cc_start: 0.8181 (mm) cc_final: 0.7952 (mm) REVERT: D 385 PHE cc_start: 0.8325 (m-80) cc_final: 0.7638 (m-80) REVERT: D 387 ARG cc_start: 0.9226 (mmp80) cc_final: 0.8899 (mmp80) REVERT: D 415 MET cc_start: 0.6366 (mmp) cc_final: 0.5718 (mmp) REVERT: D 491 LYS cc_start: 0.9301 (ptpp) cc_final: 0.8927 (ttmm) REVERT: D 531 LYS cc_start: 0.7891 (pttm) cc_final: 0.7543 (mmtt) REVERT: D 546 LEU cc_start: 0.7536 (tp) cc_final: 0.7069 (tp) REVERT: D 550 ASP cc_start: 0.8089 (t0) cc_final: 0.7446 (t0) REVERT: D 567 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8690 (tptp) REVERT: D 662 ASN cc_start: 0.9169 (p0) cc_final: 0.8768 (p0) REVERT: D 968 MET cc_start: -0.2103 (tpt) cc_final: -0.2821 (ttt) REVERT: D 1007 TYR cc_start: 0.6641 (m-80) cc_final: 0.5901 (t80) REVERT: D 1378 MET cc_start: 0.7594 (mmt) cc_final: 0.6125 (tpt) outliers start: 2 outliers final: 0 residues processed: 520 average time/residue: 0.2330 time to fit residues: 201.8229 Evaluate side-chains 418 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 90 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 487 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 480 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 344 optimal weight: 0.3980 chunk 351 optimal weight: 7.9990 chunk 507 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 483 ASN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS D 112 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 846 HIS ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.144701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.117017 restraints weight = 195984.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.119333 restraints weight = 146342.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.122142 restraints weight = 116875.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.123404 restraints weight = 83281.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.123950 restraints weight = 74691.153| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 42463 Z= 0.237 Angle : 0.950 13.765 57794 Z= 0.475 Chirality : 0.054 0.396 6686 Planarity : 0.007 0.133 7358 Dihedral : 8.489 59.619 6502 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.88 % Favored : 83.98 % Rotamer: Outliers : 0.02 % Allowed : 0.68 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.10), residues: 5220 helix: -1.47 (0.16), residues: 826 sheet: -2.55 (0.13), residues: 1357 loop : -3.49 (0.10), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C1163 TYR 0.055 0.003 TYR A1152 PHE 0.030 0.003 PHE C1049 TRP 0.037 0.003 TRP B 739 HIS 0.019 0.002 HIS D 846 Details of bonding type rmsd covalent geometry : bond 0.00521 (42374) covalent geometry : angle 0.93588 (57572) SS BOND : bond 0.00392 ( 45) SS BOND : angle 2.23822 ( 90) hydrogen bonds : bond 0.06273 ( 517) hydrogen bonds : angle 6.51141 ( 1551) link_ALPHA1-6 : bond 0.00432 ( 1) link_ALPHA1-6 : angle 1.45732 ( 3) link_BETA1-4 : bond 0.00571 ( 14) link_BETA1-4 : angle 2.49116 ( 42) link_NAG-ASN : bond 0.00820 ( 29) link_NAG-ASN : angle 3.45953 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 505 time to evaluate : 1.001 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: symmetry clash REVERT: A 63 SER cc_start: 0.7296 (t) cc_final: 0.7052 (p) REVERT: A 209 LYS cc_start: 0.8779 (mttm) cc_final: 0.7549 (mttm) REVERT: A 215 THR cc_start: 0.8990 (t) cc_final: 0.8757 (t) REVERT: A 229 PHE cc_start: 0.7659 (p90) cc_final: 0.7230 (p90) REVERT: A 415 MET cc_start: 0.4185 (ttt) cc_final: 0.3890 (ttt) REVERT: A 436 TRP cc_start: 0.7151 (m100) cc_final: 0.5488 (t-100) REVERT: A 464 MET cc_start: 0.8697 (ttt) cc_final: 0.8483 (ttt) REVERT: A 490 LEU cc_start: 0.8700 (mp) cc_final: 0.8438 (tt) REVERT: A 491 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8717 (tppt) REVERT: A 530 VAL cc_start: 0.8281 (t) cc_final: 0.8027 (t) REVERT: A 666 MET cc_start: 0.8927 (ppp) cc_final: 0.8563 (ppp) REVERT: A 916 PHE cc_start: 0.9009 (t80) cc_final: 0.8256 (t80) REVERT: A 931 LEU cc_start: 0.8632 (tp) cc_final: 0.8239 (tp) REVERT: A 959 MET cc_start: 0.6279 (mtt) cc_final: 0.5634 (ptt) REVERT: A 1133 LYS cc_start: 0.9124 (tptt) cc_final: 0.8508 (tptt) REVERT: A 1211 TYR cc_start: 0.6762 (m-80) cc_final: 0.6297 (m-80) REVERT: A 1216 TYR cc_start: 0.8661 (m-80) cc_final: 0.8271 (m-80) REVERT: A 1314 MET cc_start: 0.8155 (mpp) cc_final: 0.7774 (mpp) REVERT: A 1328 LEU cc_start: 0.9362 (tp) cc_final: 0.9119 (tp) REVERT: B 164 LEU cc_start: 0.8427 (tp) cc_final: 0.8168 (tp) REVERT: B 363 ILE cc_start: 0.8866 (tp) cc_final: 0.7873 (tp) REVERT: B 385 PHE cc_start: 0.7792 (m-80) cc_final: 0.7465 (m-80) REVERT: B 409 ILE cc_start: 0.7744 (mp) cc_final: 0.6842 (tp) REVERT: B 415 MET cc_start: 0.1018 (ttp) cc_final: 0.0210 (tpt) REVERT: B 460 HIS cc_start: 0.8052 (m90) cc_final: 0.7539 (m90) REVERT: B 461 LEU cc_start: 0.9102 (mp) cc_final: 0.8815 (tp) REVERT: B 545 VAL cc_start: 0.8043 (m) cc_final: 0.7830 (t) REVERT: B 586 ARG cc_start: 0.7357 (mtp85) cc_final: 0.6978 (mtp85) REVERT: B 619 TYR cc_start: 0.7552 (m-10) cc_final: 0.7320 (m-80) REVERT: B 977 MET cc_start: 0.8915 (mmp) cc_final: 0.8617 (mmp) REVERT: B 1183 TRP cc_start: 0.8034 (m-90) cc_final: 0.7412 (m-90) REVERT: B 1254 THR cc_start: 0.7407 (m) cc_final: 0.7194 (m) REVERT: B 1290 PHE cc_start: 0.8565 (m-10) cc_final: 0.8360 (m-10) REVERT: B 1328 LEU cc_start: 0.9660 (tp) cc_final: 0.9183 (tp) REVERT: C 101 MET cc_start: 0.7662 (mpp) cc_final: 0.7392 (mpp) REVERT: C 191 SER cc_start: 0.7991 (p) cc_final: 0.7788 (t) REVERT: C 203 TYR cc_start: 0.7953 (m-80) cc_final: 0.7742 (m-80) REVERT: C 323 GLU cc_start: 0.8977 (mp0) cc_final: 0.8669 (mp0) REVERT: C 460 HIS cc_start: 0.8481 (t-90) cc_final: 0.8278 (t-90) REVERT: C 464 MET cc_start: 0.8203 (mtm) cc_final: 0.7586 (tmm) REVERT: C 517 GLN cc_start: 0.5938 (tp-100) cc_final: 0.5529 (tp-100) REVERT: C 539 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7659 (ttp80) REVERT: C 584 HIS cc_start: 0.8769 (t-90) cc_final: 0.8347 (t70) REVERT: C 666 MET cc_start: 0.8562 (tpp) cc_final: 0.8251 (tpt) REVERT: C 787 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5694 (ttm170) REVERT: C 945 ARG cc_start: 0.8096 (tmt170) cc_final: 0.6860 (ttt-90) REVERT: C 1028 PHE cc_start: 0.8803 (m-10) cc_final: 0.8225 (m-10) REVERT: C 1042 THR cc_start: 0.3362 (p) cc_final: 0.2924 (t) REVERT: C 1123 ASN cc_start: 0.8783 (m-40) cc_final: 0.8523 (m110) REVERT: C 1126 PHE cc_start: 0.8919 (m-80) cc_final: 0.8625 (m-80) REVERT: C 1136 GLN cc_start: 0.8622 (pp30) cc_final: 0.8025 (pp30) REVERT: C 1208 MET cc_start: 0.8136 (ppp) cc_final: 0.7774 (ppp) REVERT: C 1325 GLN cc_start: 0.8972 (tt0) cc_final: 0.8699 (tt0) REVERT: D 181 PHE cc_start: 0.6404 (p90) cc_final: 0.5839 (p90) REVERT: D 320 LEU cc_start: 0.8346 (mm) cc_final: 0.8006 (mm) REVERT: D 407 PHE cc_start: 0.8279 (p90) cc_final: 0.8062 (p90) REVERT: D 415 MET cc_start: 0.6413 (mmp) cc_final: 0.5851 (mmp) REVERT: D 446 HIS cc_start: 0.6447 (t70) cc_final: 0.6184 (t-170) REVERT: D 500 MET cc_start: 0.2691 (mmm) cc_final: 0.2041 (mtt) REVERT: D 531 LYS cc_start: 0.8131 (pttm) cc_final: 0.7823 (mmtt) REVERT: D 546 LEU cc_start: 0.7792 (tp) cc_final: 0.7387 (tp) REVERT: D 550 ASP cc_start: 0.8173 (t0) cc_final: 0.7525 (t0) REVERT: D 567 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8843 (tptp) REVERT: D 662 ASN cc_start: 0.9173 (p0) cc_final: 0.8832 (p0) REVERT: D 916 PHE cc_start: 0.8188 (m-80) cc_final: 0.7945 (m-80) REVERT: D 968 MET cc_start: -0.1856 (tpt) cc_final: -0.2629 (ttt) REVERT: D 1007 TYR cc_start: 0.6564 (m-80) cc_final: 0.5780 (t80) REVERT: D 1378 MET cc_start: 0.7707 (mmt) cc_final: 0.6268 (tpt) outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.2335 time to fit residues: 195.5969 Evaluate side-chains 401 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 365 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 chunk 518 optimal weight: 3.9990 chunk 480 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 474 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 378 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1242 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 189 GLN C 483 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 389 ASN ** D 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.151526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.126710 restraints weight = 196408.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.130064 restraints weight = 133066.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.132461 restraints weight = 97765.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.134170 restraints weight = 75955.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.135599 restraints weight = 61712.639| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 42463 Z= 0.147 Angle : 0.833 13.588 57794 Z= 0.411 Chirality : 0.050 0.339 6686 Planarity : 0.006 0.122 7358 Dihedral : 8.084 59.881 6502 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.05 % Favored : 87.82 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.11), residues: 5220 helix: -0.94 (0.17), residues: 821 sheet: -2.31 (0.14), residues: 1362 loop : -3.37 (0.10), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 117 TYR 0.047 0.002 TYR A1152 PHE 0.049 0.002 PHE D1049 TRP 0.029 0.002 TRP B1237 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00328 (42374) covalent geometry : angle 0.81773 (57572) SS BOND : bond 0.00383 ( 45) SS BOND : angle 1.97671 ( 90) hydrogen bonds : bond 0.05583 ( 517) hydrogen bonds : angle 6.07778 ( 1551) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.44190 ( 3) link_BETA1-4 : bond 0.00588 ( 14) link_BETA1-4 : angle 2.43963 ( 42) link_NAG-ASN : bond 0.00612 ( 29) link_NAG-ASN : angle 3.30396 ( 87) =============================================================================== Job complete usr+sys time: 9532.82 seconds wall clock time: 165 minutes 17.99 seconds (9917.99 seconds total)