Starting phenix.real_space_refine on Tue Jul 7 00:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7s_12755/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.cif" model { file = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7s_12755/07_2026/7o7s_12755.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 9.69, per 1000 atoms: 0.23 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: 3.85 Conformation dependent library (CDL) restraints added in 1.9 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: 0.87 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: 5.45 Time building geometry restraints manager: 5.03 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 - 17.93: 21638 17.93 - 35.87: 2962 35.87 - 53.80: 537 53.80 - 71.73: 105 71.73 - 89.66: 55 Dihedral angle restraints: 25297 sinusoidal: 10041 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 25294 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 34.630 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 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 : 16.803 89.663 15336 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/Z covalent geometry : bond 0.00902 / 0.45 (42374) covalent geometry : angle 1.28156 / 0.72 (57572) SS BOND : bond 0.00665 / 0.34 ( 45) SS BOND : angle 1.96681 / 1.26 ( 90) hydrogen bonds : bond 0.10685 / 7.28 ( 517) hydrogen bonds : angle 7.70536 / 5.12 ( 1551) link_ALPHA1-6 : bond 0.00082 / 0.04 ( 1) link_ALPHA1-6 : angle 0.63283 / 0.32 ( 3) link_BETA1-4 : bond 0.00661 / 0.52 ( 14) link_BETA1-4 : angle 2.48570 / 1.61 ( 42) link_NAG-ASN : bond 0.00443 / 0.27 ( 29) link_NAG-ASN : angle 3.40551 / 2.34 ( 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 : 1.009 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: 0.2398 time to fit residues: 267.6688 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 : 1.110 ------------------------------------------------------------------------------- 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... 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 445 HIS 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 ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 106 GLN ** B 132 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 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 = 0.4857 r_free = 0.4857 target = 0.154822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.127025 restraints weight = 199246.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.130471 restraints weight = 138790.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.133089 restraints weight = 104143.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.134946 restraints weight = 81580.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.136357 restraints weight = 67234.120| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.2379 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= 0.204 Angle : 0.999 14.620 57794 Z= 0.498 Chirality : 0.056 0.556 6686 Planarity : 0.007 0.085 7358 Dihedral : 8.621 38.439 5590 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.56 % Favored : 85.19 % Rotamer: Outliers : 0.50 % Allowed : 9.57 % Favored : 89.93 % 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: -5.19 (0.09), residues: 5220 helix: -2.25 (0.15), residues: 797 sheet: -3.16 (0.13), residues: 1181 loop : -4.11 (0.09), residues: 3242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1073 TYR 0.028 0.003 TYR D1007 PHE 0.043 0.003 PHE A 980 TRP 0.028 0.003 TRP A1132 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (42374) covalent geometry : angle 0.98234 / 0.49 (57572) SS BOND : bond 0.00636 / 0.32 ( 45) SS BOND : angle 2.08284 / 1.26 ( 90) hydrogen bonds : bond 0.06810 / 4.63 ( 517) hydrogen bonds : angle 6.78247 / 4.56 ( 1551) link_ALPHA1-6 : bond 0.01031 / 0.54 ( 1) link_ALPHA1-6 : angle 1.41498 / 0.79 ( 3) link_BETA1-4 : bond 0.01236 / 0.83 ( 14) link_BETA1-4 : angle 3.08257 / 1.90 ( 42) link_NAG-ASN : bond 0.00949 / 0.65 ( 29) link_NAG-ASN : angle 3.87992 / 2.71 ( 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 623 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 600 time to evaluate : 1.501 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: A 80 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: A 82 ASP cc_start: 0.9357 (m-30) cc_final: 0.8973 (m-30) REVERT: A 121 MET cc_start: 0.8653 (ttt) cc_final: 0.8440 (ttt) REVERT: A 215 THR cc_start: 0.8633 (t) cc_final: 0.8298 (p) REVERT: A 229 PHE cc_start: 0.7163 (p90) cc_final: 0.6607 (p90) REVERT: A 399 THR cc_start: 0.7740 (p) cc_final: 0.7326 (t) REVERT: A 415 MET cc_start: 0.3389 (ttt) cc_final: 0.3082 (ttt) REVERT: A 436 TRP cc_start: 0.6827 (m100) cc_final: 0.5919 (t-100) REVERT: A 440 GLU cc_start: 0.5805 (tt0) cc_final: 0.4946 (mp0) REVERT: A 464 MET cc_start: 0.8744 (ttt) cc_final: 0.8302 (ttt) REVERT: A 481 ILE cc_start: 0.8859 (mp) cc_final: 0.8581 (mp) REVERT: A 530 VAL cc_start: 0.7942 (t) cc_final: 0.7605 (t) REVERT: A 567 LYS cc_start: 0.8746 (tttt) cc_final: 0.8291 (mptt) REVERT: A 586 ARG cc_start: 0.7604 (ttt90) cc_final: 0.6926 (mmm-85) REVERT: A 597 LEU cc_start: 0.6091 (mp) cc_final: 0.5878 (mp) REVERT: A 673 MET cc_start: 0.8505 (tpt) cc_final: 0.8057 (tpp) REVERT: A 933 LEU cc_start: 0.8357 (mt) cc_final: 0.8119 (mp) REVERT: A 959 MET cc_start: 0.5942 (mtt) cc_final: 0.5237 (ptt) REVERT: A 995 GLN cc_start: 0.3233 (tt0) cc_final: 0.3023 (mt0) REVERT: A 1040 TRP cc_start: 0.5473 (t60) cc_final: 0.3766 (t60) REVERT: A 1064 THR cc_start: 0.7739 (m) cc_final: 0.7512 (p) REVERT: A 1136 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 1154 PHE cc_start: 0.5177 (m-80) cc_final: 0.4879 (m-80) REVERT: B 293 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7883 (pp30) REVERT: B 309 PHE cc_start: 0.7321 (m-80) cc_final: 0.6769 (m-80) REVERT: B 325 GLN cc_start: 0.9088 (tt0) cc_final: 0.8744 (tm-30) REVERT: B 461 LEU cc_start: 0.7722 (mp) cc_final: 0.6740 (tp) REVERT: B 479 HIS cc_start: 0.8110 (m170) cc_final: 0.7816 (m-70) REVERT: B 510 THR cc_start: 0.7123 (t) cc_final: 0.6911 (t) REVERT: B 520 MET cc_start: 0.9173 (pmm) cc_final: 0.8708 (ppp) REVERT: B 531 LYS cc_start: 0.7911 (pttm) cc_final: 0.7656 (tttt) REVERT: B 550 ASP cc_start: 0.8662 (t70) cc_final: 0.8338 (m-30) REVERT: B 619 TYR cc_start: 0.6754 (m-10) cc_final: 0.6511 (m-80) REVERT: B 789 PHE cc_start: 0.6257 (t80) cc_final: 0.5916 (t80) REVERT: B 1022 ASP cc_start: 0.8851 (p0) cc_final: 0.8637 (p0) REVERT: B 1258 LEU cc_start: 0.8552 (mt) cc_final: 0.8348 (tp) REVERT: B 1296 ASN cc_start: 0.8698 (t0) cc_final: 0.8461 (t0) REVERT: C 151 MET cc_start: 0.2712 (mmm) cc_final: 0.0830 (mmm) REVERT: C 177 GLN cc_start: 0.7351 (tt0) cc_final: 0.6826 (tm-30) REVERT: C 189 GLN cc_start: 0.7907 (pm20) cc_final: 0.7627 (tm-30) REVERT: C 363 ILE cc_start: 0.8355 (tp) cc_final: 0.8043 (tp) REVERT: C 373 ASP cc_start: 0.7712 (t70) cc_final: 0.7407 (m-30) REVERT: C 418 SER cc_start: 0.9332 (m) cc_final: 0.8935 (p) REVERT: C 464 MET cc_start: 0.7717 (ttm) cc_final: 0.7374 (mtm) REVERT: C 558 TYR cc_start: 0.7068 (m-80) cc_final: 0.6218 (m-80) REVERT: C 569 ASP cc_start: 0.7986 (t0) cc_final: 0.7712 (t70) REVERT: C 1005 ILE cc_start: 0.4905 (mt) cc_final: 0.4566 (mt) REVERT: C 1104 TYR cc_start: 0.5056 (t80) cc_final: 0.3571 (t80) REVERT: C 1126 PHE cc_start: 0.8695 (m-80) cc_final: 0.8379 (m-80) REVERT: C 1325 GLN cc_start: 0.9086 (tt0) cc_final: 0.8759 (tt0) REVERT: C 1328 LEU cc_start: 0.7869 (tp) cc_final: 0.7448 (tp) REVERT: D 117 ARG cc_start: 0.7279 (ptm160) cc_final: 0.6909 (ptt180) REVERT: D 130 PHE cc_start: 0.9154 (p90) cc_final: 0.8826 (p90) REVERT: D 149 VAL cc_start: 0.5836 (t) cc_final: 0.5256 (t) REVERT: D 181 PHE cc_start: 0.6327 (p90) cc_final: 0.5864 (p90) REVERT: D 286 PHE cc_start: 0.8150 (m-80) cc_final: 0.7825 (m-80) REVERT: D 446 HIS cc_start: 0.5826 (t70) cc_final: 0.5571 (t-90) REVERT: D 449 TYR cc_start: 0.6653 (m-80) cc_final: 0.5881 (m-80) REVERT: D 483 ASN cc_start: 0.7475 (m110) cc_final: 0.7178 (p0) REVERT: D 491 LYS cc_start: 0.9317 (ptpp) cc_final: 0.8869 (ttmm) REVERT: D 554 ASP cc_start: 0.8471 (p0) cc_final: 0.8014 (p0) REVERT: D 567 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8893 (tptp) REVERT: D 853 ARG cc_start: 0.9184 (tmm160) cc_final: 0.8979 (mmt-90) REVERT: D 963 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 968 MET cc_start: -0.1467 (tpt) cc_final: -0.2006 (ttt) REVERT: D 1007 TYR cc_start: 0.6734 (m-80) cc_final: 0.5886 (t80) REVERT: D 1173 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 1378 MET cc_start: 0.7648 (mmt) cc_final: 0.6105 (tpt) outliers start: 23 outliers final: 5 residues processed: 623 average time/residue: 0.2268 time to fit residues: 235.2772 Evaluate side-chains 445 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 438 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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: 0.4980 chunk 152 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 502 optimal weight: 8.9990 chunk 465 optimal weight: 50.0000 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN ** 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** A1035 ASN A1259 HIS ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** 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 C 392 ASN C 413 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN C1243 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 217 HIS ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.152362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.124094 restraints weight = 199693.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.127154 restraints weight = 144652.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.129429 restraints weight = 111515.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.131050 restraints weight = 90353.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.132413 restraints weight = 76114.096| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 42463 Z= 0.216 Angle : 0.947 11.702 57794 Z= 0.476 Chirality : 0.054 0.438 6686 Planarity : 0.007 0.081 7358 Dihedral : 8.126 37.122 5590 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.42 % Favored : 84.39 % Rotamer: Outliers : 0.20 % Allowed : 7.12 % Favored : 92.68 % 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: -4.90 (0.10), residues: 5220 helix: -1.94 (0.15), residues: 798 sheet: -2.96 (0.13), residues: 1269 loop : -3.95 (0.09), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1073 TYR 0.034 0.003 TYR D 619 PHE 0.047 0.003 PHE D1049 TRP 0.027 0.003 TRP A 739 HIS 0.012 0.002 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (42374) covalent geometry : angle 0.93311 / 0.47 (57572) SS BOND : bond 0.00474 / 0.26 ( 45) SS BOND : angle 1.97119 / 1.17 ( 90) hydrogen bonds : bond 0.06606 / 4.48 ( 517) hydrogen bonds : angle 6.67075 / 4.47 ( 1551) link_ALPHA1-6 : bond 0.00774 / 0.41 ( 1) link_ALPHA1-6 : angle 1.54348 / 0.85 ( 3) link_BETA1-4 : bond 0.01119 / 0.65 ( 14) link_BETA1-4 : angle 2.45126 / 1.48 ( 42) link_NAG-ASN : bond 0.00746 / 0.49 ( 29) link_NAG-ASN : angle 3.60057 / 2.47 ( 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 560 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 551 time to evaluate : 1.611 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: A 82 ASP cc_start: 0.9543 (m-30) cc_final: 0.8892 (m-30) REVERT: A 121 MET cc_start: 0.8985 (ttt) cc_final: 0.8677 (ttt) REVERT: A 209 LYS cc_start: 0.7679 (mttt) cc_final: 0.7233 (mttt) REVERT: A 215 THR cc_start: 0.8783 (t) cc_final: 0.8361 (p) REVERT: A 229 PHE cc_start: 0.7171 (p90) cc_final: 0.6618 (p90) REVERT: A 237 LYS cc_start: 0.8917 (tppt) cc_final: 0.8342 (tppt) REVERT: A 310 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8590 (tp-100) REVERT: A 436 TRP cc_start: 0.6816 (m100) cc_final: 0.5744 (t-100) REVERT: A 440 GLU cc_start: 0.5721 (tt0) cc_final: 0.4574 (mp0) REVERT: A 464 MET cc_start: 0.8760 (ttt) cc_final: 0.8378 (ttt) REVERT: A 530 VAL cc_start: 0.8194 (t) cc_final: 0.7837 (t) REVERT: A 567 LYS cc_start: 0.8862 (tttt) cc_final: 0.8460 (mptt) REVERT: A 586 ARG cc_start: 0.7880 (ttt90) cc_final: 0.6926 (mmm-85) REVERT: A 597 LEU cc_start: 0.6269 (mp) cc_final: 0.5915 (mp) REVERT: A 933 LEU cc_start: 0.8857 (mt) cc_final: 0.8292 (mp) REVERT: A 959 MET cc_start: 0.6236 (mtt) cc_final: 0.5539 (ptt) REVERT: A 995 GLN cc_start: 0.3643 (tt0) cc_final: 0.3238 (mt0) REVERT: A 1112 ILE cc_start: 0.7760 (mt) cc_final: 0.7553 (mt) REVERT: A 1133 LYS cc_start: 0.9022 (tptt) cc_final: 0.8796 (tptp) REVERT: A 1136 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 1154 PHE cc_start: 0.5431 (m-80) cc_final: 0.5115 (m-80) REVERT: A 1259 HIS cc_start: 0.5265 (OUTLIER) cc_final: 0.4725 (m90) REVERT: A 1263 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8441 (mmmt) REVERT: B 32 MET cc_start: 0.3751 (tmm) cc_final: 0.3530 (tmm) REVERT: B 256 TYR cc_start: 0.8513 (t80) cc_final: 0.8082 (t80) REVERT: B 409 ILE cc_start: 0.7800 (mp) cc_final: 0.7100 (tp) REVERT: B 461 LEU cc_start: 0.7928 (mp) cc_final: 0.7225 (tp) REVERT: B 500 MET cc_start: 0.6448 (tmm) cc_final: 0.5944 (ttt) REVERT: B 531 LYS cc_start: 0.8104 (pttm) cc_final: 0.7809 (tttt) REVERT: B 619 TYR cc_start: 0.7202 (m-10) cc_final: 0.6838 (m-80) REVERT: B 627 LEU cc_start: 0.7878 (tp) cc_final: 0.7636 (mt) REVERT: B 789 PHE cc_start: 0.6349 (t80) cc_final: 0.6041 (t80) REVERT: B 959 MET cc_start: 0.6559 (ttp) cc_final: 0.6289 (ttp) REVERT: B 977 MET cc_start: 0.8990 (mmp) cc_final: 0.8740 (mmp) REVERT: B 1183 TRP cc_start: 0.7606 (m100) cc_final: 0.6946 (m100) REVERT: B 1328 LEU cc_start: 0.9515 (tp) cc_final: 0.8985 (tp) REVERT: C 101 MET cc_start: 0.7635 (mpp) cc_final: 0.7322 (mpp) REVERT: C 189 GLN cc_start: 0.8051 (pm20) cc_final: 0.7686 (tm-30) REVERT: C 363 ILE cc_start: 0.8554 (tp) cc_final: 0.8210 (tp) REVERT: C 373 ASP cc_start: 0.7751 (t70) cc_final: 0.7404 (m-30) REVERT: C 418 SER cc_start: 0.9321 (m) cc_final: 0.8992 (p) REVERT: C 569 ASP cc_start: 0.8287 (t0) cc_final: 0.8009 (t70) REVERT: C 667 TYR cc_start: 0.8883 (t80) cc_final: 0.8528 (t80) REVERT: C 1042 THR cc_start: 0.2590 (p) cc_final: 0.1983 (t) REVERT: C 1104 TYR cc_start: 0.5341 (t80) cc_final: 0.3779 (t80) REVERT: C 1126 PHE cc_start: 0.8861 (m-80) cc_final: 0.8498 (m-80) REVERT: C 1325 GLN cc_start: 0.9189 (tt0) cc_final: 0.8861 (tt0) REVERT: D 121 MET cc_start: 0.8987 (tmm) cc_final: 0.8717 (tmm) REVERT: D 181 PHE cc_start: 0.6271 (p90) cc_final: 0.5651 (p90) REVERT: D 214 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7633 (ttt90) REVERT: D 286 PHE cc_start: 0.8406 (m-80) cc_final: 0.8167 (m-80) REVERT: D 358 HIS cc_start: 0.7192 (p-80) cc_final: 0.6939 (p-80) REVERT: D 385 PHE cc_start: 0.8253 (m-10) cc_final: 0.7773 (m-10) REVERT: D 387 ARG cc_start: 0.9203 (mmp80) cc_final: 0.8982 (mmp80) REVERT: D 446 HIS cc_start: 0.6163 (t70) cc_final: 0.5952 (t-90) REVERT: D 449 TYR cc_start: 0.6698 (m-80) cc_final: 0.5958 (m-80) REVERT: D 483 ASN cc_start: 0.7661 (m110) cc_final: 0.7309 (p0) REVERT: D 546 LEU cc_start: 0.6911 (tp) cc_final: 0.6504 (tp) REVERT: D 550 ASP cc_start: 0.7859 (t0) cc_final: 0.7386 (t0) REVERT: D 567 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8915 (tptp) REVERT: D 662 ASN cc_start: 0.9252 (p0) cc_final: 0.8949 (p0) REVERT: D 968 MET cc_start: -0.1774 (tpt) cc_final: -0.2328 (ttt) REVERT: D 1007 TYR cc_start: 0.6845 (m-80) cc_final: 0.5982 (t80) REVERT: D 1173 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 1378 MET cc_start: 0.7698 (mmt) cc_final: 0.6142 (tpt) outliers start: 9 outliers final: 2 residues processed: 558 average time/residue: 0.2475 time to fit residues: 228.9640 Evaluate side-chains 431 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 428 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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: 4.9990 chunk 332 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 345 optimal weight: 2.9990 chunk 479 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 438 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 365 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 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 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 302 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 413 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.146683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.119425 restraints weight = 198183.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.122273 restraints weight = 143066.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.124078 restraints weight = 117102.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.125906 restraints weight = 87093.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.127083 restraints weight = 70517.783| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 42463 Z= 0.261 Angle : 1.001 13.059 57794 Z= 0.504 Chirality : 0.056 0.437 6686 Planarity : 0.007 0.131 7358 Dihedral : 8.111 35.857 5590 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.49 % Favored : 83.33 % Rotamer: Outliers : 0.20 % Allowed : 8.00 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -4.83 (0.10), residues: 5220 helix: -2.00 (0.15), residues: 811 sheet: -2.93 (0.13), residues: 1241 loop : -3.86 (0.09), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C1163 TYR 0.039 0.003 TYR A 619 PHE 0.053 0.003 PHE D1049 TRP 0.026 0.003 TRP A 765 HIS 0.012 0.002 HIS C 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 (42374) covalent geometry : angle 0.98847 / 0.50 (57572) SS BOND : bond 0.00515 / 0.28 ( 45) SS BOND : angle 1.98564 / 1.20 ( 90) hydrogen bonds : bond 0.06824 / 4.62 ( 517) hydrogen bonds : angle 6.84718 / 4.59 ( 1551) link_ALPHA1-6 : bond 0.00631 / 0.33 ( 1) link_ALPHA1-6 : angle 1.25898 / 0.69 ( 3) link_BETA1-4 : bond 0.00673 / 0.42 ( 14) link_BETA1-4 : angle 2.37906 / 1.45 ( 42) link_NAG-ASN : bond 0.00793 / 0.51 ( 29) link_NAG-ASN : angle 3.43293 / 2.44 ( 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 523 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 514 time to evaluate : 1.496 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: A 121 MET cc_start: 0.9097 (ttt) cc_final: 0.8870 (ttt) REVERT: A 229 PHE cc_start: 0.7356 (p90) cc_final: 0.6382 (p90) REVERT: A 237 LYS cc_start: 0.8918 (tppt) cc_final: 0.8478 (tppt) REVERT: A 415 MET cc_start: 0.4349 (ttt) cc_final: 0.3834 (ttt) REVERT: A 436 TRP cc_start: 0.6948 (m100) cc_final: 0.5807 (t-100) REVERT: A 440 GLU cc_start: 0.5836 (tt0) cc_final: 0.4559 (mp0) REVERT: A 464 MET cc_start: 0.8717 (ttt) cc_final: 0.8374 (ttt) REVERT: A 481 ILE cc_start: 0.8902 (mp) cc_final: 0.8633 (mp) REVERT: A 490 LEU cc_start: 0.8768 (mp) cc_final: 0.8543 (tt) REVERT: A 530 VAL cc_start: 0.8139 (t) cc_final: 0.7894 (t) REVERT: A 567 LYS cc_start: 0.8991 (tttt) cc_final: 0.8682 (mptt) REVERT: A 586 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7224 (mtp85) REVERT: A 597 LEU cc_start: 0.6934 (mp) cc_final: 0.6382 (mp) REVERT: A 916 PHE cc_start: 0.9058 (t80) cc_final: 0.8744 (t80) REVERT: A 959 MET cc_start: 0.6568 (mtt) cc_final: 0.5997 (ptt) REVERT: A 1122 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8479 (mmm160) REVERT: A 1133 LYS cc_start: 0.9018 (tptt) cc_final: 0.8657 (tptp) REVERT: A 1154 PHE cc_start: 0.5782 (m-80) cc_final: 0.5484 (m-80) REVERT: A 1263 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8359 (mmmt) REVERT: B 189 GLN cc_start: 0.8854 (pm20) cc_final: 0.8635 (mm-40) REVERT: B 256 TYR cc_start: 0.8409 (t80) cc_final: 0.8041 (t80) REVERT: B 325 GLN cc_start: 0.9276 (tt0) cc_final: 0.8832 (pp30) REVERT: B 385 PHE cc_start: 0.7725 (m-80) cc_final: 0.7358 (m-80) REVERT: B 461 LEU cc_start: 0.8226 (mp) cc_final: 0.7663 (tp) REVERT: B 500 MET cc_start: 0.6847 (tmm) cc_final: 0.6189 (ttt) REVERT: B 531 LYS cc_start: 0.8132 (pttm) cc_final: 0.7790 (tttt) REVERT: B 571 SER cc_start: 0.8224 (t) cc_final: 0.7633 (t) REVERT: B 586 ARG cc_start: 0.7249 (mtp85) cc_final: 0.6532 (mtp85) REVERT: B 666 MET cc_start: 0.7707 (ttp) cc_final: 0.7414 (ttp) REVERT: B 959 MET cc_start: 0.6371 (ttp) cc_final: 0.6127 (ttp) REVERT: B 977 MET cc_start: 0.9051 (mmp) cc_final: 0.8727 (mmp) REVERT: B 1012 TYR cc_start: 0.7927 (t80) cc_final: 0.7718 (t80) REVERT: B 1163 ARG cc_start: 0.8316 (ttt90) cc_final: 0.7990 (ttp80) REVERT: B 1184 GLU cc_start: 0.6564 (pt0) cc_final: 0.6234 (pt0) REVERT: B 1328 LEU cc_start: 0.9586 (tp) cc_final: 0.9135 (tp) REVERT: C 101 MET cc_start: 0.7852 (mpp) cc_final: 0.7583 (mpp) REVERT: C 203 TYR cc_start: 0.7868 (m-80) cc_final: 0.7564 (m-80) REVERT: C 363 ILE cc_start: 0.8623 (tp) cc_final: 0.8388 (tp) REVERT: C 373 ASP cc_start: 0.7746 (t70) cc_final: 0.7469 (m-30) REVERT: C 464 MET cc_start: 0.7819 (mtm) cc_final: 0.7590 (mtm) REVERT: C 558 TYR cc_start: 0.7720 (m-80) cc_final: 0.6497 (m-80) REVERT: C 569 ASP cc_start: 0.8510 (t0) cc_final: 0.8260 (t70) REVERT: C 977 MET cc_start: 0.5786 (ptt) cc_final: 0.5518 (ptt) REVERT: C 1005 ILE cc_start: 0.4640 (mt) cc_final: 0.4367 (mt) REVERT: C 1123 ASN cc_start: 0.8382 (m110) cc_final: 0.8020 (m110) REVERT: C 1126 PHE cc_start: 0.8954 (m-80) cc_final: 0.8554 (m-80) REVERT: C 1325 GLN cc_start: 0.9268 (tt0) cc_final: 0.9018 (tt0) REVERT: D 151 MET cc_start: 0.5347 (ttm) cc_final: 0.5144 (tpp) REVERT: D 181 PHE cc_start: 0.6446 (p90) cc_final: 0.5927 (p90) REVERT: D 246 MET cc_start: 0.0239 (ttm) cc_final: -0.0445 (mtt) REVERT: D 358 HIS cc_start: 0.7518 (p-80) cc_final: 0.7157 (p-80) REVERT: D 359 PHE cc_start: 0.7781 (p90) cc_final: 0.7535 (p90) REVERT: D 385 PHE cc_start: 0.8081 (m-10) cc_final: 0.7747 (m-10) REVERT: D 387 ARG cc_start: 0.9198 (mmp80) cc_final: 0.8906 (mmp80) REVERT: D 393 TYR cc_start: 0.8464 (t80) cc_final: 0.8254 (t80) REVERT: D 415 MET cc_start: 0.7026 (mmp) cc_final: 0.6374 (mmp) REVERT: D 449 TYR cc_start: 0.7235 (m-80) cc_final: 0.6726 (m-80) REVERT: D 483 ASN cc_start: 0.7698 (m110) cc_final: 0.7329 (p0) REVERT: D 546 LEU cc_start: 0.7131 (tp) cc_final: 0.6733 (tp) REVERT: D 550 ASP cc_start: 0.7987 (t0) cc_final: 0.7581 (t0) REVERT: D 567 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8800 (tptp) REVERT: D 662 ASN cc_start: 0.9343 (p0) cc_final: 0.8940 (p0) REVERT: D 961 ASN cc_start: 0.7492 (t0) cc_final: 0.7030 (m-40) REVERT: D 968 MET cc_start: -0.1848 (tpt) cc_final: -0.2311 (ttt) REVERT: D 1007 TYR cc_start: 0.7009 (m-80) cc_final: 0.6039 (t80) REVERT: D 1378 MET cc_start: 0.7829 (mmt) cc_final: 0.5946 (tpp) outliers start: 9 outliers final: 2 residues processed: 523 average time/residue: 0.2431 time to fit residues: 211.0139 Evaluate side-chains 411 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 409 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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: 0.2980 chunk 67 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 513 optimal weight: 30.0000 chunk 369 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 406 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1358 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.151595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.120864 restraints weight = 195148.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.123309 restraints weight = 153284.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.125250 restraints weight = 125145.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.126705 restraints weight = 97026.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.127102 restraints weight = 86357.644| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42463 Z= 0.182 Angle : 0.899 20.210 57794 Z= 0.448 Chirality : 0.052 0.463 6686 Planarity : 0.006 0.128 7358 Dihedral : 7.702 34.452 5590 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.08 % Favored : 85.79 % Rotamer: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.24 % 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: -4.54 (0.10), residues: 5220 helix: -1.57 (0.16), residues: 807 sheet: -2.78 (0.13), residues: 1292 loop : -3.70 (0.09), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 684 TYR 0.043 0.002 TYR C1152 PHE 0.062 0.002 PHE B1049 TRP 0.022 0.002 TRP A1132 HIS 0.009 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (42374) covalent geometry : angle 0.88440 / 0.44 (57572) SS BOND : bond 0.00467 / 0.24 ( 45) SS BOND : angle 2.33658 / 1.74 ( 90) hydrogen bonds : bond 0.06220 / 4.22 ( 517) hydrogen bonds : angle 6.45864 / 4.31 ( 1551) link_ALPHA1-6 : bond 0.00557 / 0.29 ( 1) link_ALPHA1-6 : angle 1.37377 / 0.77 ( 3) link_BETA1-4 : bond 0.00415 / 0.30 ( 14) link_BETA1-4 : angle 2.23545 / 1.36 ( 42) link_NAG-ASN : bond 0.00670 / 0.40 ( 29) link_NAG-ASN : angle 3.33853 / 2.52 ( 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 545 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 542 time to evaluate : 1.566 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: 0.7185 (t) cc_final: 0.6810 (p) REVERT: A 121 MET cc_start: 0.8990 (ttt) cc_final: 0.8705 (ttt) REVERT: A 215 THR cc_start: 0.8885 (t) cc_final: 0.8435 (p) REVERT: A 229 PHE cc_start: 0.7523 (p90) cc_final: 0.6405 (p90) REVERT: A 237 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8566 (tppt) REVERT: A 384 ILE cc_start: 0.9435 (pt) cc_final: 0.9041 (mm) REVERT: A 436 TRP cc_start: 0.6898 (m100) cc_final: 0.5512 (t-100) REVERT: A 464 MET cc_start: 0.8771 (ttt) cc_final: 0.8505 (ttt) REVERT: A 530 VAL cc_start: 0.7985 (t) cc_final: 0.7725 (t) REVERT: A 567 LYS cc_start: 0.8828 (tttt) cc_final: 0.8612 (mptt) REVERT: A 586 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7655 (mmm-85) REVERT: A 619 TYR cc_start: 0.7417 (m-80) cc_final: 0.7093 (m-80) REVERT: A 673 MET cc_start: 0.8310 (tpp) cc_final: 0.8104 (tpp) REVERT: A 916 PHE cc_start: 0.9008 (t80) cc_final: 0.8474 (t80) REVERT: A 931 LEU cc_start: 0.8714 (tp) cc_final: 0.8134 (tp) REVERT: A 959 MET cc_start: 0.5875 (mtt) cc_final: 0.5610 (ptt) REVERT: A 1112 ILE cc_start: 0.7873 (mt) cc_final: 0.7659 (mt) REVERT: A 1122 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8481 (mmm160) REVERT: A 1133 LYS cc_start: 0.9219 (tptt) cc_final: 0.8741 (tptp) REVERT: A 1136 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 142 GLN cc_start: 0.8826 (pm20) cc_final: 0.8449 (pm20) REVERT: B 256 TYR cc_start: 0.8437 (t80) cc_final: 0.8034 (t80) REVERT: B 385 PHE cc_start: 0.7835 (m-80) cc_final: 0.7434 (m-80) REVERT: B 461 LEU cc_start: 0.8280 (mp) cc_final: 0.7771 (tp) REVERT: B 500 MET cc_start: 0.6598 (tmm) cc_final: 0.6006 (ttt) REVERT: B 531 LYS cc_start: 0.8217 (pttm) cc_final: 0.7869 (tttt) REVERT: B 557 LYS cc_start: 0.8357 (pttt) cc_final: 0.7891 (pttt) REVERT: B 571 SER cc_start: 0.8193 (t) cc_final: 0.7600 (t) REVERT: B 586 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6330 (mtp85) REVERT: B 619 TYR cc_start: 0.7359 (m-10) cc_final: 0.6585 (m-80) REVERT: B 666 MET cc_start: 0.7899 (ttp) cc_final: 0.7605 (ttp) REVERT: B 739 TRP cc_start: 0.8324 (t60) cc_final: 0.6579 (t60) REVERT: B 959 MET cc_start: 0.6569 (ttp) cc_final: 0.6288 (ttp) REVERT: B 977 MET cc_start: 0.8971 (mmp) cc_final: 0.8692 (mmp) REVERT: B 1012 TYR cc_start: 0.7950 (t80) cc_final: 0.7660 (t80) REVERT: B 1040 TRP cc_start: 0.6664 (t60) cc_final: 0.6394 (t60) REVERT: B 1041 LEU cc_start: 0.9407 (tp) cc_final: 0.9063 (tp) REVERT: B 1172 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8674 (tm-30) REVERT: B 1184 GLU cc_start: 0.6586 (pt0) cc_final: 0.6195 (pt0) REVERT: C 207 VAL cc_start: 0.8641 (m) cc_final: 0.8380 (t) REVERT: C 323 GLU cc_start: 0.8764 (mp0) cc_final: 0.8516 (mp0) REVERT: C 373 ASP cc_start: 0.8166 (t70) cc_final: 0.7848 (m-30) REVERT: C 460 HIS cc_start: 0.8230 (t-90) cc_final: 0.8014 (t-90) REVERT: C 569 ASP cc_start: 0.8327 (t0) cc_final: 0.8123 (t70) REVERT: C 787 ARG cc_start: 0.6086 (mtp180) cc_final: 0.5494 (ttm170) REVERT: C 945 ARG cc_start: 0.7796 (tmt170) cc_final: 0.7446 (ttt180) REVERT: C 1104 TYR cc_start: 0.5548 (t80) cc_final: 0.4132 (t80) REVERT: C 1126 PHE cc_start: 0.8904 (m-80) cc_final: 0.8542 (m-80) REVERT: C 1325 GLN cc_start: 0.9095 (tt0) cc_final: 0.8820 (tt0) REVERT: D 151 MET cc_start: 0.5345 (ttm) cc_final: 0.5097 (tpp) REVERT: D 181 PHE cc_start: 0.6597 (p90) cc_final: 0.5995 (p90) REVERT: D 214 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7786 (ttt90) REVERT: D 358 HIS cc_start: 0.7458 (p-80) cc_final: 0.7173 (p-80) REVERT: D 385 PHE cc_start: 0.7989 (m-10) cc_final: 0.7576 (m-10) REVERT: D 387 ARG cc_start: 0.9165 (mmp80) cc_final: 0.8866 (mmp80) REVERT: D 393 TYR cc_start: 0.8542 (t80) cc_final: 0.8220 (t80) REVERT: D 449 TYR cc_start: 0.6943 (m-80) cc_final: 0.6421 (m-80) REVERT: D 464 MET cc_start: 0.8403 (ptt) cc_final: 0.8061 (ptt) REVERT: D 483 ASN cc_start: 0.8107 (m110) cc_final: 0.7882 (p0) REVERT: D 500 MET cc_start: 0.2575 (mmm) cc_final: 0.2367 (mmm) REVERT: D 546 LEU cc_start: 0.7331 (tp) cc_final: 0.6953 (tp) REVERT: D 550 ASP cc_start: 0.8080 (t0) cc_final: 0.7519 (t0) REVERT: D 567 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8828 (tptp) REVERT: D 662 ASN cc_start: 0.9289 (p0) cc_final: 0.8883 (p0) REVERT: D 968 MET cc_start: -0.1613 (tpt) cc_final: -0.2152 (ttt) REVERT: D 1007 TYR cc_start: 0.6589 (m-80) cc_final: 0.5806 (t80) REVERT: D 1378 MET cc_start: 0.8040 (mmt) cc_final: 0.6291 (tpp) outliers start: 3 outliers final: 1 residues processed: 545 average time/residue: 0.2306 time to fit residues: 208.7859 Evaluate side-chains 418 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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: 9.9990 chunk 255 optimal weight: 0.9990 chunk 340 optimal weight: 0.0170 chunk 224 optimal weight: 4.9990 chunk 413 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 447 optimal weight: 0.0040 chunk 126 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 461 optimal weight: 50.0000 overall best weight: 1.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** 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** A1143 HIS ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** 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** B1252 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 511 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 GLN C 651 ASN ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 ASN C1302 GLN 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 424 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1143 HIS D1277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.153229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.128602 restraints weight = 198839.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.131992 restraints weight = 135640.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.134484 restraints weight = 99592.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.136228 restraints weight = 77355.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.137627 restraints weight = 62891.437| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42463 Z= 0.153 Angle : 0.849 13.787 57794 Z= 0.421 Chirality : 0.051 0.460 6686 Planarity : 0.006 0.102 7358 Dihedral : 7.211 38.200 5590 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.20 % Favored : 86.67 % Rotamer: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % 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: -4.26 (0.10), residues: 5220 helix: -1.28 (0.16), residues: 821 sheet: -2.54 (0.14), residues: 1306 loop : -3.58 (0.10), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 684 TYR 0.058 0.002 TYR A1152 PHE 0.053 0.002 PHE D1049 TRP 0.018 0.002 TRP C1132 HIS 0.014 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (42374) covalent geometry : angle 0.83517 / 0.42 (57572) SS BOND : bond 0.00593 / 0.31 ( 45) SS BOND : angle 2.22788 / 1.57 ( 90) hydrogen bonds : bond 0.05920 / 3.99 ( 517) hydrogen bonds : angle 6.19701 / 4.13 ( 1551) link_ALPHA1-6 : bond 0.00410 / 0.22 ( 1) link_ALPHA1-6 : angle 1.40594 / 0.78 ( 3) link_BETA1-4 : bond 0.00505 / 0.34 ( 14) link_BETA1-4 : angle 2.25169 / 1.40 ( 42) link_NAG-ASN : bond 0.00630 / 0.35 ( 29) link_NAG-ASN : angle 3.07219 / 2.34 ( 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 563 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 561 time to evaluate : 1.902 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: A 38 LEU cc_start: 0.8275 (tt) cc_final: 0.7545 (tt) REVERT: A 45 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5666 (mm-30) REVERT: A 63 SER cc_start: 0.7126 (t) cc_final: 0.6778 (p) REVERT: A 82 ASP cc_start: 0.9341 (m-30) cc_final: 0.9001 (m-30) REVERT: A 121 MET cc_start: 0.8878 (ttt) cc_final: 0.8656 (ttt) REVERT: A 126 ASP cc_start: 0.7824 (p0) cc_final: 0.7547 (p0) REVERT: A 215 THR cc_start: 0.8667 (t) cc_final: 0.8261 (p) REVERT: A 229 PHE cc_start: 0.7563 (p90) cc_final: 0.7231 (p90) REVERT: A 237 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8648 (tppt) REVERT: A 318 MET cc_start: 0.8276 (tpt) cc_final: 0.8014 (tpt) REVERT: A 384 ILE cc_start: 0.9427 (pt) cc_final: 0.9067 (mm) REVERT: A 385 PHE cc_start: 0.9025 (m-10) cc_final: 0.8815 (m-10) REVERT: A 399 THR cc_start: 0.7904 (p) cc_final: 0.7410 (t) REVERT: A 436 TRP cc_start: 0.6612 (m100) cc_final: 0.5617 (t-100) REVERT: A 440 GLU cc_start: 0.4779 (tt0) cc_final: 0.4027 (mp0) REVERT: A 464 MET cc_start: 0.8673 (ttt) cc_final: 0.8357 (ttt) REVERT: A 491 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8443 (tppt) REVERT: A 530 VAL cc_start: 0.8050 (t) cc_final: 0.7775 (t) REVERT: A 567 LYS cc_start: 0.8839 (tttt) cc_final: 0.8545 (mptt) REVERT: A 916 PHE cc_start: 0.9043 (t80) cc_final: 0.8704 (t80) REVERT: A 931 LEU cc_start: 0.8628 (tp) cc_final: 0.7750 (tp) REVERT: A 959 MET cc_start: 0.5838 (mtt) cc_final: 0.5590 (ptt) REVERT: A 961 ASN cc_start: 0.8576 (t0) cc_final: 0.8329 (t0) REVERT: A 1112 ILE cc_start: 0.7884 (mt) cc_final: 0.7670 (mt) REVERT: A 1122 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8404 (mmm160) REVERT: A 1154 PHE cc_start: 0.5559 (m-80) cc_final: 0.5010 (m-80) REVERT: A 1315 LYS cc_start: 0.8790 (tmmt) cc_final: 0.8587 (tmmt) REVERT: B 142 GLN cc_start: 0.8549 (pm20) cc_final: 0.7990 (pm20) REVERT: B 256 TYR cc_start: 0.8297 (t80) cc_final: 0.7874 (t80) REVERT: B 348 THR cc_start: 0.8129 (m) cc_final: 0.7275 (p) REVERT: B 385 PHE cc_start: 0.7711 (m-80) cc_final: 0.7345 (m-80) REVERT: B 415 MET cc_start: -0.1282 (ttt) cc_final: -0.1873 (tpt) REVERT: B 461 LEU cc_start: 0.8468 (mp) cc_final: 0.8000 (tp) REVERT: B 557 LYS cc_start: 0.8254 (pttt) cc_final: 0.7949 (pttt) REVERT: B 586 ARG cc_start: 0.6957 (mtp85) cc_final: 0.6318 (mtp85) REVERT: B 619 TYR cc_start: 0.7191 (m-10) cc_final: 0.6506 (m-80) REVERT: B 666 MET cc_start: 0.7832 (ttp) cc_final: 0.7610 (ttp) REVERT: B 739 TRP cc_start: 0.8255 (t60) cc_final: 0.7068 (t60) REVERT: B 808 PHE cc_start: 0.8511 (p90) cc_final: 0.8203 (p90) REVERT: B 959 MET cc_start: 0.6573 (ttp) cc_final: 0.6119 (ttp) REVERT: B 1012 TYR cc_start: 0.7822 (t80) cc_final: 0.7505 (t80) REVERT: B 1172 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 1184 GLU cc_start: 0.6269 (pt0) cc_final: 0.5831 (pt0) REVERT: B 1290 PHE cc_start: 0.8373 (m-10) cc_final: 0.8009 (m-10) REVERT: B 1328 LEU cc_start: 0.9513 (tp) cc_final: 0.8804 (tp) REVERT: C 101 MET cc_start: 0.7632 (mpp) cc_final: 0.7399 (mpp) REVERT: C 323 GLU cc_start: 0.8782 (mp0) cc_final: 0.8524 (mp0) REVERT: C 460 HIS cc_start: 0.8021 (t-90) cc_final: 0.7773 (t-90) REVERT: C 666 MET cc_start: 0.8366 (tpp) cc_final: 0.8103 (tpt) REVERT: C 945 ARG cc_start: 0.7826 (tmt170) cc_final: 0.6627 (ttt180) REVERT: C 1042 THR cc_start: 0.1785 (p) cc_final: 0.0493 (t) REVERT: C 1104 TYR cc_start: 0.5138 (t80) cc_final: 0.3844 (t80) REVERT: C 1123 ASN cc_start: 0.8175 (m-40) cc_final: 0.7901 (m110) REVERT: C 1126 PHE cc_start: 0.8795 (m-80) cc_final: 0.8452 (m-80) REVERT: D 151 MET cc_start: 0.5608 (ttm) cc_final: 0.5379 (tpp) REVERT: D 181 PHE cc_start: 0.6146 (p90) cc_final: 0.5615 (p90) REVERT: D 214 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7897 (ttt90) REVERT: D 246 MET cc_start: -0.0628 (ttm) cc_final: -0.1157 (mtt) REVERT: D 385 PHE cc_start: 0.8027 (m-10) cc_final: 0.7824 (m-10) REVERT: D 387 ARG cc_start: 0.9152 (mmp80) cc_final: 0.8892 (mmp80) REVERT: D 449 TYR cc_start: 0.6731 (m-80) cc_final: 0.6313 (m-80) REVERT: D 491 LYS cc_start: 0.9339 (ptpp) cc_final: 0.8873 (ttmm) REVERT: D 546 LEU cc_start: 0.7520 (tp) cc_final: 0.7098 (tp) REVERT: D 550 ASP cc_start: 0.7446 (t0) cc_final: 0.6820 (t0) REVERT: D 567 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8677 (tptp) REVERT: D 662 ASN cc_start: 0.9227 (p0) cc_final: 0.8823 (p0) REVERT: D 968 MET cc_start: -0.1772 (tpt) cc_final: -0.2393 (ttt) REVERT: D 1007 TYR cc_start: 0.6761 (m-80) cc_final: 0.5958 (t80) REVERT: D 1378 MET cc_start: 0.7888 (mmt) cc_final: 0.6183 (tpp) outliers start: 2 outliers final: 0 residues processed: 563 average time/residue: 0.2514 time to fit residues: 234.2575 Evaluate side-chains 432 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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: 0.6980 chunk 447 optimal weight: 0.0980 chunk 412 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 466 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 chunk 480 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 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 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.150972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.122464 restraints weight = 196921.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.125875 restraints weight = 137469.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.128352 restraints weight = 103410.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.130244 restraints weight = 82087.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.131548 restraints weight = 68069.352| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42463 Z= 0.166 Angle : 0.844 13.931 57794 Z= 0.418 Chirality : 0.051 0.445 6686 Planarity : 0.006 0.093 7358 Dihedral : 7.028 36.347 5590 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.20 % Favored : 86.69 % Rotamer: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % 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: -4.18 (0.10), residues: 5220 helix: -1.20 (0.16), residues: 826 sheet: -2.45 (0.14), residues: 1317 loop : -3.55 (0.09), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 684 TYR 0.045 0.002 TYR A1152 PHE 0.048 0.002 PHE D1049 TRP 0.019 0.002 TRP B1183 HIS 0.011 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (42374) covalent geometry : angle 0.83040 / 0.41 (57572) SS BOND : bond 0.00709 / 0.41 ( 45) SS BOND : angle 2.20167 / 1.48 ( 90) hydrogen bonds : bond 0.05847 / 3.93 ( 517) hydrogen bonds : angle 6.20589 / 4.13 ( 1551) link_ALPHA1-6 : bond 0.00314 / 0.17 ( 1) link_ALPHA1-6 : angle 1.40292 / 0.78 ( 3) link_BETA1-4 : bond 0.00521 / 0.35 ( 14) link_BETA1-4 : angle 2.20956 / 1.36 ( 42) link_NAG-ASN : bond 0.00670 / 0.40 ( 29) link_NAG-ASN : angle 3.04622 / 2.35 ( 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 533 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 1.415 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 38 LEU cc_start: 0.8323 (tt) cc_final: 0.7694 (tt) REVERT: A 63 SER cc_start: 0.7197 (t) cc_final: 0.6862 (p) REVERT: A 82 ASP cc_start: 0.9404 (m-30) cc_final: 0.9035 (m-30) REVERT: A 126 ASP cc_start: 0.7874 (p0) cc_final: 0.7614 (p0) REVERT: A 138 TYR cc_start: 0.4283 (m-80) cc_final: 0.3489 (m-80) REVERT: A 215 THR cc_start: 0.8652 (t) cc_final: 0.8273 (p) REVERT: A 229 PHE cc_start: 0.7469 (p90) cc_final: 0.7250 (p90) REVERT: A 237 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8427 (tppt) REVERT: A 384 ILE cc_start: 0.9461 (pt) cc_final: 0.9152 (mm) REVERT: A 399 THR cc_start: 0.8050 (p) cc_final: 0.7563 (t) REVERT: A 415 MET cc_start: 0.3255 (ttt) cc_final: 0.2522 (ttt) REVERT: A 436 TRP cc_start: 0.6829 (m100) cc_final: 0.5680 (t-100) REVERT: A 440 GLU cc_start: 0.5110 (tt0) cc_final: 0.4218 (mp0) REVERT: A 464 MET cc_start: 0.8658 (ttt) cc_final: 0.8335 (ttt) REVERT: A 490 LEU cc_start: 0.8610 (mp) cc_final: 0.8331 (tt) REVERT: A 530 VAL cc_start: 0.8040 (t) cc_final: 0.7813 (t) REVERT: A 567 LYS cc_start: 0.8888 (tttt) cc_final: 0.8595 (mptt) REVERT: A 669 PHE cc_start: 0.8589 (m-10) cc_final: 0.8355 (m-80) REVERT: A 916 PHE cc_start: 0.9077 (t80) cc_final: 0.8715 (t80) REVERT: A 931 LEU cc_start: 0.8636 (tp) cc_final: 0.7832 (tp) REVERT: A 959 MET cc_start: 0.6003 (mtt) cc_final: 0.5702 (ptt) REVERT: A 1112 ILE cc_start: 0.7915 (mt) cc_final: 0.7691 (mt) REVERT: A 1122 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8496 (mmm160) REVERT: A 1216 TYR cc_start: 0.8302 (m-10) cc_final: 0.8084 (m-10) REVERT: B 142 GLN cc_start: 0.8822 (pm20) cc_final: 0.8268 (pm20) REVERT: B 256 TYR cc_start: 0.8394 (t80) cc_final: 0.7954 (t80) REVERT: B 348 THR cc_start: 0.8249 (m) cc_final: 0.7542 (p) REVERT: B 385 PHE cc_start: 0.7767 (m-80) cc_final: 0.7408 (m-80) REVERT: B 415 MET cc_start: -0.1334 (ttt) cc_final: -0.1923 (tpt) REVERT: B 461 LEU cc_start: 0.8709 (mp) cc_final: 0.8129 (tp) REVERT: B 545 VAL cc_start: 0.8036 (m) cc_final: 0.7719 (p) REVERT: B 557 LYS cc_start: 0.8406 (pttt) cc_final: 0.7936 (pttt) REVERT: B 586 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6455 (mtp85) REVERT: B 619 TYR cc_start: 0.7253 (m-10) cc_final: 0.6573 (m-80) REVERT: B 666 MET cc_start: 0.7999 (ttp) cc_final: 0.7786 (ttp) REVERT: B 808 PHE cc_start: 0.8617 (p90) cc_final: 0.8264 (p90) REVERT: B 959 MET cc_start: 0.6698 (ttp) cc_final: 0.6228 (ttp) REVERT: B 1132 TRP cc_start: 0.8484 (t60) cc_final: 0.8127 (t60) REVERT: B 1172 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 1183 TRP cc_start: 0.7812 (m-90) cc_final: 0.7317 (m-90) REVERT: B 1184 GLU cc_start: 0.6431 (pt0) cc_final: 0.6202 (pt0) REVERT: B 1328 LEU cc_start: 0.9549 (tp) cc_final: 0.8801 (tp) REVERT: C 207 VAL cc_start: 0.8533 (m) cc_final: 0.8252 (t) REVERT: C 323 GLU cc_start: 0.8785 (mp0) cc_final: 0.8474 (mp0) REVERT: C 460 HIS cc_start: 0.8210 (t-90) cc_final: 0.7969 (t-90) REVERT: C 945 ARG cc_start: 0.7958 (tmt170) cc_final: 0.6816 (ttt180) REVERT: C 1104 TYR cc_start: 0.5394 (t80) cc_final: 0.4015 (t80) REVERT: C 1123 ASN cc_start: 0.8307 (m-40) cc_final: 0.8035 (m110) REVERT: C 1126 PHE cc_start: 0.8772 (m-80) cc_final: 0.8468 (m-80) REVERT: C 1208 MET cc_start: 0.8251 (ppp) cc_final: 0.7882 (ppp) REVERT: C 1314 MET cc_start: 0.9312 (ppp) cc_final: 0.8722 (mpp) REVERT: D 181 PHE cc_start: 0.6407 (p90) cc_final: 0.5838 (p90) REVERT: D 214 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.7722 (ttt90) REVERT: D 246 MET cc_start: -0.0590 (ttm) cc_final: -0.1044 (mtt) REVERT: D 387 ARG cc_start: 0.9150 (mmp80) cc_final: 0.8901 (mmp80) REVERT: D 394 TYR cc_start: 0.8886 (t80) cc_final: 0.8555 (t80) REVERT: D 449 TYR cc_start: 0.6823 (m-80) cc_final: 0.6388 (m-80) REVERT: D 491 LYS cc_start: 0.9366 (ptpp) cc_final: 0.8900 (ttmm) REVERT: D 500 MET cc_start: 0.2552 (mmm) cc_final: 0.1737 (mtt) REVERT: D 531 LYS cc_start: 0.7766 (pttp) cc_final: 0.7398 (pttm) REVERT: D 546 LEU cc_start: 0.7548 (tp) cc_final: 0.7133 (tp) REVERT: D 550 ASP cc_start: 0.7642 (t0) cc_final: 0.7058 (t0) REVERT: D 567 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8760 (tptp) REVERT: D 662 ASN cc_start: 0.9232 (p0) cc_final: 0.8869 (p0) REVERT: D 968 MET cc_start: -0.2000 (tpt) cc_final: -0.2636 (ttt) REVERT: D 1007 TYR cc_start: 0.6741 (m-80) cc_final: 0.5821 (t80) REVERT: D 1378 MET cc_start: 0.7936 (mmt) cc_final: 0.6383 (tpp) outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.2473 time to fit residues: 217.7734 Evaluate side-chains 425 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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: 5.9990 chunk 345 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 chunk 280 optimal weight: 50.0000 chunk 399 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 0.0030 chunk 257 optimal weight: 1.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 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 602 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 ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 HIS ** C 511 HIS ** 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 132 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.126223 restraints weight = 196319.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.129612 restraints weight = 133644.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.132020 restraints weight = 98107.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.133806 restraints weight = 76418.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.135108 restraints weight = 62192.147| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 42463 Z= 0.159 Angle : 0.833 13.804 57794 Z= 0.413 Chirality : 0.051 0.457 6686 Planarity : 0.006 0.148 7358 Dihedral : 6.849 36.076 5590 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.20 % Favored : 86.69 % Rotamer: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.07 (0.10), residues: 5220 helix: -1.06 (0.17), residues: 817 sheet: -2.35 (0.13), residues: 1347 loop : -3.50 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1122 TYR 0.043 0.002 TYR A1152 PHE 0.041 0.002 PHE B1126 TRP 0.022 0.002 TRP A1132 HIS 0.011 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (42374) covalent geometry : angle 0.82067 / 0.41 (57572) SS BOND : bond 0.00486 / 0.26 ( 45) SS BOND : angle 2.10048 / 1.45 ( 90) hydrogen bonds : bond 0.05746 / 3.89 ( 517) hydrogen bonds : angle 6.16920 / 4.10 ( 1551) link_ALPHA1-6 : bond 0.00408 / 0.21 ( 1) link_ALPHA1-6 : angle 1.42895 / 0.79 ( 3) link_BETA1-4 : bond 0.00573 / 0.41 ( 14) link_BETA1-4 : angle 2.19067 / 1.35 ( 42) link_NAG-ASN : bond 0.00595 / 0.34 ( 29) link_NAG-ASN : angle 2.97777 / 2.32 ( 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 528 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 526 time to evaluate : 1.652 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: A 45 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5969 (mm-30) REVERT: A 63 SER cc_start: 0.7181 (t) cc_final: 0.6882 (p) REVERT: A 82 ASP cc_start: 0.9326 (m-30) cc_final: 0.8943 (m-30) REVERT: A 126 ASP cc_start: 0.7932 (p0) cc_final: 0.7681 (p0) REVERT: A 138 TYR cc_start: 0.4293 (m-80) cc_final: 0.3538 (m-80) REVERT: A 215 THR cc_start: 0.8685 (t) cc_final: 0.8271 (p) REVERT: A 229 PHE cc_start: 0.7499 (p90) cc_final: 0.7107 (p90) REVERT: A 245 GLU cc_start: 0.8951 (mp0) cc_final: 0.8651 (mp0) REVERT: A 384 ILE cc_start: 0.9420 (pt) cc_final: 0.9154 (mm) REVERT: A 399 THR cc_start: 0.8020 (p) cc_final: 0.7522 (t) REVERT: A 436 TRP cc_start: 0.6770 (m100) cc_final: 0.5669 (t-100) REVERT: A 440 GLU cc_start: 0.5237 (tt0) cc_final: 0.4329 (mp0) REVERT: A 464 MET cc_start: 0.8692 (ttt) cc_final: 0.8356 (ttt) REVERT: A 481 ILE cc_start: 0.8901 (mp) cc_final: 0.8648 (mp) REVERT: A 519 ASP cc_start: 0.8498 (t70) cc_final: 0.8165 (t70) REVERT: A 520 MET cc_start: 0.6344 (mmp) cc_final: 0.6018 (mmt) REVERT: A 530 VAL cc_start: 0.7947 (t) cc_final: 0.7681 (t) REVERT: A 567 LYS cc_start: 0.8878 (tttt) cc_final: 0.8580 (mptt) REVERT: A 669 PHE cc_start: 0.8628 (m-10) cc_final: 0.8404 (m-80) REVERT: A 959 MET cc_start: 0.5996 (mtt) cc_final: 0.5756 (ptt) REVERT: A 961 ASN cc_start: 0.8625 (t0) cc_final: 0.8421 (t0) REVERT: A 1112 ILE cc_start: 0.7894 (mt) cc_final: 0.7662 (mt) REVERT: A 1122 ARG cc_start: 0.8770 (mtp180) cc_final: 0.8489 (mmm160) REVERT: A 1263 LYS cc_start: 0.8522 (mmmt) cc_final: 0.7612 (tttt) REVERT: A 1280 ILE cc_start: 0.8381 (mp) cc_final: 0.7829 (mp) REVERT: A 1314 MET cc_start: 0.8203 (mpp) cc_final: 0.7619 (mpp) REVERT: B 142 GLN cc_start: 0.8722 (pm20) cc_final: 0.8199 (pm20) REVERT: B 256 TYR cc_start: 0.8331 (t80) cc_final: 0.7845 (t80) REVERT: B 363 ILE cc_start: 0.8905 (tp) cc_final: 0.7888 (tp) REVERT: B 385 PHE cc_start: 0.7789 (m-80) cc_final: 0.7468 (m-80) REVERT: B 393 TYR cc_start: 0.8585 (t80) cc_final: 0.8163 (t80) REVERT: B 461 LEU cc_start: 0.8610 (mp) cc_final: 0.8191 (tp) REVERT: B 545 VAL cc_start: 0.7954 (m) cc_final: 0.7657 (p) REVERT: B 557 LYS cc_start: 0.8519 (pttt) cc_final: 0.8041 (pttt) REVERT: B 558 TYR cc_start: 0.7971 (m-80) cc_final: 0.7628 (m-80) REVERT: B 619 TYR cc_start: 0.7316 (m-10) cc_final: 0.6607 (m-80) REVERT: B 808 PHE cc_start: 0.8512 (p90) cc_final: 0.8167 (p90) REVERT: B 968 MET cc_start: 0.6709 (tpt) cc_final: 0.6391 (tpp) REVERT: B 1172 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 1183 TRP cc_start: 0.7692 (m-90) cc_final: 0.7322 (m-90) REVERT: C 101 MET cc_start: 0.7752 (mpp) cc_final: 0.7532 (mpp) REVERT: C 203 TYR cc_start: 0.8045 (m-80) cc_final: 0.7836 (m-80) REVERT: C 207 VAL cc_start: 0.8536 (m) cc_final: 0.8267 (t) REVERT: C 460 HIS cc_start: 0.8209 (t-90) cc_final: 0.7963 (t-90) REVERT: C 666 MET cc_start: 0.8431 (tpp) cc_final: 0.8083 (tpt) REVERT: C 754 VAL cc_start: 0.8651 (t) cc_final: 0.8427 (t) REVERT: C 787 ARG cc_start: 0.5988 (mtp180) cc_final: 0.5202 (ttm170) REVERT: C 945 ARG cc_start: 0.7961 (tmt170) cc_final: 0.6758 (ttt180) REVERT: C 1104 TYR cc_start: 0.5353 (t80) cc_final: 0.4036 (t80) REVERT: C 1123 ASN cc_start: 0.8309 (m-40) cc_final: 0.8027 (m110) REVERT: C 1126 PHE cc_start: 0.8806 (m-80) cc_final: 0.8487 (m-80) REVERT: C 1208 MET cc_start: 0.8107 (ppp) cc_final: 0.7811 (ppp) REVERT: C 1325 GLN cc_start: 0.8918 (tt0) cc_final: 0.8635 (tt0) REVERT: D 181 PHE cc_start: 0.6287 (p90) cc_final: 0.5734 (p90) REVERT: D 359 PHE cc_start: 0.7536 (p90) cc_final: 0.7294 (p90) REVERT: D 387 ARG cc_start: 0.9125 (mmp80) cc_final: 0.8841 (mmp80) REVERT: D 394 TYR cc_start: 0.8785 (t80) cc_final: 0.8539 (t80) REVERT: D 449 TYR cc_start: 0.6713 (m-80) cc_final: 0.6364 (m-80) REVERT: D 491 LYS cc_start: 0.9345 (ptpp) cc_final: 0.8868 (ttmm) REVERT: D 500 MET cc_start: 0.2226 (mmm) cc_final: 0.1475 (ttm) REVERT: D 546 LEU cc_start: 0.7659 (tp) cc_final: 0.7228 (tp) REVERT: D 550 ASP cc_start: 0.7583 (t0) cc_final: 0.7082 (t0) REVERT: D 567 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8696 (tptp) REVERT: D 662 ASN cc_start: 0.9202 (p0) cc_final: 0.8835 (p0) REVERT: D 798 MET cc_start: 0.7690 (ppp) cc_final: 0.7485 (ppp) REVERT: D 916 PHE cc_start: 0.8497 (m-80) cc_final: 0.8271 (m-80) REVERT: D 968 MET cc_start: -0.2015 (tpt) cc_final: -0.2711 (ttt) REVERT: D 1007 TYR cc_start: 0.6628 (m-80) cc_final: 0.5748 (t80) REVERT: D 1378 MET cc_start: 0.7654 (mmt) cc_final: 0.6120 (tpp) outliers start: 2 outliers final: 0 residues processed: 528 average time/residue: 0.2500 time to fit residues: 218.9334 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 : 1.626 ------------------------------------------------------------------------------- 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: 7.9990 chunk 221 optimal weight: 10.0000 chunk 447 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 HIS C 483 ASN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 995 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1062 HIS C1123 ASN C1143 HIS D 112 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** D 483 ASN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.142635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.115865 restraints weight = 198862.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.118478 restraints weight = 147636.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.120347 restraints weight = 112906.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.121590 restraints weight = 88109.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.121748 restraints weight = 77805.405| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 42463 Z= 0.286 Angle : 1.024 14.626 57794 Z= 0.515 Chirality : 0.058 0.416 6686 Planarity : 0.007 0.134 7358 Dihedral : 7.579 33.501 5590 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 33.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.76 % Favored : 83.07 % Rotamer: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -4.49 (0.10), residues: 5220 helix: -1.82 (0.16), residues: 818 sheet: -2.69 (0.13), residues: 1304 loop : -3.61 (0.09), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C1163 TYR 0.048 0.003 TYR A1152 PHE 0.042 0.003 PHE C1080 TRP 0.048 0.004 TRP C 765 HIS 0.018 0.002 HIS B1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (42374) covalent geometry : angle 1.01203 / 0.51 (57572) SS BOND : bond 0.00516 / 0.34 ( 45) SS BOND : angle 2.11520 / 1.35 ( 90) hydrogen bonds : bond 0.06760 / 4.60 ( 517) hydrogen bonds : angle 6.82607 / 4.56 ( 1551) link_ALPHA1-6 : bond 0.00332 / 0.17 ( 1) link_ALPHA1-6 : angle 1.42447 / 0.79 ( 3) link_BETA1-4 : bond 0.00683 / 0.55 ( 14) link_BETA1-4 : angle 2.43529 / 1.49 ( 42) link_NAG-ASN : bond 0.00915 / 0.57 ( 29) link_NAG-ASN : angle 3.45145 / 2.62 ( 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 510 residues out of total 4577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 509 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7255 (t) cc_final: 0.6983 (p) REVERT: A 126 ASP cc_start: 0.8187 (p0) cc_final: 0.7879 (p0) REVERT: A 138 TYR cc_start: 0.5268 (m-80) cc_final: 0.4270 (m-80) REVERT: A 179 GLN cc_start: 0.6446 (tm-30) cc_final: 0.5822 (tm-30) REVERT: A 229 PHE cc_start: 0.7661 (p90) cc_final: 0.7242 (p90) REVERT: A 415 MET cc_start: 0.4309 (ttt) cc_final: 0.3680 (ttt) REVERT: A 436 TRP cc_start: 0.7293 (m100) cc_final: 0.5597 (t-100) REVERT: A 440 GLU cc_start: 0.5813 (tt0) cc_final: 0.4780 (mp0) REVERT: A 464 MET cc_start: 0.8646 (ttt) cc_final: 0.8374 (ttt) REVERT: A 491 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8772 (tppt) REVERT: A 519 ASP cc_start: 0.8568 (t70) cc_final: 0.8353 (t70) REVERT: A 530 VAL cc_start: 0.7975 (t) cc_final: 0.7750 (t) REVERT: A 586 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7614 (mmm-85) REVERT: A 669 PHE cc_start: 0.8740 (m-10) cc_final: 0.8527 (m-80) REVERT: A 916 PHE cc_start: 0.9157 (t80) cc_final: 0.8639 (t80) REVERT: A 931 LEU cc_start: 0.8963 (tp) cc_final: 0.8177 (tp) REVERT: A 959 MET cc_start: 0.6475 (mtt) cc_final: 0.6120 (ptt) REVERT: A 961 ASN cc_start: 0.8468 (t0) cc_final: 0.8216 (t0) REVERT: A 1280 ILE cc_start: 0.8435 (mp) cc_final: 0.7807 (mp) REVERT: A 1308 LEU cc_start: 0.8448 (mp) cc_final: 0.8091 (mm) REVERT: A 1314 MET cc_start: 0.8168 (mpp) cc_final: 0.7617 (mpp) REVERT: A 1328 LEU cc_start: 0.9365 (tp) cc_final: 0.9106 (tp) REVERT: B 164 LEU cc_start: 0.8519 (tp) cc_final: 0.8297 (tp) REVERT: B 256 TYR cc_start: 0.8343 (t80) cc_final: 0.7833 (t80) REVERT: B 325 GLN cc_start: 0.9381 (tt0) cc_final: 0.8906 (pp30) REVERT: B 363 ILE cc_start: 0.8871 (tp) cc_final: 0.7949 (tp) REVERT: B 385 PHE cc_start: 0.7878 (m-80) cc_final: 0.7567 (m-80) REVERT: B 460 HIS cc_start: 0.8251 (m90) cc_final: 0.7765 (m90) REVERT: B 461 LEU cc_start: 0.9199 (mp) cc_final: 0.8956 (tp) REVERT: B 496 TYR cc_start: 0.6873 (m-10) cc_final: 0.6577 (m-80) REVERT: B 510 THR cc_start: 0.6979 (t) cc_final: 0.6552 (t) REVERT: B 545 VAL cc_start: 0.8049 (m) cc_final: 0.7738 (p) REVERT: B 557 LYS cc_start: 0.8716 (pttt) cc_final: 0.8481 (pttt) REVERT: B 571 SER cc_start: 0.8527 (t) cc_final: 0.7812 (p) REVERT: B 586 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6720 (mtp85) REVERT: B 619 TYR cc_start: 0.7661 (m-10) cc_final: 0.6726 (m-80) REVERT: B 789 PHE cc_start: 0.6799 (t80) cc_final: 0.6465 (t80) REVERT: B 1163 ARG cc_start: 0.8587 (ttt90) cc_final: 0.7936 (tpt-90) REVERT: B 1172 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 1290 PHE cc_start: 0.8667 (m-10) cc_final: 0.8464 (m-10) REVERT: B 1328 LEU cc_start: 0.9658 (tp) cc_final: 0.9168 (tp) REVERT: C 101 MET cc_start: 0.8001 (mpp) cc_final: 0.7768 (mpp) REVERT: C 203 TYR cc_start: 0.7984 (m-80) cc_final: 0.7772 (m-80) REVERT: C 322 THR cc_start: 0.9017 (p) cc_final: 0.8798 (p) REVERT: C 323 GLU cc_start: 0.8767 (mp0) cc_final: 0.8452 (mp0) REVERT: C 441 HIS cc_start: 0.6420 (t70) cc_final: 0.6170 (t-170) REVERT: C 460 HIS cc_start: 0.8560 (t-90) cc_final: 0.8350 (t-90) REVERT: C 945 ARG cc_start: 0.8171 (tmt170) cc_final: 0.7000 (ttt-90) REVERT: C 1005 ILE cc_start: 0.4779 (mt) cc_final: 0.4571 (mt) REVERT: C 1028 PHE cc_start: 0.8802 (m-10) cc_final: 0.8218 (m-10) REVERT: C 1123 ASN cc_start: 0.8789 (m110) cc_final: 0.8462 (m110) REVERT: C 1126 PHE cc_start: 0.8927 (m-80) cc_final: 0.8664 (m-80) REVERT: C 1136 GLN cc_start: 0.8709 (pp30) cc_final: 0.8105 (pp30) REVERT: C 1325 GLN cc_start: 0.9106 (tt0) cc_final: 0.8840 (tt0) REVERT: D 181 PHE cc_start: 0.6427 (p90) cc_final: 0.5880 (p90) REVERT: D 214 ARG cc_start: 0.8646 (mtp-110) cc_final: 0.8445 (ptm160) REVERT: D 246 MET cc_start: -0.0000 (ttm) cc_final: -0.0659 (mtt) REVERT: D 359 PHE cc_start: 0.8042 (p90) cc_final: 0.7703 (p90) REVERT: D 449 TYR cc_start: 0.7448 (m-80) cc_final: 0.7093 (m-80) REVERT: D 531 LYS cc_start: 0.7901 (pttp) cc_final: 0.7080 (mmtt) REVERT: D 546 LEU cc_start: 0.7661 (tp) cc_final: 0.7235 (tp) REVERT: D 550 ASP cc_start: 0.8195 (t0) cc_final: 0.7743 (t0) REVERT: D 662 ASN cc_start: 0.9303 (p0) cc_final: 0.8942 (p0) REVERT: D 798 MET cc_start: 0.7753 (ppp) cc_final: 0.7537 (ppp) REVERT: D 916 PHE cc_start: 0.8361 (m-80) cc_final: 0.8126 (m-80) REVERT: D 968 MET cc_start: -0.1744 (tpt) cc_final: -0.2503 (ttt) REVERT: D 1007 TYR cc_start: 0.6616 (m-80) cc_final: 0.5675 (t80) REVERT: D 1378 MET cc_start: 0.7800 (mmt) cc_final: 0.6204 (tpp) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.2417 time to fit residues: 203.0467 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 : 1.489 ------------------------------------------------------------------------------- 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: 2.9990 chunk 246 optimal weight: 1.9990 chunk 487 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 480 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 351 optimal weight: 4.9990 chunk 507 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 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 562 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 517 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.146796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.119800 restraints weight = 194168.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.122515 restraints weight = 146710.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.124827 restraints weight = 108839.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.125970 restraints weight = 88623.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.126764 restraints weight = 71647.706| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 42463 Z= 0.191 Angle : 0.904 13.644 57794 Z= 0.449 Chirality : 0.053 0.477 6686 Planarity : 0.006 0.128 7358 Dihedral : 7.279 33.272 5590 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.27 % Favored : 85.59 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.28 (0.10), residues: 5220 helix: -1.45 (0.16), residues: 814 sheet: -2.52 (0.14), residues: 1306 loop : -3.54 (0.09), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1163 TYR 0.056 0.002 TYR A1152 PHE 0.040 0.002 PHE C1080 TRP 0.055 0.003 TRP B1237 HIS 0.011 0.001 HIS B1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (42374) covalent geometry : angle 0.88733 / 0.44 (57572) SS BOND : bond 0.00508 / 0.29 ( 45) SS BOND : angle 2.40520 / 1.59 ( 90) hydrogen bonds : bond 0.06195 / 4.23 ( 517) hydrogen bonds : angle 6.45210 / 4.27 ( 1551) link_ALPHA1-6 : bond 0.00346 / 0.18 ( 1) link_ALPHA1-6 : angle 1.43554 / 0.80 ( 3) link_BETA1-4 : bond 0.00557 / 0.42 ( 14) link_BETA1-4 : angle 2.57357 / 1.54 ( 42) link_NAG-ASN : bond 0.00708 / 0.41 ( 29) link_NAG-ASN : angle 3.50159 / 2.51 ( 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: 0 poor density : 506 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.7220 (t) cc_final: 0.7011 (p) REVERT: A 138 TYR cc_start: 0.4556 (m-80) cc_final: 0.3523 (m-80) REVERT: A 179 GLN cc_start: 0.6500 (tm-30) cc_final: 0.6102 (tm-30) REVERT: A 209 LYS cc_start: 0.8691 (mttm) cc_final: 0.7464 (mttm) REVERT: A 215 THR cc_start: 0.8896 (t) cc_final: 0.8416 (p) REVERT: A 229 PHE cc_start: 0.7618 (p90) cc_final: 0.7199 (p90) REVERT: A 384 ILE cc_start: 0.9411 (pt) cc_final: 0.9034 (mm) REVERT: A 399 THR cc_start: 0.8006 (p) cc_final: 0.7508 (t) REVERT: A 415 MET cc_start: 0.4057 (ttt) cc_final: 0.3750 (ttt) REVERT: A 436 TRP cc_start: 0.7118 (m100) cc_final: 0.5747 (t60) REVERT: A 440 GLU cc_start: 0.5543 (tt0) cc_final: 0.4478 (mp0) REVERT: A 490 LEU cc_start: 0.8693 (mt) cc_final: 0.8478 (mp) REVERT: A 519 ASP cc_start: 0.8187 (t70) cc_final: 0.7958 (t70) REVERT: A 520 MET cc_start: 0.6321 (mmp) cc_final: 0.6071 (mmt) REVERT: A 530 VAL cc_start: 0.7723 (t) cc_final: 0.7486 (t) REVERT: A 916 PHE cc_start: 0.9048 (t80) cc_final: 0.8606 (t80) REVERT: A 931 LEU cc_start: 0.8783 (tp) cc_final: 0.7943 (tp) REVERT: A 959 MET cc_start: 0.6180 (mtt) cc_final: 0.5811 (ptt) REVERT: A 961 ASN cc_start: 0.8506 (t0) cc_final: 0.8229 (t0) REVERT: A 1112 ILE cc_start: 0.8052 (mt) cc_final: 0.7849 (mt) REVERT: A 1211 TYR cc_start: 0.6665 (m-80) cc_final: 0.6212 (m-80) REVERT: A 1314 MET cc_start: 0.8031 (mpp) cc_final: 0.7670 (mpp) REVERT: A 1328 LEU cc_start: 0.9338 (tp) cc_final: 0.9124 (tp) REVERT: B 142 GLN cc_start: 0.8826 (pm20) cc_final: 0.8063 (pm20) REVERT: B 164 LEU cc_start: 0.8433 (tp) cc_final: 0.8224 (tp) REVERT: B 202 SER cc_start: 0.9008 (t) cc_final: 0.8718 (p) REVERT: B 256 TYR cc_start: 0.8212 (t80) cc_final: 0.7701 (t80) REVERT: B 363 ILE cc_start: 0.8681 (tp) cc_final: 0.7855 (tp) REVERT: B 385 PHE cc_start: 0.7822 (m-80) cc_final: 0.7498 (m-80) REVERT: B 460 HIS cc_start: 0.7692 (m90) cc_final: 0.7334 (m90) REVERT: B 461 LEU cc_start: 0.9193 (mp) cc_final: 0.8881 (tp) REVERT: B 496 TYR cc_start: 0.6726 (m-10) cc_final: 0.6431 (m-80) REVERT: B 500 MET cc_start: 0.6775 (tmm) cc_final: 0.6119 (ttt) REVERT: B 510 THR cc_start: 0.7176 (t) cc_final: 0.6803 (t) REVERT: B 520 MET cc_start: 0.9281 (pmm) cc_final: 0.8945 (pmm) REVERT: B 545 VAL cc_start: 0.7968 (m) cc_final: 0.7679 (p) REVERT: B 557 LYS cc_start: 0.8545 (pttt) cc_final: 0.8152 (pttt) REVERT: B 571 SER cc_start: 0.8356 (t) cc_final: 0.7776 (p) REVERT: B 586 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6706 (mtp85) REVERT: B 619 TYR cc_start: 0.7679 (m-10) cc_final: 0.6831 (m-80) REVERT: B 627 LEU cc_start: 0.7628 (tp) cc_final: 0.7403 (mp) REVERT: B 789 PHE cc_start: 0.6669 (t80) cc_final: 0.6346 (t80) REVERT: B 959 MET cc_start: 0.6174 (ttm) cc_final: 0.5640 (ttm) REVERT: B 1172 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 1183 TRP cc_start: 0.8101 (m-90) cc_final: 0.7608 (m-90) REVERT: B 1328 LEU cc_start: 0.9634 (tp) cc_final: 0.9171 (tp) REVERT: C 101 MET cc_start: 0.7761 (mpp) cc_final: 0.7464 (mpp) REVERT: C 323 GLU cc_start: 0.8696 (mp0) cc_final: 0.8327 (mp0) REVERT: C 460 HIS cc_start: 0.8437 (t-90) cc_final: 0.8204 (t-90) REVERT: C 673 MET cc_start: 0.8075 (mpp) cc_final: 0.7785 (mpp) REVERT: C 945 ARG cc_start: 0.8120 (tmt170) cc_final: 0.6939 (ttt-90) REVERT: C 1123 ASN cc_start: 0.8685 (m110) cc_final: 0.8311 (m110) REVERT: C 1126 PHE cc_start: 0.8893 (m-80) cc_final: 0.8585 (m-80) REVERT: C 1208 MET cc_start: 0.8045 (ppp) cc_final: 0.7695 (ppp) REVERT: C 1325 GLN cc_start: 0.8878 (tt0) cc_final: 0.8571 (tt0) REVERT: D 181 PHE cc_start: 0.6363 (p90) cc_final: 0.5783 (p90) REVERT: D 214 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8002 (ttt90) REVERT: D 246 MET cc_start: -0.0448 (ttm) cc_final: -0.1002 (mtt) REVERT: D 318 MET cc_start: 0.8442 (mmp) cc_final: 0.7522 (tpp) REVERT: D 320 LEU cc_start: 0.8262 (mm) cc_final: 0.7884 (mm) REVERT: D 359 PHE cc_start: 0.7886 (p90) cc_final: 0.7629 (p90) REVERT: D 387 ARG cc_start: 0.9224 (mmp80) cc_final: 0.8854 (mmp80) REVERT: D 449 TYR cc_start: 0.7146 (m-80) cc_final: 0.6813 (m-80) REVERT: D 491 LYS cc_start: 0.9400 (ptpp) cc_final: 0.8944 (ttmm) REVERT: D 546 LEU cc_start: 0.7776 (tp) cc_final: 0.7353 (tp) REVERT: D 550 ASP cc_start: 0.8029 (t0) cc_final: 0.7564 (t0) REVERT: D 662 ASN cc_start: 0.9258 (p0) cc_final: 0.8894 (p0) REVERT: D 916 PHE cc_start: 0.8358 (m-80) cc_final: 0.8120 (m-80) REVERT: D 963 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7821 (tp40) REVERT: D 968 MET cc_start: -0.1909 (tpt) cc_final: -0.2708 (ttt) REVERT: D 1007 TYR cc_start: 0.6523 (m-80) cc_final: 0.5800 (t80) REVERT: D 1378 MET cc_start: 0.7584 (mmt) cc_final: 0.6111 (tpp) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.2514 time to fit residues: 210.0838 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 : 1.567 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 518 optimal weight: 2.9990 chunk 480 optimal weight: 0.4980 chunk 207 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 474 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 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 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN ** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1252 GLN C 168 GLN C 293 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 995 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.120119 restraints weight = 193226.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.123474 restraints weight = 134632.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.125837 restraints weight = 101617.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.127541 restraints weight = 81583.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.128761 restraints weight = 68660.279| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42463 Z= 0.171 Angle : 0.873 15.268 57794 Z= 0.431 Chirality : 0.052 0.400 6686 Planarity : 0.006 0.070 7358 Dihedral : 7.009 32.631 5590 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.18 % Favored : 85.69 % Rotamer: Outliers : 0.02 % Allowed : 0.70 % Favored : 99.28 % 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: -4.14 (0.10), residues: 5220 helix: -1.26 (0.17), residues: 822 sheet: -2.47 (0.13), residues: 1338 loop : -3.47 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1163 TYR 0.052 0.002 TYR A1152 PHE 0.064 0.002 PHE D 669 TRP 0.051 0.003 TRP B1237 HIS 0.012 0.001 HIS A1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (42374) covalent geometry : angle 0.85728 / 0.43 (57572) SS BOND : bond 0.00368 / 0.23 ( 45) SS BOND : angle 2.15210 / 1.44 ( 90) hydrogen bonds : bond 0.05893 / 4.00 ( 517) hydrogen bonds : angle 6.30518 / 4.17 ( 1551) link_ALPHA1-6 : bond 0.00205 / 0.11 ( 1) link_ALPHA1-6 : angle 1.68352 / 0.95 ( 3) link_BETA1-4 : bond 0.00489 / 0.32 ( 14) link_BETA1-4 : angle 2.31943 / 1.38 ( 42) link_NAG-ASN : bond 0.00708 / 0.40 ( 29) link_NAG-ASN : angle 3.46252 / 2.53 ( 87) =============================================================================== Job complete usr+sys time: 9719.33 seconds wall clock time: 168 minutes 53.49 seconds (10133.49 seconds total)