Starting phenix.real_space_refine on Thu Dec 26 09:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7l_12747/12_2024/7o7l_12747.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 192 5.16 5 C 28336 2.51 5 N 7398 2.21 5 O 8688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44614 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} 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: "B" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} Chain breaks: 2 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: J, D, C, H, I Time building chain proxies: 64.17, per 1000 atoms: 1.44 Number of scatterers: 44614 At special positions: 0 Unit cell: (210.447, 166.473, 217.776, 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 192 16.00 O 8688 8.00 N 7398 7.00 C 28336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, 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=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.04 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.10 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=2.04 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.05 Simple disulfide: pdb=" SG CYS A1352 " - pdb=" SG CYS A1467 " distance=2.04 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.04 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.05 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.04 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B1352 " - pdb=" SG CYS B1467 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM44430 O5 NAG B2005 .*. O " rejected from bonding due to valence issues. Atom "HETATM44612 O5 NAG D2005 .*. O " rejected from bonding due to valence issues. Atom "HETATM44234 O5 NAG J 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM44117 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " 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 A2006 " - " ASN A 869 " " NAG A2007 " - " ASN A 991 " " NAG A2008 " - " ASN A1424 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2004 " - " ASN B 869 " " NAG B2005 " - " ASN B 991 " " 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 C2006 " - " ASN C 869 " " NAG C2007 " - " ASN C 991 " " NAG C2008 " - " ASN C1424 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2004 " - " ASN D 869 " " NAG D2005 " - " ASN D 991 " " NAG E 1 " - " ASN B 396 " " NAG F 1 " - " ASN B 410 " " NAG G 1 " - " ASN B1424 " " NAG H 1 " - " ASN D 396 " " NAG I 1 " - " ASN D 410 " " NAG J 1 " - " ASN D1424 " Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 5.7 seconds 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 15.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 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 removed outlier: 3.702A pdb=" N LEU A 670 " --> pdb=" O MET A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 962 removed outlier: 6.631A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 962' Processing helix chain 'A' and resid 973 through 993 removed outlier: 5.012A pdb=" N MET A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) Proline residue: A 982 - end of helix removed outlier: 5.240A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 992 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 993 " --> pdb=" O TYR A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 removed outlier: 4.199A pdb=" N THR A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLN A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1052 removed outlier: 4.107A pdb=" N LYS A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1073 removed outlier: 3.611A pdb=" N ALA A1066 " --> pdb=" O HIS A1062 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A1073 " --> pdb=" O TRP A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1111 removed outlier: 3.811A pdb=" N THR A1106 " --> pdb=" O SER A1102 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A1111 " --> pdb=" O ILE A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1137 Processing helix chain 'A' and resid 1144 through 1157 removed outlier: 4.194A pdb=" N ALA A1148 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A1151 " --> pdb=" O LYS A1147 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A1152 " --> pdb=" O ALA A1148 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A1156 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1172 removed outlier: 3.732A pdb=" N LYS A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 3.975A pdb=" N TYR A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1241 removed outlier: 3.897A pdb=" N THR A1229 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A1238 " --> pdb=" O ILE A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1268 removed outlier: 5.459A pdb=" N VAL A1255 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A1256 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1258 " --> pdb=" O THR A1254 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A1259 " --> pdb=" O VAL A1255 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A1261 " --> pdb=" O ALA A1257 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A1265 " --> pdb=" O LEU A1261 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'A' and resid 1393 through 1400 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 958 through 962 removed outlier: 6.963A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 962' Processing helix chain 'B' and resid 973 through 993 removed outlier: 5.301A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 981 " --> pdb=" O MET B 977 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 3.972A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B 989 " --> pdb=" O TYR B 985 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASN B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 992 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 4.457A pdb=" N GLY B1006 " --> pdb=" O SER B1002 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN B1013 " --> pdb=" O ASN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1052 removed outlier: 3.740A pdb=" N VAL B1045 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B1048 " --> pdb=" O PHE B1044 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 3.959A pdb=" N LEU B1070 " --> pdb=" O ALA B1066 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B1073 " --> pdb=" O TRP B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 4.250A pdb=" N THR B1106 " --> pdb=" O SER B1102 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B1108 " --> pdb=" O TYR B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1137 removed outlier: 3.526A pdb=" N ARG B1122 " --> pdb=" O HIS B1118 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1124 " --> pdb=" O VAL B1120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B1130 " --> pdb=" O PHE B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.772A pdb=" N ALA B1148 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B1151 " --> pdb=" O LYS B1147 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B1155 " --> pdb=" O ALA B1151 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B1156 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 3.690A pdb=" N VAL B1166 " --> pdb=" O LYS B1162 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1167 " --> pdb=" O ARG B1163 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS B1168 " --> pdb=" O LYS B1164 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B1170 " --> pdb=" O VAL B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1217 removed outlier: 3.842A pdb=" N THR B1209 " --> pdb=" O GLU B1205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B1211 " --> pdb=" O GLU B1207 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B1215 " --> pdb=" O TYR B1211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B1217 " --> pdb=" O LEU B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 4.603A pdb=" N THR B1229 " --> pdb=" O SER B1225 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B1231 " --> pdb=" O ASP B1227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B1233 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE B1238 " --> pdb=" O ILE B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 5.208A pdb=" N VAL B1255 " --> pdb=" O THR B1251 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL B1256 " --> pdb=" O GLN B1252 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B1260 " --> pdb=" O VAL B1256 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B1261 " --> pdb=" O ALA B1257 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR B1264 " --> pdb=" O ALA B1260 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY B1265 " --> pdb=" O LEU B1261 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA B1266 " --> pdb=" O SER B1262 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'B' and resid 1393 through 1400 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 removed outlier: 3.702A pdb=" N LEU C 670 " --> pdb=" O MET C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 962 removed outlier: 6.631A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 962' Processing helix chain 'C' and resid 973 through 993 removed outlier: 5.012A pdb=" N MET C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL C 978 " --> pdb=" O GLU C 974 " (cutoff:3.500A) Proline residue: C 982 - end of helix removed outlier: 5.240A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR C 989 " --> pdb=" O TYR C 985 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 992 " --> pdb=" O ASP C 988 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 993 " --> pdb=" O TYR C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 removed outlier: 4.199A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1052 removed outlier: 4.107A pdb=" N LYS C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C1048 " --> pdb=" O PHE C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1073 removed outlier: 3.611A pdb=" N ALA C1066 " --> pdb=" O HIS C1062 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG C1073 " --> pdb=" O TRP C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1111 removed outlier: 3.811A pdb=" N THR C1106 " --> pdb=" O SER C1102 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C1111 " --> pdb=" O ILE C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1137 Processing helix chain 'C' and resid 1144 through 1157 removed outlier: 4.194A pdb=" N ALA C1148 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA C1151 " --> pdb=" O LYS C1147 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C1152 " --> pdb=" O ALA C1148 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C1154 " --> pdb=" O LEU C1150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C1156 " --> pdb=" O TYR C1152 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA C1157 " --> pdb=" O ALA C1153 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1172 removed outlier: 3.732A pdb=" N LYS C1168 " --> pdb=" O LYS C1164 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C1169 " --> pdb=" O GLU C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1217 removed outlier: 3.975A pdb=" N TYR C1211 " --> pdb=" O GLU C1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 1225 through 1241 removed outlier: 3.897A pdb=" N THR C1229 " --> pdb=" O SER C1225 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C1237 " --> pdb=" O ASN C1233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C1238 " --> pdb=" O ILE C1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 1251 through 1268 removed outlier: 5.459A pdb=" N VAL C1255 " --> pdb=" O THR C1251 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL C1256 " --> pdb=" O GLN C1252 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C1258 " --> pdb=" O THR C1254 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS C1259 " --> pdb=" O VAL C1255 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C1260 " --> pdb=" O VAL C1256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C1261 " --> pdb=" O ALA C1257 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C1264 " --> pdb=" O ALA C1260 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C1265 " --> pdb=" O LEU C1261 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA C1266 " --> pdb=" O SER C1262 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1267 " --> pdb=" O LYS C1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'C' and resid 1393 through 1400 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 Processing helix chain 'D' and resid 958 through 962 removed outlier: 6.963A 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: 5.301A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 978 " --> pdb=" O GLU D 974 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 981 " --> pdb=" O MET D 977 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 3.972A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR D 989 " --> pdb=" O TYR D 985 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASN D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 992 " --> pdb=" O ASP D 988 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR D 993 " --> pdb=" O TYR D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 4.457A pdb=" N GLY D1006 " --> pdb=" O SER D1002 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN D1013 " --> pdb=" O ASN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 3.740A pdb=" N VAL D1045 " --> pdb=" O LEU D1041 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D1048 " --> pdb=" O PHE D1044 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D1050 " --> pdb=" O LEU D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.959A pdb=" N LEU D1070 " --> pdb=" O ALA D1066 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D1073 " --> pdb=" O TRP D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 removed outlier: 4.250A pdb=" N THR D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D1108 " --> pdb=" O TYR D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 removed outlier: 3.526A pdb=" N ARG D1122 " --> pdb=" O HIS D1118 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D1124 " --> pdb=" O VAL D1120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D1130 " --> pdb=" O PHE D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.772A pdb=" N ALA D1148 " --> pdb=" O VAL D1144 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D1151 " --> pdb=" O LYS D1147 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D1155 " --> pdb=" O ALA D1151 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 3.690A pdb=" N VAL D1166 " --> pdb=" O LYS D1162 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D1167 " --> pdb=" O ARG D1163 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS D1168 " --> pdb=" O LYS D1164 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1217 removed outlier: 3.842A pdb=" N THR D1209 " --> pdb=" O GLU D1205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D1215 " --> pdb=" O TYR D1211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.603A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D1231 " --> pdb=" O ASP D1227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 5.208A pdb=" N VAL D1255 " --> pdb=" O THR D1251 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D1256 " --> pdb=" O GLN D1252 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D1261 " --> pdb=" O ALA D1257 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR D1264 " --> pdb=" O ALA D1260 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY D1265 " --> pdb=" O LEU D1261 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA D1266 " --> pdb=" O SER D1262 " (cutoff:3.500A) removed outlier: 4.103A 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 384 hydrogen bonds defined for protein. 1152 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: 10.50 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 13390 1.34 - 1.48: 12514 1.48 - 1.63: 19404 1.63 - 1.78: 10 1.78 - 1.92: 274 Bond restraints: 45592 Sorted by residual: bond pdb=" CA SER B1372 " pdb=" CB SER B1372 " ideal model delta sigma weight residual 1.530 1.482 0.049 9.80e-03 1.04e+04 2.45e+01 bond pdb=" CA SER D1372 " pdb=" CB SER D1372 " ideal model delta sigma weight residual 1.530 1.482 0.049 9.80e-03 1.04e+04 2.45e+01 bond pdb=" C LYS C 271 " pdb=" O LYS C 271 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.10e-02 8.26e+03 1.79e+01 bond pdb=" C LYS A 271 " pdb=" O LYS A 271 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.10e-02 8.26e+03 1.79e+01 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.22e-02 6.72e+03 1.48e+01 ... (remaining 45587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 61206 4.05 - 8.10: 692 8.10 - 12.14: 34 12.14 - 16.19: 14 16.19 - 20.24: 4 Bond angle restraints: 61950 Sorted by residual: angle pdb=" N ALA D 391 " pdb=" CA ALA D 391 " pdb=" C ALA D 391 " ideal model delta sigma weight residual 114.12 98.01 16.11 1.39e+00 5.18e-01 1.34e+02 angle pdb=" N ALA B 391 " pdb=" CA ALA B 391 " pdb=" C ALA B 391 " ideal model delta sigma weight residual 114.12 98.01 16.11 1.39e+00 5.18e-01 1.34e+02 angle pdb=" N PRO A 845 " pdb=" CA PRO A 845 " pdb=" C PRO A 845 " ideal model delta sigma weight residual 111.26 93.43 17.83 1.63e+00 3.76e-01 1.20e+02 angle pdb=" N PRO C 845 " pdb=" CA PRO C 845 " pdb=" C PRO C 845 " ideal model delta sigma weight residual 111.26 93.43 17.83 1.63e+00 3.76e-01 1.20e+02 angle pdb=" N SER B 801 " pdb=" CA SER B 801 " pdb=" C SER B 801 " ideal model delta sigma weight residual 108.96 92.95 16.01 1.59e+00 3.96e-01 1.01e+02 ... (remaining 61945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 25501 21.46 - 42.92: 2176 42.92 - 64.38: 313 64.38 - 85.84: 91 85.84 - 107.30: 22 Dihedral angle restraints: 28103 sinusoidal: 11645 harmonic: 16458 Sorted by residual: dihedral pdb=" C GLU C1184 " pdb=" N GLU C1184 " pdb=" CA GLU C1184 " pdb=" CB GLU C1184 " ideal model delta harmonic sigma weight residual -122.60 -156.36 33.76 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" C GLU A1184 " pdb=" N GLU A1184 " pdb=" CA GLU A1184 " pdb=" CB GLU A1184 " ideal model delta harmonic sigma weight residual -122.60 -156.36 33.76 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N GLU C1184 " pdb=" C GLU C1184 " pdb=" CA GLU C1184 " pdb=" CB GLU C1184 " ideal model delta harmonic sigma weight residual 122.80 155.88 -33.08 0 2.50e+00 1.60e-01 1.75e+02 ... (remaining 28100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 7154 0.370 - 0.741: 34 0.741 - 1.111: 4 1.111 - 1.482: 4 1.482 - 1.852: 2 Chirality restraints: 7198 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.47e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.47e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.85e+01 ... (remaining 7195 not shown) Planarity restraints: 7946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D2005 " 0.358 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG D2005 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG D2005 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG D2005 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG D2005 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2005 " -0.358 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG B2005 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B2005 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG B2005 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG B2005 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2002 " -0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG A2002 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A2002 " -0.134 2.00e-02 2.50e+03 pdb=" N2 NAG A2002 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG A2002 " -0.140 2.00e-02 2.50e+03 ... (remaining 7943 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1133 2.59 - 3.17: 43548 3.17 - 3.75: 72866 3.75 - 4.32: 98165 4.32 - 4.90: 148466 Nonbonded interactions: 364178 Sorted by model distance: nonbonded pdb=" SG CYS D 642 " pdb=" SG CYS D 689 " model vdw 2.015 3.760 nonbonded pdb=" SG CYS C 251 " pdb=" SG CYS C 299 " model vdw 2.027 3.760 nonbonded pdb=" OG SER D 94 " pdb=" O SER D 96 " model vdw 2.027 3.040 nonbonded pdb=" OG SER B 94 " pdb=" O SER B 96 " model vdw 2.027 3.040 nonbonded pdb=" SG CYS C 470 " pdb=" SG CYS C 563 " model vdw 2.028 3.760 ... (remaining 364173 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 26 through 1468 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1468 or resid 2001 through 2005)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.810 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 125.390 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 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 : 0.008 0.117 45592 Z= 0.502 Angle : 1.161 20.241 61950 Z= 0.630 Chirality : 0.083 1.852 7198 Planarity : 0.020 0.308 7916 Dihedral : 16.568 107.301 17426 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.83 % Favored : 82.49 % Rotamer: Outliers : 0.49 % Allowed : 4.25 % Favored : 95.27 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.09), residues: 5620 helix: -3.65 (0.13), residues: 692 sheet: -3.24 (0.11), residues: 1506 loop : -4.02 (0.08), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1183 HIS 0.012 0.002 HIS B 321 PHE 0.050 0.003 PHE D1057 TYR 0.036 0.003 TYR B1418 ARG 0.013 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 972 time to evaluate : 5.138 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 281 GLU cc_start: 0.4605 (OUTLIER) cc_final: 0.3449 (mp0) REVERT: A 381 ASN cc_start: 0.9679 (t0) cc_final: 0.9461 (m-40) REVERT: A 460 HIS cc_start: 0.6647 (t-170) cc_final: 0.4405 (t-170) REVERT: A 607 MET cc_start: 0.5321 (mtt) cc_final: 0.4966 (mtt) REVERT: A 985 TYR cc_start: 0.5883 (m-10) cc_final: 0.5214 (m-10) REVERT: B 197 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 200 GLN cc_start: 0.8011 (tt0) cc_final: 0.7736 (tm-30) REVERT: B 318 MET cc_start: 0.9231 (ttp) cc_final: 0.8976 (ttm) REVERT: B 333 VAL cc_start: 0.7678 (t) cc_final: 0.7380 (p) REVERT: B 347 ILE cc_start: 0.1549 (mm) cc_final: 0.0450 (mm) REVERT: B 381 ASN cc_start: 0.9423 (m110) cc_final: 0.9100 (t0) REVERT: B 428 ARG cc_start: 0.8928 (ptp90) cc_final: 0.8212 (ttp80) REVERT: B 500 MET cc_start: 0.7871 (ttm) cc_final: 0.6935 (ttm) REVERT: B 520 MET cc_start: 0.3701 (ttt) cc_final: 0.3171 (ttt) REVERT: B 539 ARG cc_start: 0.7376 (mtt-85) cc_final: 0.6957 (mtt180) REVERT: B 569 ASP cc_start: 0.8588 (t0) cc_final: 0.8362 (t0) REVERT: B 735 PHE cc_start: 0.9275 (m-80) cc_final: 0.9018 (m-80) REVERT: B 840 GLU cc_start: 0.7368 (pm20) cc_final: 0.6554 (tp30) REVERT: B 877 LEU cc_start: 0.8832 (tt) cc_final: 0.8555 (mm) REVERT: B 916 PHE cc_start: 0.8740 (m-80) cc_final: 0.8392 (m-80) REVERT: B 933 LEU cc_start: 0.9172 (mp) cc_final: 0.7687 (mp) REVERT: B 1047 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7497 (pttp) REVERT: B 1152 TYR cc_start: 0.7502 (t80) cc_final: 0.7218 (t80) REVERT: B 1172 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7869 (mm-30) REVERT: B 1312 TYR cc_start: 0.8948 (m-80) cc_final: 0.8615 (m-80) REVERT: B 1330 TYR cc_start: 0.9011 (p90) cc_final: 0.8541 (p90) REVERT: B 1331 ASN cc_start: 0.8735 (m110) cc_final: 0.8484 (m-40) REVERT: B 1390 ILE cc_start: 0.9625 (tt) cc_final: 0.9280 (tp) REVERT: B 1446 ILE cc_start: 0.8348 (pt) cc_final: 0.8039 (pt) REVERT: C 281 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.3451 (mp0) REVERT: C 381 ASN cc_start: 0.9680 (t0) cc_final: 0.9461 (m-40) REVERT: C 460 HIS cc_start: 0.6640 (t-170) cc_final: 0.4398 (t-170) REVERT: C 607 MET cc_start: 0.5325 (mtt) cc_final: 0.4961 (mtt) REVERT: C 985 TYR cc_start: 0.5878 (m-10) cc_final: 0.5214 (m-10) REVERT: D 197 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 200 GLN cc_start: 0.8009 (tt0) cc_final: 0.7735 (tm-30) REVERT: D 318 MET cc_start: 0.9234 (ttp) cc_final: 0.8977 (ttm) REVERT: D 333 VAL cc_start: 0.7679 (t) cc_final: 0.7384 (p) REVERT: D 347 ILE cc_start: 0.1550 (mm) cc_final: 0.0454 (mm) REVERT: D 381 ASN cc_start: 0.9423 (m110) cc_final: 0.9101 (t0) REVERT: D 428 ARG cc_start: 0.8927 (ptp90) cc_final: 0.8210 (ttp80) REVERT: D 500 MET cc_start: 0.7871 (ttm) cc_final: 0.6937 (ttm) REVERT: D 520 MET cc_start: 0.3700 (ttt) cc_final: 0.3169 (ttt) REVERT: D 539 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.6960 (mtt180) REVERT: D 569 ASP cc_start: 0.8589 (t0) cc_final: 0.8364 (t0) REVERT: D 735 PHE cc_start: 0.9276 (m-80) cc_final: 0.9019 (m-80) REVERT: D 840 GLU cc_start: 0.7364 (pm20) cc_final: 0.6552 (tp30) REVERT: D 877 LEU cc_start: 0.8832 (tt) cc_final: 0.8554 (mm) REVERT: D 916 PHE cc_start: 0.8736 (m-80) cc_final: 0.8389 (m-80) REVERT: D 933 LEU cc_start: 0.9174 (mp) cc_final: 0.7694 (mp) REVERT: D 1047 LYS cc_start: 0.8268 (ptpt) cc_final: 0.7489 (pttp) REVERT: D 1152 TYR cc_start: 0.7507 (t80) cc_final: 0.7243 (t80) REVERT: D 1172 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 1312 TYR cc_start: 0.8949 (m-80) cc_final: 0.8615 (m-80) REVERT: D 1330 TYR cc_start: 0.9010 (p90) cc_final: 0.8541 (p90) REVERT: D 1331 ASN cc_start: 0.8735 (m110) cc_final: 0.8489 (m-40) REVERT: D 1390 ILE cc_start: 0.9625 (tt) cc_final: 0.9281 (tp) REVERT: D 1446 ILE cc_start: 0.8351 (pt) cc_final: 0.8040 (pt) outliers start: 24 outliers final: 4 residues processed: 992 average time/residue: 0.6303 time to fit residues: 995.9525 Evaluate side-chains 643 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 637 time to evaluate : 4.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 7.9990 chunk 427 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 146 optimal weight: 0.0270 chunk 288 optimal weight: 40.0000 chunk 228 optimal weight: 10.0000 chunk 442 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 329 optimal weight: 8.9990 chunk 512 optimal weight: 3.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 279 HIS A 302 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 168 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 303 GLN B 460 HIS B 511 HIS B 644 ASN B 647 ASN B 693 GLN ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 ASN B1259 HIS ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 263 HIS ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN C 302 GLN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1259 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 168 GLN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN D 303 GLN D 460 HIS D 511 HIS D 647 ASN D 693 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1179 ASN D1259 HIS ** D1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 45592 Z= 0.266 Angle : 0.937 11.781 61950 Z= 0.463 Chirality : 0.055 0.546 7198 Planarity : 0.006 0.085 7916 Dihedral : 9.868 70.807 6934 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.84 % Favored : 85.77 % Rotamer: Outliers : 0.42 % Allowed : 8.17 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.09), residues: 5620 helix: -2.89 (0.15), residues: 698 sheet: -2.76 (0.12), residues: 1550 loop : -3.79 (0.09), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C1183 HIS 0.012 0.001 HIS B 321 PHE 0.040 0.002 PHE B 452 TYR 0.031 0.002 TYR C1418 ARG 0.007 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 818 time to evaluate : 4.827 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 230 GLU cc_start: 0.7928 (mp0) cc_final: 0.7716 (mp0) REVERT: A 318 MET cc_start: 0.4844 (mtt) cc_final: 0.4480 (mtt) REVERT: A 381 ASN cc_start: 0.9697 (t0) cc_final: 0.9451 (m-40) REVERT: A 385 PHE cc_start: 0.8920 (m-80) cc_final: 0.8577 (m-80) REVERT: A 460 HIS cc_start: 0.7347 (t-170) cc_final: 0.6718 (t-170) REVERT: A 607 MET cc_start: 0.5339 (mtt) cc_final: 0.4797 (mtt) REVERT: A 648 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6193 (t) REVERT: A 916 PHE cc_start: 0.8040 (m-10) cc_final: 0.7711 (m-10) REVERT: A 968 MET cc_start: 0.5938 (mmp) cc_final: 0.5522 (mmm) REVERT: A 985 TYR cc_start: 0.5848 (m-10) cc_final: 0.5486 (m-10) REVERT: A 1311 GLU cc_start: 0.8450 (pm20) cc_final: 0.8152 (pm20) REVERT: A 1330 TYR cc_start: 0.9604 (p90) cc_final: 0.9271 (p90) REVERT: B 121 MET cc_start: 0.7382 (mmp) cc_final: 0.6880 (mpp) REVERT: B 145 LYS cc_start: 0.8466 (mptt) cc_final: 0.8122 (mmtm) REVERT: B 177 GLN cc_start: 0.8882 (tt0) cc_final: 0.8483 (tm-30) REVERT: B 194 LEU cc_start: 0.9350 (mt) cc_final: 0.9129 (mt) REVERT: B 197 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7761 (pp20) REVERT: B 333 VAL cc_start: 0.7713 (t) cc_final: 0.6954 (t) REVERT: B 381 ASN cc_start: 0.9450 (m110) cc_final: 0.9028 (t0) REVERT: B 415 MET cc_start: 0.7981 (mmp) cc_final: 0.7731 (mmp) REVERT: B 428 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8332 (ttp80) REVERT: B 520 MET cc_start: 0.4610 (ttt) cc_final: 0.4330 (ttt) REVERT: B 539 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6169 (mtt180) REVERT: B 557 LYS cc_start: 0.9337 (mtpt) cc_final: 0.9020 (mmtp) REVERT: B 625 LYS cc_start: 0.8693 (pptt) cc_final: 0.8343 (ptmm) REVERT: B 735 PHE cc_start: 0.9256 (m-80) cc_final: 0.8964 (m-80) REVERT: B 764 GLU cc_start: 0.9245 (mp0) cc_final: 0.9035 (pm20) REVERT: B 840 GLU cc_start: 0.7507 (pm20) cc_final: 0.6370 (tp30) REVERT: B 916 PHE cc_start: 0.8498 (m-80) cc_final: 0.8239 (m-80) REVERT: B 1047 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7404 (pttp) REVERT: B 1172 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8250 (mm-30) REVERT: B 1212 VAL cc_start: 0.8814 (t) cc_final: 0.8601 (t) REVERT: B 1248 PHE cc_start: 0.8014 (t80) cc_final: 0.7721 (t80) REVERT: B 1279 THR cc_start: 0.9095 (p) cc_final: 0.8748 (p) REVERT: B 1292 VAL cc_start: 0.9433 (t) cc_final: 0.9226 (t) REVERT: B 1314 MET cc_start: 0.8953 (mmp) cc_final: 0.8700 (mmp) REVERT: B 1315 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8788 (mtpp) REVERT: B 1330 TYR cc_start: 0.8892 (p90) cc_final: 0.8458 (p90) REVERT: B 1331 ASN cc_start: 0.8676 (m110) cc_final: 0.8363 (m-40) REVERT: B 1393 LYS cc_start: 0.8873 (tmmt) cc_final: 0.8573 (tmmt) REVERT: B 1446 ILE cc_start: 0.7994 (pt) cc_final: 0.7770 (pt) REVERT: C 318 MET cc_start: 0.4869 (mtt) cc_final: 0.4493 (mtt) REVERT: C 381 ASN cc_start: 0.9697 (t0) cc_final: 0.9452 (m-40) REVERT: C 385 PHE cc_start: 0.8923 (m-80) cc_final: 0.8581 (m-80) REVERT: C 460 HIS cc_start: 0.7343 (t-170) cc_final: 0.6713 (t-170) REVERT: C 607 MET cc_start: 0.5344 (mtt) cc_final: 0.4795 (mtt) REVERT: C 648 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6194 (t) REVERT: C 916 PHE cc_start: 0.8038 (m-10) cc_final: 0.7710 (m-10) REVERT: C 968 MET cc_start: 0.5930 (mmp) cc_final: 0.5518 (mmm) REVERT: C 985 TYR cc_start: 0.5850 (m-10) cc_final: 0.5491 (m-10) REVERT: C 1311 GLU cc_start: 0.8454 (pm20) cc_final: 0.8157 (pm20) REVERT: C 1330 TYR cc_start: 0.9602 (p90) cc_final: 0.9269 (p90) REVERT: D 121 MET cc_start: 0.7386 (mmp) cc_final: 0.6878 (mpp) REVERT: D 145 LYS cc_start: 0.8470 (mptt) cc_final: 0.8125 (mmtm) REVERT: D 177 GLN cc_start: 0.8884 (tt0) cc_final: 0.8483 (tm-30) REVERT: D 194 LEU cc_start: 0.9352 (mt) cc_final: 0.9130 (mt) REVERT: D 197 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7762 (pp20) REVERT: D 318 MET cc_start: 0.9150 (ttp) cc_final: 0.8883 (ttt) REVERT: D 333 VAL cc_start: 0.7717 (t) cc_final: 0.7015 (t) REVERT: D 381 ASN cc_start: 0.9448 (m110) cc_final: 0.9024 (t0) REVERT: D 415 MET cc_start: 0.7983 (mmp) cc_final: 0.7733 (mmp) REVERT: D 428 ARG cc_start: 0.8936 (ptp90) cc_final: 0.8331 (ttp80) REVERT: D 520 MET cc_start: 0.4615 (ttt) cc_final: 0.4338 (ttt) REVERT: D 539 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.7110 (mtt180) REVERT: D 625 LYS cc_start: 0.8691 (pptt) cc_final: 0.8337 (ptmm) REVERT: D 689 CYS cc_start: 0.0397 (OUTLIER) cc_final: -0.0206 (m) REVERT: D 735 PHE cc_start: 0.9258 (m-80) cc_final: 0.8964 (m-80) REVERT: D 764 GLU cc_start: 0.9246 (mp0) cc_final: 0.9035 (pm20) REVERT: D 840 GLU cc_start: 0.7521 (pm20) cc_final: 0.6386 (tp30) REVERT: D 916 PHE cc_start: 0.8504 (m-80) cc_final: 0.8245 (m-80) REVERT: D 1047 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7396 (pttp) REVERT: D 1172 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 1212 VAL cc_start: 0.8811 (t) cc_final: 0.8599 (t) REVERT: D 1248 PHE cc_start: 0.8014 (t80) cc_final: 0.7720 (t80) REVERT: D 1279 THR cc_start: 0.9096 (p) cc_final: 0.8747 (p) REVERT: D 1292 VAL cc_start: 0.9433 (t) cc_final: 0.9226 (t) REVERT: D 1314 MET cc_start: 0.8951 (mmp) cc_final: 0.8697 (mmp) REVERT: D 1315 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8786 (mtpp) REVERT: D 1330 TYR cc_start: 0.8891 (p90) cc_final: 0.8460 (p90) REVERT: D 1331 ASN cc_start: 0.8676 (m110) cc_final: 0.8366 (m-40) REVERT: D 1393 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8569 (tmmt) REVERT: D 1446 ILE cc_start: 0.7993 (pt) cc_final: 0.7766 (pt) outliers start: 21 outliers final: 3 residues processed: 839 average time/residue: 0.6139 time to fit residues: 835.1558 Evaluate side-chains 622 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 616 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 284 optimal weight: 0.6980 chunk 158 optimal weight: 0.0570 chunk 426 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 513 optimal weight: 4.9990 chunk 554 optimal weight: 9.9990 chunk 456 optimal weight: 0.7980 chunk 508 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 411 optimal weight: 0.1980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN A 511 HIS A 646 HIS A1179 ASN A1187 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1404 HIS ** B1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 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 279 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 511 HIS C 646 HIS C 880 GLN C1015 GLN C1179 ASN C1187 GLN ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1404 HIS ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 45592 Z= 0.235 Angle : 0.862 12.017 61950 Z= 0.425 Chirality : 0.051 0.286 7198 Planarity : 0.006 0.078 7916 Dihedral : 8.606 57.708 6934 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.38 % Favored : 86.26 % Rotamer: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.10), residues: 5620 helix: -2.50 (0.16), residues: 708 sheet: -2.48 (0.12), residues: 1586 loop : -3.60 (0.09), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1183 HIS 0.015 0.001 HIS B 321 PHE 0.035 0.002 PHE D1049 TYR 0.033 0.002 TYR B1007 ARG 0.007 0.001 ARG D 945 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 796 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 230 GLU cc_start: 0.7824 (mp0) cc_final: 0.7622 (mp0) REVERT: A 270 ARG cc_start: 0.3172 (mtp180) cc_final: 0.2379 (mmm160) REVERT: A 318 MET cc_start: 0.4847 (mtt) cc_final: 0.4380 (mtt) REVERT: A 327 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5983 (pp30) REVERT: A 381 ASN cc_start: 0.9674 (t0) cc_final: 0.9460 (m-40) REVERT: A 385 PHE cc_start: 0.8873 (m-80) cc_final: 0.8600 (m-80) REVERT: A 392 ASN cc_start: 0.9205 (p0) cc_final: 0.8998 (p0) REVERT: A 456 LYS cc_start: 0.9105 (pttm) cc_final: 0.8476 (tptt) REVERT: A 460 HIS cc_start: 0.7660 (t-170) cc_final: 0.7065 (t-170) REVERT: A 607 MET cc_start: 0.5483 (mtt) cc_final: 0.4968 (mtt) REVERT: A 655 TYR cc_start: 0.2558 (p90) cc_final: 0.1588 (p90) REVERT: A 673 MET cc_start: 0.2796 (mmp) cc_final: 0.2201 (mmm) REVERT: A 1259 HIS cc_start: 0.9442 (t70) cc_final: 0.9184 (t70) REVERT: A 1314 MET cc_start: 0.0369 (tmm) cc_final: -0.0071 (tmm) REVERT: A 1330 TYR cc_start: 0.9589 (p90) cc_final: 0.9209 (p90) REVERT: B 121 MET cc_start: 0.7318 (mmp) cc_final: 0.6849 (mpp) REVERT: B 145 LYS cc_start: 0.8406 (mptt) cc_final: 0.8088 (mmtm) REVERT: B 177 GLN cc_start: 0.8843 (tt0) cc_final: 0.8583 (tm-30) REVERT: B 197 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7780 (pp20) REVERT: B 221 VAL cc_start: 0.9408 (t) cc_final: 0.8945 (p) REVERT: B 254 TYR cc_start: 0.9139 (m-10) cc_final: 0.8883 (m-10) REVERT: B 319 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8330 (mmpt) REVERT: B 321 HIS cc_start: 0.8869 (p-80) cc_final: 0.8334 (p-80) REVERT: B 333 VAL cc_start: 0.7783 (t) cc_final: 0.7218 (t) REVERT: B 381 ASN cc_start: 0.9489 (m110) cc_final: 0.8985 (t0) REVERT: B 441 HIS cc_start: 0.7998 (m-70) cc_final: 0.7787 (m-70) REVERT: B 496 TYR cc_start: 0.8101 (m-10) cc_final: 0.7899 (m-10) REVERT: B 500 MET cc_start: 0.7419 (mtt) cc_final: 0.5624 (mtt) REVERT: B 520 MET cc_start: 0.4712 (ttt) cc_final: 0.4421 (ttt) REVERT: B 539 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.6202 (mtt180) REVERT: B 557 LYS cc_start: 0.9294 (mtpt) cc_final: 0.9004 (mmtp) REVERT: B 586 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8312 (tpt-90) REVERT: B 625 LYS cc_start: 0.8884 (pptt) cc_final: 0.8531 (ptmm) REVERT: B 673 MET cc_start: 0.8268 (tpt) cc_final: 0.7775 (tpt) REVERT: B 735 PHE cc_start: 0.9209 (m-80) cc_final: 0.8918 (m-80) REVERT: B 764 GLU cc_start: 0.9271 (mp0) cc_final: 0.9045 (pm20) REVERT: B 787 ARG cc_start: 0.8517 (tmt170) cc_final: 0.8292 (ttp80) REVERT: B 840 GLU cc_start: 0.7602 (pm20) cc_final: 0.6244 (tp30) REVERT: B 933 LEU cc_start: 0.8605 (mp) cc_final: 0.6233 (mp) REVERT: B 1047 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7847 (pptt) REVERT: B 1208 MET cc_start: 0.8255 (ppp) cc_final: 0.8013 (ppp) REVERT: B 1209 THR cc_start: 0.8551 (m) cc_final: 0.8336 (m) REVERT: B 1212 VAL cc_start: 0.8769 (t) cc_final: 0.8514 (p) REVERT: B 1248 PHE cc_start: 0.7939 (t80) cc_final: 0.7663 (t80) REVERT: B 1312 TYR cc_start: 0.8330 (m-10) cc_final: 0.7921 (m-10) REVERT: B 1315 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8752 (mtpp) REVERT: B 1329 LYS cc_start: 0.9457 (pttt) cc_final: 0.9242 (ptpt) REVERT: B 1436 ASP cc_start: 0.7612 (m-30) cc_final: 0.7072 (m-30) REVERT: B 1446 ILE cc_start: 0.7913 (pt) cc_final: 0.7603 (pt) REVERT: C 270 ARG cc_start: 0.3004 (mtp180) cc_final: 0.2252 (mmm160) REVERT: C 318 MET cc_start: 0.5061 (mtt) cc_final: 0.4552 (mtt) REVERT: C 327 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5993 (pp30) REVERT: C 381 ASN cc_start: 0.9674 (t0) cc_final: 0.9461 (m-40) REVERT: C 385 PHE cc_start: 0.8874 (m-80) cc_final: 0.8603 (m-80) REVERT: C 392 ASN cc_start: 0.9206 (p0) cc_final: 0.8999 (p0) REVERT: C 456 LYS cc_start: 0.9105 (pttm) cc_final: 0.8477 (tptt) REVERT: C 460 HIS cc_start: 0.7654 (t-170) cc_final: 0.7062 (t-170) REVERT: C 607 MET cc_start: 0.5484 (mtt) cc_final: 0.4962 (mtt) REVERT: C 655 TYR cc_start: 0.2563 (p90) cc_final: 0.1592 (p90) REVERT: C 673 MET cc_start: 0.2798 (mmp) cc_final: 0.2203 (mmm) REVERT: C 778 LEU cc_start: 0.8433 (pp) cc_final: 0.8203 (pp) REVERT: C 1259 HIS cc_start: 0.9444 (t70) cc_final: 0.9185 (t70) REVERT: C 1311 GLU cc_start: 0.8436 (pm20) cc_final: 0.8061 (pm20) REVERT: C 1314 MET cc_start: 0.0615 (tmm) cc_final: 0.0301 (tmm) REVERT: C 1330 TYR cc_start: 0.9585 (p90) cc_final: 0.9205 (p90) REVERT: D 121 MET cc_start: 0.7328 (mmp) cc_final: 0.6858 (mpp) REVERT: D 145 LYS cc_start: 0.8414 (mptt) cc_final: 0.8096 (mmtm) REVERT: D 177 GLN cc_start: 0.8844 (tt0) cc_final: 0.8582 (tm-30) REVERT: D 197 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7780 (pp20) REVERT: D 221 VAL cc_start: 0.9407 (t) cc_final: 0.8949 (p) REVERT: D 254 TYR cc_start: 0.9202 (m-10) cc_final: 0.8981 (m-10) REVERT: D 321 HIS cc_start: 0.8883 (p-80) cc_final: 0.8478 (p-80) REVERT: D 333 VAL cc_start: 0.7792 (t) cc_final: 0.7253 (t) REVERT: D 381 ASN cc_start: 0.9489 (m110) cc_final: 0.8983 (t0) REVERT: D 441 HIS cc_start: 0.7997 (m-70) cc_final: 0.7777 (m-70) REVERT: D 500 MET cc_start: 0.7430 (mtt) cc_final: 0.5696 (mtt) REVERT: D 520 MET cc_start: 0.4714 (ttt) cc_final: 0.4419 (ttt) REVERT: D 539 ARG cc_start: 0.7377 (mtt-85) cc_final: 0.6218 (mtt180) REVERT: D 557 LYS cc_start: 0.9295 (mtpt) cc_final: 0.9005 (mmtp) REVERT: D 586 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8310 (tpt-90) REVERT: D 625 LYS cc_start: 0.8885 (pptt) cc_final: 0.8536 (ptmm) REVERT: D 638 ASP cc_start: 0.9425 (p0) cc_final: 0.9223 (p0) REVERT: D 673 MET cc_start: 0.8247 (tpt) cc_final: 0.7783 (tpt) REVERT: D 735 PHE cc_start: 0.9213 (m-80) cc_final: 0.8917 (m-80) REVERT: D 764 GLU cc_start: 0.9271 (mp0) cc_final: 0.9045 (pm20) REVERT: D 787 ARG cc_start: 0.8514 (tmt170) cc_final: 0.8292 (ttp80) REVERT: D 840 GLU cc_start: 0.7628 (pm20) cc_final: 0.6273 (tp30) REVERT: D 1047 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7842 (pptt) REVERT: D 1164 LYS cc_start: 0.6867 (tptt) cc_final: 0.6662 (tptt) REVERT: D 1208 MET cc_start: 0.8257 (ppp) cc_final: 0.8016 (ppp) REVERT: D 1209 THR cc_start: 0.8558 (m) cc_final: 0.8347 (m) REVERT: D 1212 VAL cc_start: 0.8771 (t) cc_final: 0.8518 (p) REVERT: D 1248 PHE cc_start: 0.7933 (t80) cc_final: 0.7659 (t80) REVERT: D 1312 TYR cc_start: 0.8331 (m-10) cc_final: 0.8072 (m-10) REVERT: D 1315 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8745 (mtpp) REVERT: D 1329 LYS cc_start: 0.9456 (pttt) cc_final: 0.9239 (ptpt) REVERT: D 1436 ASP cc_start: 0.7494 (m-30) cc_final: 0.6939 (m-30) REVERT: D 1446 ILE cc_start: 0.7935 (pt) cc_final: 0.7633 (pt) outliers start: 6 outliers final: 2 residues processed: 802 average time/residue: 0.6134 time to fit residues: 794.6340 Evaluate side-chains 615 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 611 time to evaluate : 5.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 506 optimal weight: 1.9990 chunk 385 optimal weight: 0.2980 chunk 266 optimal weight: 5.9990 chunk 56 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 514 optimal weight: 0.0980 chunk 545 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 488 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN A 460 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 562 ASN B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 85 HIS ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1089 ASN ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1403 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45592 Z= 0.227 Angle : 0.824 10.949 61950 Z= 0.405 Chirality : 0.051 0.348 7198 Planarity : 0.006 0.071 7916 Dihedral : 8.196 59.258 6934 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.02 % Favored : 86.62 % Rotamer: Outliers : 0.14 % Allowed : 6.33 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.10), residues: 5620 helix: -2.17 (0.17), residues: 706 sheet: -2.33 (0.12), residues: 1548 loop : -3.44 (0.09), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1183 HIS 0.013 0.001 HIS D 321 PHE 0.024 0.002 PHE D1049 TYR 0.028 0.002 TYR A1018 ARG 0.009 0.001 ARG D 853 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 744 time to evaluate : 5.142 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 151 MET cc_start: 0.6672 (tpp) cc_final: 0.6157 (tpp) REVERT: A 230 GLU cc_start: 0.7661 (mp0) cc_final: 0.7370 (mp0) REVERT: A 270 ARG cc_start: 0.3536 (mtp180) cc_final: 0.3072 (mmm-85) REVERT: A 318 MET cc_start: 0.5123 (mtt) cc_final: 0.4582 (mtt) REVERT: A 381 ASN cc_start: 0.9688 (t0) cc_final: 0.9406 (m-40) REVERT: A 385 PHE cc_start: 0.8915 (m-80) cc_final: 0.8606 (m-80) REVERT: A 409 ILE cc_start: 0.8338 (pt) cc_final: 0.8070 (tt) REVERT: A 456 LYS cc_start: 0.9310 (pttm) cc_final: 0.8577 (tptt) REVERT: A 460 HIS cc_start: 0.7777 (t-90) cc_final: 0.7218 (t-170) REVERT: A 607 MET cc_start: 0.5587 (mtt) cc_final: 0.5124 (mtt) REVERT: A 655 TYR cc_start: 0.2262 (p90) cc_final: 0.1563 (p90) REVERT: A 673 MET cc_start: 0.2296 (mmp) cc_final: 0.1566 (mmm) REVERT: A 968 MET cc_start: 0.5903 (mmp) cc_final: 0.5701 (mmp) REVERT: A 985 TYR cc_start: 0.5746 (m-10) cc_final: 0.5433 (m-10) REVERT: A 987 LEU cc_start: 0.8317 (tt) cc_final: 0.8107 (mt) REVERT: A 1314 MET cc_start: 0.1068 (tmm) cc_final: 0.0856 (tmm) REVERT: A 1330 TYR cc_start: 0.9624 (p90) cc_final: 0.9302 (p90) REVERT: B 101 MET cc_start: 0.2461 (ptm) cc_final: 0.0504 (ttp) REVERT: B 121 MET cc_start: 0.7387 (mmp) cc_final: 0.6944 (mpp) REVERT: B 145 LYS cc_start: 0.8350 (mptt) cc_final: 0.8045 (mmtm) REVERT: B 151 MET cc_start: 0.8394 (tpp) cc_final: 0.8142 (tpp) REVERT: B 221 VAL cc_start: 0.9305 (t) cc_final: 0.9092 (p) REVERT: B 254 TYR cc_start: 0.9166 (m-10) cc_final: 0.8879 (m-10) REVERT: B 321 HIS cc_start: 0.8937 (p-80) cc_final: 0.8393 (p-80) REVERT: B 333 VAL cc_start: 0.7983 (t) cc_final: 0.7527 (t) REVERT: B 381 ASN cc_start: 0.9503 (m110) cc_final: 0.9001 (t0) REVERT: B 384 ILE cc_start: 0.9455 (pt) cc_final: 0.9091 (tp) REVERT: B 385 PHE cc_start: 0.9025 (m-80) cc_final: 0.8663 (m-80) REVERT: B 441 HIS cc_start: 0.7997 (m-70) cc_final: 0.7542 (m-70) REVERT: B 496 TYR cc_start: 0.8196 (m-80) cc_final: 0.7928 (m-10) REVERT: B 520 MET cc_start: 0.5338 (ttt) cc_final: 0.4990 (ttt) REVERT: B 539 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.6540 (mtt180) REVERT: B 557 LYS cc_start: 0.9353 (mtpt) cc_final: 0.9073 (mmtp) REVERT: B 586 ARG cc_start: 0.8874 (ttt180) cc_final: 0.8377 (tpt-90) REVERT: B 625 LYS cc_start: 0.8873 (pptt) cc_final: 0.8534 (ptmm) REVERT: B 734 TYR cc_start: 0.7702 (m-80) cc_final: 0.7423 (m-80) REVERT: B 735 PHE cc_start: 0.9263 (m-80) cc_final: 0.8991 (m-80) REVERT: B 938 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 1047 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7931 (pptt) REVERT: B 1172 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8431 (mm-30) REVERT: B 1208 MET cc_start: 0.8467 (ppp) cc_final: 0.8024 (ppp) REVERT: B 1209 THR cc_start: 0.8668 (m) cc_final: 0.8374 (m) REVERT: B 1213 LEU cc_start: 0.9336 (tp) cc_final: 0.9099 (tp) REVERT: B 1248 PHE cc_start: 0.8006 (t80) cc_final: 0.7712 (t80) REVERT: B 1264 TYR cc_start: 0.7658 (t80) cc_final: 0.7420 (t80) REVERT: B 1315 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8721 (mtpp) REVERT: B 1323 TYR cc_start: 0.6281 (t80) cc_final: 0.6025 (t80) REVERT: B 1378 MET cc_start: 0.6885 (mtm) cc_final: 0.6187 (mtm) REVERT: B 1398 MET cc_start: 0.7890 (tmm) cc_final: 0.7593 (tpp) REVERT: B 1436 ASP cc_start: 0.7731 (m-30) cc_final: 0.7193 (m-30) REVERT: B 1446 ILE cc_start: 0.7928 (pt) cc_final: 0.7623 (pt) REVERT: C 151 MET cc_start: 0.6760 (tpt) cc_final: 0.6506 (tpt) REVERT: C 230 GLU cc_start: 0.7889 (mp0) cc_final: 0.7623 (mp0) REVERT: C 270 ARG cc_start: 0.3272 (mtp180) cc_final: 0.2950 (mmm-85) REVERT: C 318 MET cc_start: 0.5039 (mtt) cc_final: 0.4710 (mtt) REVERT: C 381 ASN cc_start: 0.9689 (t0) cc_final: 0.9404 (m-40) REVERT: C 385 PHE cc_start: 0.8913 (m-80) cc_final: 0.8607 (m-80) REVERT: C 409 ILE cc_start: 0.8338 (pt) cc_final: 0.8068 (tt) REVERT: C 456 LYS cc_start: 0.9311 (pttm) cc_final: 0.8578 (tptt) REVERT: C 460 HIS cc_start: 0.7770 (t-90) cc_final: 0.7208 (t-170) REVERT: C 607 MET cc_start: 0.5594 (mtt) cc_final: 0.5121 (mtt) REVERT: C 655 TYR cc_start: 0.2267 (p90) cc_final: 0.1566 (p90) REVERT: C 673 MET cc_start: 0.2300 (mmp) cc_final: 0.1573 (mmm) REVERT: C 968 MET cc_start: 0.5903 (mmp) cc_final: 0.5698 (mmp) REVERT: C 985 TYR cc_start: 0.5747 (m-10) cc_final: 0.5435 (m-10) REVERT: C 987 LEU cc_start: 0.8312 (tt) cc_final: 0.8103 (mt) REVERT: C 1330 TYR cc_start: 0.9621 (p90) cc_final: 0.9301 (p90) REVERT: D 101 MET cc_start: 0.2465 (ptm) cc_final: 0.0499 (ttp) REVERT: D 121 MET cc_start: 0.7410 (mmp) cc_final: 0.6962 (mpp) REVERT: D 145 LYS cc_start: 0.8358 (mptt) cc_final: 0.8048 (mmtm) REVERT: D 151 MET cc_start: 0.8385 (tpp) cc_final: 0.8132 (tpp) REVERT: D 221 VAL cc_start: 0.9305 (t) cc_final: 0.9092 (p) REVERT: D 254 TYR cc_start: 0.9264 (m-10) cc_final: 0.9014 (m-10) REVERT: D 319 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8426 (mmmt) REVERT: D 321 HIS cc_start: 0.8883 (p-80) cc_final: 0.8399 (p-80) REVERT: D 333 VAL cc_start: 0.7990 (t) cc_final: 0.7560 (t) REVERT: D 381 ASN cc_start: 0.9503 (m110) cc_final: 0.9000 (t0) REVERT: D 384 ILE cc_start: 0.9457 (pt) cc_final: 0.9098 (tp) REVERT: D 385 PHE cc_start: 0.9032 (m-80) cc_final: 0.8687 (m-80) REVERT: D 500 MET cc_start: 0.7662 (mtt) cc_final: 0.6962 (mtt) REVERT: D 502 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8328 (ptmt) REVERT: D 520 MET cc_start: 0.5339 (ttt) cc_final: 0.4986 (ttt) REVERT: D 539 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7303 (mtt180) REVERT: D 586 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8393 (tpt-90) REVERT: D 625 LYS cc_start: 0.8874 (pptt) cc_final: 0.8538 (ptmm) REVERT: D 734 TYR cc_start: 0.7704 (m-80) cc_final: 0.7419 (m-80) REVERT: D 735 PHE cc_start: 0.9265 (m-80) cc_final: 0.8992 (m-80) REVERT: D 1047 LYS cc_start: 0.8332 (ptpt) cc_final: 0.7927 (pptt) REVERT: D 1172 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8436 (mm-30) REVERT: D 1208 MET cc_start: 0.8463 (ppp) cc_final: 0.8023 (ppp) REVERT: D 1209 THR cc_start: 0.8670 (m) cc_final: 0.8386 (m) REVERT: D 1213 LEU cc_start: 0.9330 (tp) cc_final: 0.9100 (tp) REVERT: D 1248 PHE cc_start: 0.8001 (t80) cc_final: 0.7711 (t80) REVERT: D 1264 TYR cc_start: 0.7653 (t80) cc_final: 0.7431 (t80) REVERT: D 1315 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8732 (mtpp) REVERT: D 1323 TYR cc_start: 0.6110 (t80) cc_final: 0.5908 (t80) REVERT: D 1378 MET cc_start: 0.6885 (mtm) cc_final: 0.6188 (mtm) REVERT: D 1398 MET cc_start: 0.7922 (tmm) cc_final: 0.7529 (tpp) REVERT: D 1436 ASP cc_start: 0.7725 (m-30) cc_final: 0.7195 (m-30) REVERT: D 1446 ILE cc_start: 0.7972 (pt) cc_final: 0.7689 (pt) outliers start: 7 outliers final: 4 residues processed: 751 average time/residue: 0.6039 time to fit residues: 736.3063 Evaluate side-chains 586 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 581 time to evaluate : 4.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 454 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 405 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 465 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 278 optimal weight: 2.9990 chunk 489 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A1015 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B 967 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 ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 ASN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS C 662 ASN C 843 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN C1301 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 ASN D 693 GLN ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1179 ASN ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45592 Z= 0.283 Angle : 0.870 13.484 61950 Z= 0.431 Chirality : 0.053 0.408 7198 Planarity : 0.006 0.072 7916 Dihedral : 8.128 59.667 6934 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.04 % Favored : 85.71 % Rotamer: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.10), residues: 5620 helix: -1.89 (0.17), residues: 710 sheet: -2.27 (0.12), residues: 1566 loop : -3.53 (0.09), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 741 HIS 0.014 0.002 HIS C1259 PHE 0.034 0.002 PHE B1044 TYR 0.025 0.002 TYR D1418 ARG 0.018 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 697 time to evaluate : 5.008 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 151 MET cc_start: 0.6864 (tpp) cc_final: 0.6326 (tpp) REVERT: A 318 MET cc_start: 0.5293 (mtt) cc_final: 0.5086 (mtt) REVERT: A 381 ASN cc_start: 0.9680 (t0) cc_final: 0.9394 (m-40) REVERT: A 385 PHE cc_start: 0.9012 (m-80) cc_final: 0.8723 (m-80) REVERT: A 409 ILE cc_start: 0.8386 (pt) cc_final: 0.8091 (tt) REVERT: A 456 LYS cc_start: 0.9352 (pttm) cc_final: 0.8683 (tptt) REVERT: A 460 HIS cc_start: 0.8238 (t70) cc_final: 0.7285 (t-170) REVERT: A 464 MET cc_start: 0.7418 (tmm) cc_final: 0.7182 (tmm) REVERT: A 607 MET cc_start: 0.5627 (mtt) cc_final: 0.5178 (mtt) REVERT: A 655 TYR cc_start: 0.2572 (p90) cc_final: 0.1981 (p90) REVERT: A 673 MET cc_start: 0.3197 (mmp) cc_final: 0.2265 (mmm) REVERT: A 966 LEU cc_start: 0.8788 (tp) cc_final: 0.8551 (mp) REVERT: A 968 MET cc_start: 0.6164 (mmp) cc_final: 0.5863 (mmp) REVERT: A 985 TYR cc_start: 0.6057 (m-10) cc_final: 0.5497 (m-10) REVERT: A 1314 MET cc_start: 0.1037 (tmm) cc_final: 0.0810 (tmm) REVERT: A 1330 TYR cc_start: 0.9686 (p90) cc_final: 0.9455 (p90) REVERT: A 1398 MET cc_start: 0.0737 (ppp) cc_final: 0.0498 (ppp) REVERT: B 121 MET cc_start: 0.7782 (mmp) cc_final: 0.7422 (mpp) REVERT: B 183 LEU cc_start: 0.9403 (mp) cc_final: 0.9178 (mp) REVERT: B 221 VAL cc_start: 0.9354 (t) cc_final: 0.9120 (p) REVERT: B 254 TYR cc_start: 0.9230 (m-10) cc_final: 0.8919 (m-10) REVERT: B 321 HIS cc_start: 0.9096 (p-80) cc_final: 0.8858 (p-80) REVERT: B 333 VAL cc_start: 0.7968 (t) cc_final: 0.7496 (t) REVERT: B 381 ASN cc_start: 0.9526 (m110) cc_final: 0.9101 (t0) REVERT: B 384 ILE cc_start: 0.9312 (pt) cc_final: 0.8882 (tp) REVERT: B 385 PHE cc_start: 0.8971 (m-80) cc_final: 0.8660 (m-80) REVERT: B 425 TYR cc_start: 0.9216 (t80) cc_final: 0.8859 (t80) REVERT: B 479 HIS cc_start: 0.8686 (m-70) cc_final: 0.8370 (m-70) REVERT: B 520 MET cc_start: 0.5835 (ttt) cc_final: 0.5526 (ttt) REVERT: B 569 ASP cc_start: 0.8854 (t0) cc_final: 0.8532 (t0) REVERT: B 625 LYS cc_start: 0.8980 (pptt) cc_final: 0.8662 (ptmm) REVERT: B 735 PHE cc_start: 0.9272 (m-80) cc_final: 0.8999 (m-80) REVERT: B 933 LEU cc_start: 0.8981 (mp) cc_final: 0.8776 (mp) REVERT: B 1047 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8156 (pptt) REVERT: B 1172 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8582 (mm-30) REVERT: B 1208 MET cc_start: 0.8806 (ppp) cc_final: 0.8452 (ppp) REVERT: B 1209 THR cc_start: 0.8815 (m) cc_final: 0.8609 (m) REVERT: B 1216 TYR cc_start: 0.7572 (m-80) cc_final: 0.7315 (m-80) REVERT: B 1264 TYR cc_start: 0.7668 (t80) cc_final: 0.7355 (t80) REVERT: B 1293 ASP cc_start: 0.8772 (m-30) cc_final: 0.8447 (m-30) REVERT: B 1315 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8810 (mtpp) REVERT: B 1323 TYR cc_start: 0.6304 (t80) cc_final: 0.6075 (t80) REVERT: B 1331 ASN cc_start: 0.9226 (m-40) cc_final: 0.8863 (m-40) REVERT: B 1378 MET cc_start: 0.7062 (mtm) cc_final: 0.6362 (mtm) REVERT: B 1393 LYS cc_start: 0.9311 (tptt) cc_final: 0.9104 (tptp) REVERT: B 1436 ASP cc_start: 0.8003 (m-30) cc_final: 0.7617 (m-30) REVERT: B 1446 ILE cc_start: 0.8133 (pt) cc_final: 0.7861 (pt) REVERT: C 151 MET cc_start: 0.6856 (tpt) cc_final: 0.6345 (tpt) REVERT: C 230 GLU cc_start: 0.7795 (mp0) cc_final: 0.7451 (mp0) REVERT: C 381 ASN cc_start: 0.9679 (t0) cc_final: 0.9392 (m-40) REVERT: C 385 PHE cc_start: 0.9009 (m-80) cc_final: 0.8723 (m-80) REVERT: C 409 ILE cc_start: 0.8383 (pt) cc_final: 0.8084 (tt) REVERT: C 456 LYS cc_start: 0.9354 (pttm) cc_final: 0.8687 (tptt) REVERT: C 460 HIS cc_start: 0.8230 (t70) cc_final: 0.7308 (t-90) REVERT: C 607 MET cc_start: 0.5623 (mtt) cc_final: 0.5173 (mtt) REVERT: C 655 TYR cc_start: 0.2571 (p90) cc_final: 0.1980 (p90) REVERT: C 673 MET cc_start: 0.3065 (mmp) cc_final: 0.2134 (mmm) REVERT: C 966 LEU cc_start: 0.8786 (tp) cc_final: 0.8545 (mp) REVERT: C 968 MET cc_start: 0.6161 (mmp) cc_final: 0.5863 (mmp) REVERT: C 985 TYR cc_start: 0.6064 (m-10) cc_final: 0.5502 (m-10) REVERT: C 1314 MET cc_start: 0.0587 (tmm) cc_final: 0.0309 (tmm) REVERT: C 1330 TYR cc_start: 0.9690 (p90) cc_final: 0.9463 (p90) REVERT: C 1398 MET cc_start: 0.0748 (ppp) cc_final: 0.0508 (ppp) REVERT: D 121 MET cc_start: 0.7789 (mmp) cc_final: 0.7429 (mpp) REVERT: D 151 MET cc_start: 0.8507 (tpp) cc_final: 0.8197 (tpp) REVERT: D 183 LEU cc_start: 0.9405 (mp) cc_final: 0.9183 (mp) REVERT: D 221 VAL cc_start: 0.9354 (t) cc_final: 0.9120 (p) REVERT: D 254 TYR cc_start: 0.9309 (m-10) cc_final: 0.9035 (m-10) REVERT: D 321 HIS cc_start: 0.9043 (p-80) cc_final: 0.8838 (p-80) REVERT: D 333 VAL cc_start: 0.7947 (t) cc_final: 0.7483 (t) REVERT: D 381 ASN cc_start: 0.9529 (m110) cc_final: 0.9102 (t0) REVERT: D 384 ILE cc_start: 0.9317 (pt) cc_final: 0.8853 (tp) REVERT: D 385 PHE cc_start: 0.9003 (m-80) cc_final: 0.8675 (m-80) REVERT: D 425 TYR cc_start: 0.9177 (t80) cc_final: 0.8753 (t80) REVERT: D 479 HIS cc_start: 0.8677 (m-70) cc_final: 0.8372 (m-70) REVERT: D 502 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8282 (ptmt) REVERT: D 520 MET cc_start: 0.5834 (ttt) cc_final: 0.5528 (ttt) REVERT: D 569 ASP cc_start: 0.8884 (t0) cc_final: 0.8569 (t0) REVERT: D 625 LYS cc_start: 0.8977 (pptt) cc_final: 0.8660 (ptmm) REVERT: D 638 ASP cc_start: 0.9535 (p0) cc_final: 0.9324 (p0) REVERT: D 735 PHE cc_start: 0.9273 (m-80) cc_final: 0.8997 (m-80) REVERT: D 933 LEU cc_start: 0.8979 (mp) cc_final: 0.8774 (mp) REVERT: D 1047 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8142 (ptmm) REVERT: D 1164 LYS cc_start: 0.7366 (tptt) cc_final: 0.7081 (tptt) REVERT: D 1172 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8616 (mm-30) REVERT: D 1208 MET cc_start: 0.8794 (ppp) cc_final: 0.8445 (ppp) REVERT: D 1216 TYR cc_start: 0.7679 (m-80) cc_final: 0.7279 (m-80) REVERT: D 1264 TYR cc_start: 0.7617 (t80) cc_final: 0.7326 (t80) REVERT: D 1293 ASP cc_start: 0.8773 (m-30) cc_final: 0.8447 (m-30) REVERT: D 1315 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8794 (mtpp) REVERT: D 1331 ASN cc_start: 0.9268 (m-40) cc_final: 0.8908 (m-40) REVERT: D 1378 MET cc_start: 0.7059 (mtm) cc_final: 0.6369 (mtm) REVERT: D 1398 MET cc_start: 0.8105 (tmm) cc_final: 0.7622 (tpp) REVERT: D 1446 ILE cc_start: 0.8235 (pt) cc_final: 0.7974 (pt) outliers start: 2 outliers final: 2 residues processed: 699 average time/residue: 0.6142 time to fit residues: 699.6866 Evaluate side-chains 554 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 183 optimal weight: 7.9990 chunk 490 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 545 optimal weight: 10.0000 chunk 452 optimal weight: 9.9990 chunk 252 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 843 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 566 ASN B 938 ASN ** B 994 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 ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 GLN ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 843 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1358 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45592 Z= 0.250 Angle : 0.826 10.073 61950 Z= 0.412 Chirality : 0.054 1.032 7198 Planarity : 0.006 0.070 7916 Dihedral : 8.107 59.738 6934 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.10), residues: 5620 helix: -1.74 (0.18), residues: 704 sheet: -2.15 (0.13), residues: 1518 loop : -3.45 (0.09), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 741 HIS 0.013 0.001 HIS C1259 PHE 0.043 0.002 PHE B1049 TYR 0.039 0.002 TYR B1216 ARG 0.006 0.001 ARG D 853 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 690 time to evaluate : 4.898 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 381 ASN cc_start: 0.9668 (t0) cc_final: 0.9368 (m-40) REVERT: A 385 PHE cc_start: 0.8987 (m-80) cc_final: 0.8706 (m-80) REVERT: A 409 ILE cc_start: 0.8401 (pt) cc_final: 0.8105 (tt) REVERT: A 456 LYS cc_start: 0.9387 (pttm) cc_final: 0.8672 (tptt) REVERT: A 460 HIS cc_start: 0.8286 (t70) cc_final: 0.7291 (t-90) REVERT: A 607 MET cc_start: 0.5930 (mtt) cc_final: 0.5507 (mtt) REVERT: A 655 TYR cc_start: 0.2133 (p90) cc_final: 0.1785 (p90) REVERT: A 673 MET cc_start: 0.3501 (mmp) cc_final: 0.2565 (mmm) REVERT: A 968 MET cc_start: 0.6277 (mmp) cc_final: 0.5843 (mmp) REVERT: A 985 TYR cc_start: 0.6014 (m-10) cc_final: 0.5579 (m-10) REVERT: A 1314 MET cc_start: 0.0727 (tmm) cc_final: -0.0763 (tmm) REVERT: A 1330 TYR cc_start: 0.9692 (p90) cc_final: 0.9449 (p90) REVERT: B 50 LEU cc_start: 0.9002 (mt) cc_final: 0.8366 (mp) REVERT: B 121 MET cc_start: 0.7784 (mmp) cc_final: 0.7445 (mpp) REVERT: B 139 LYS cc_start: 0.9314 (tmtt) cc_final: 0.8889 (tmtt) REVERT: B 183 LEU cc_start: 0.9367 (mp) cc_final: 0.9147 (mp) REVERT: B 221 VAL cc_start: 0.9384 (t) cc_final: 0.9124 (p) REVERT: B 254 TYR cc_start: 0.9180 (m-10) cc_final: 0.8853 (m-10) REVERT: B 321 HIS cc_start: 0.8998 (p-80) cc_final: 0.8413 (p-80) REVERT: B 333 VAL cc_start: 0.8009 (t) cc_final: 0.7446 (p) REVERT: B 381 ASN cc_start: 0.9535 (m110) cc_final: 0.9092 (t0) REVERT: B 384 ILE cc_start: 0.9209 (pt) cc_final: 0.8968 (tp) REVERT: B 385 PHE cc_start: 0.8943 (m-80) cc_final: 0.8633 (m-80) REVERT: B 407 PHE cc_start: 0.9006 (p90) cc_final: 0.8793 (p90) REVERT: B 425 TYR cc_start: 0.9207 (t80) cc_final: 0.8751 (t80) REVERT: B 479 HIS cc_start: 0.8777 (m90) cc_final: 0.8473 (m-70) REVERT: B 496 TYR cc_start: 0.8449 (m-10) cc_final: 0.7847 (m-80) REVERT: B 500 MET cc_start: 0.7647 (mtt) cc_final: 0.7412 (mmt) REVERT: B 502 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8170 (ptmt) REVERT: B 505 ILE cc_start: 0.9776 (mm) cc_final: 0.8957 (mm) REVERT: B 520 MET cc_start: 0.6539 (ttt) cc_final: 0.6309 (ttt) REVERT: B 569 ASP cc_start: 0.8870 (t0) cc_final: 0.8481 (t0) REVERT: B 570 LEU cc_start: 0.8644 (pp) cc_final: 0.8404 (pp) REVERT: B 625 LYS cc_start: 0.8959 (pptt) cc_final: 0.8677 (ptmm) REVERT: B 735 PHE cc_start: 0.9322 (m-80) cc_final: 0.9091 (m-80) REVERT: B 1164 LYS cc_start: 0.7580 (tptt) cc_final: 0.7305 (tptt) REVERT: B 1172 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8487 (mm-30) REVERT: B 1208 MET cc_start: 0.8772 (ppp) cc_final: 0.8481 (ppp) REVERT: B 1264 TYR cc_start: 0.7597 (t80) cc_final: 0.7269 (t80) REVERT: B 1293 ASP cc_start: 0.8712 (m-30) cc_final: 0.8424 (m-30) REVERT: B 1378 MET cc_start: 0.7867 (mtm) cc_final: 0.7272 (mtm) REVERT: B 1446 ILE cc_start: 0.8127 (pt) cc_final: 0.7918 (pt) REVERT: C 151 MET cc_start: 0.6505 (tpt) cc_final: 0.5929 (tpp) REVERT: C 230 GLU cc_start: 0.8029 (mp0) cc_final: 0.7675 (mp0) REVERT: C 381 ASN cc_start: 0.9663 (t0) cc_final: 0.9366 (m-40) REVERT: C 385 PHE cc_start: 0.8984 (m-80) cc_final: 0.8705 (m-80) REVERT: C 409 ILE cc_start: 0.8397 (pt) cc_final: 0.8102 (tt) REVERT: C 456 LYS cc_start: 0.9397 (pttm) cc_final: 0.8702 (tptt) REVERT: C 460 HIS cc_start: 0.8287 (t70) cc_final: 0.7297 (t-90) REVERT: C 607 MET cc_start: 0.5926 (mtt) cc_final: 0.5530 (mtt) REVERT: C 655 TYR cc_start: 0.2123 (p90) cc_final: 0.1773 (p90) REVERT: C 673 MET cc_start: 0.3076 (mmp) cc_final: 0.2163 (mmm) REVERT: C 968 MET cc_start: 0.6272 (mmp) cc_final: 0.5948 (mmp) REVERT: C 985 TYR cc_start: 0.6020 (m-10) cc_final: 0.5587 (m-10) REVERT: C 1314 MET cc_start: 0.0869 (tmm) cc_final: -0.0697 (tmm) REVERT: C 1330 TYR cc_start: 0.9697 (p90) cc_final: 0.9456 (p90) REVERT: C 1398 MET cc_start: 0.1234 (ppp) cc_final: 0.1032 (ppp) REVERT: D 121 MET cc_start: 0.7792 (mmp) cc_final: 0.7447 (mpp) REVERT: D 139 LYS cc_start: 0.9313 (tmtt) cc_final: 0.8888 (tmtt) REVERT: D 151 MET cc_start: 0.8393 (tpp) cc_final: 0.8104 (tpp) REVERT: D 183 LEU cc_start: 0.9370 (mp) cc_final: 0.9154 (mp) REVERT: D 221 VAL cc_start: 0.9385 (t) cc_final: 0.9130 (p) REVERT: D 254 TYR cc_start: 0.9291 (m-10) cc_final: 0.8984 (m-10) REVERT: D 286 PHE cc_start: 0.8505 (m-80) cc_final: 0.8292 (m-80) REVERT: D 318 MET cc_start: 0.9102 (tpt) cc_final: 0.8640 (tpp) REVERT: D 319 LYS cc_start: 0.8774 (mmpt) cc_final: 0.8541 (mmmt) REVERT: D 321 HIS cc_start: 0.9018 (p-80) cc_final: 0.8366 (p-80) REVERT: D 333 VAL cc_start: 0.8077 (t) cc_final: 0.7518 (p) REVERT: D 381 ASN cc_start: 0.9533 (m110) cc_final: 0.9090 (t0) REVERT: D 385 PHE cc_start: 0.8961 (m-80) cc_final: 0.8658 (m-80) REVERT: D 407 PHE cc_start: 0.9003 (p90) cc_final: 0.8790 (p90) REVERT: D 425 TYR cc_start: 0.9173 (t80) cc_final: 0.8833 (t80) REVERT: D 479 HIS cc_start: 0.8785 (m90) cc_final: 0.8478 (m-70) REVERT: D 520 MET cc_start: 0.6541 (ttt) cc_final: 0.6310 (ttt) REVERT: D 569 ASP cc_start: 0.8911 (t0) cc_final: 0.8544 (t0) REVERT: D 570 LEU cc_start: 0.8631 (pp) cc_final: 0.8392 (pp) REVERT: D 625 LYS cc_start: 0.8960 (pptt) cc_final: 0.8670 (ptmm) REVERT: D 735 PHE cc_start: 0.9326 (m-80) cc_final: 0.9087 (m-80) REVERT: D 1164 LYS cc_start: 0.7267 (tptt) cc_final: 0.7056 (tptt) REVERT: D 1172 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8485 (mm-30) REVERT: D 1208 MET cc_start: 0.8819 (ppp) cc_final: 0.8523 (ppp) REVERT: D 1264 TYR cc_start: 0.7579 (t80) cc_final: 0.7251 (t80) REVERT: D 1293 ASP cc_start: 0.8712 (m-30) cc_final: 0.8422 (m-30) REVERT: D 1331 ASN cc_start: 0.9196 (m-40) cc_final: 0.8986 (m-40) REVERT: D 1378 MET cc_start: 0.7870 (mtm) cc_final: 0.7277 (mtm) REVERT: D 1398 MET cc_start: 0.7943 (tmm) cc_final: 0.7728 (tpp) REVERT: D 1446 ILE cc_start: 0.8187 (pt) cc_final: 0.7973 (pt) outliers start: 2 outliers final: 2 residues processed: 692 average time/residue: 0.6187 time to fit residues: 698.0366 Evaluate side-chains 563 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 561 time to evaluate : 5.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 526 optimal weight: 7.9990 chunk 61 optimal weight: 0.0670 chunk 310 optimal weight: 9.9990 chunk 398 optimal weight: 10.0000 chunk 308 optimal weight: 7.9990 chunk 459 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 543 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN B1143 HIS ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1281 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN D1143 HIS ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1296 ASN D1301 GLN ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 45592 Z= 0.227 Angle : 0.818 16.394 61950 Z= 0.401 Chirality : 0.050 0.314 7198 Planarity : 0.006 0.070 7916 Dihedral : 7.878 59.199 6934 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.10), residues: 5620 helix: -1.71 (0.18), residues: 724 sheet: -2.11 (0.12), residues: 1566 loop : -3.40 (0.09), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 741 HIS 0.012 0.001 HIS D 321 PHE 0.040 0.002 PHE B1049 TYR 0.037 0.002 TYR B1216 ARG 0.008 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 670 time to evaluate : 4.781 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 381 ASN cc_start: 0.9645 (t0) cc_final: 0.9351 (m-40) REVERT: A 385 PHE cc_start: 0.8968 (m-80) cc_final: 0.8715 (m-80) REVERT: A 409 ILE cc_start: 0.8403 (pt) cc_final: 0.8099 (tt) REVERT: A 456 LYS cc_start: 0.9417 (pttm) cc_final: 0.8746 (tptt) REVERT: A 460 HIS cc_start: 0.8302 (t70) cc_final: 0.7333 (t-90) REVERT: A 607 MET cc_start: 0.5948 (mtt) cc_final: 0.5534 (mtt) REVERT: A 655 TYR cc_start: 0.2347 (p90) cc_final: 0.1992 (p90) REVERT: A 673 MET cc_start: 0.3693 (mmp) cc_final: 0.2774 (mmm) REVERT: A 968 MET cc_start: 0.6177 (mmp) cc_final: 0.5738 (mmp) REVERT: A 985 TYR cc_start: 0.6017 (m-10) cc_final: 0.5506 (m-10) REVERT: A 1314 MET cc_start: 0.0811 (tmm) cc_final: -0.0005 (tmm) REVERT: A 1330 TYR cc_start: 0.9677 (p90) cc_final: 0.9414 (p90) REVERT: B 50 LEU cc_start: 0.8931 (mt) cc_final: 0.8249 (mp) REVERT: B 84 LEU cc_start: 0.6578 (mp) cc_final: 0.6260 (mt) REVERT: B 139 LYS cc_start: 0.9296 (tmtt) cc_final: 0.8909 (tmtt) REVERT: B 173 ASN cc_start: 0.9491 (p0) cc_final: 0.9181 (p0) REVERT: B 183 LEU cc_start: 0.9348 (mp) cc_final: 0.9129 (mp) REVERT: B 221 VAL cc_start: 0.9412 (t) cc_final: 0.9126 (p) REVERT: B 254 TYR cc_start: 0.9173 (m-10) cc_final: 0.8832 (m-10) REVERT: B 321 HIS cc_start: 0.9056 (p-80) cc_final: 0.8709 (p-80) REVERT: B 333 VAL cc_start: 0.8133 (t) cc_final: 0.7577 (p) REVERT: B 381 ASN cc_start: 0.9520 (m110) cc_final: 0.9100 (t0) REVERT: B 384 ILE cc_start: 0.9414 (pt) cc_final: 0.9132 (tp) REVERT: B 385 PHE cc_start: 0.8931 (m-80) cc_final: 0.8615 (m-80) REVERT: B 407 PHE cc_start: 0.9026 (p90) cc_final: 0.8781 (p90) REVERT: B 425 TYR cc_start: 0.9246 (t80) cc_final: 0.8891 (t80) REVERT: B 479 HIS cc_start: 0.8752 (m90) cc_final: 0.8458 (m-70) REVERT: B 502 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8291 (ptmt) REVERT: B 505 ILE cc_start: 0.9778 (mm) cc_final: 0.8648 (mm) REVERT: B 520 MET cc_start: 0.6487 (ttt) cc_final: 0.6283 (ttt) REVERT: B 569 ASP cc_start: 0.8857 (t0) cc_final: 0.8472 (t0) REVERT: B 570 LEU cc_start: 0.8730 (pp) cc_final: 0.8512 (pp) REVERT: B 625 LYS cc_start: 0.8974 (pptt) cc_final: 0.8720 (ptmm) REVERT: B 672 ASP cc_start: 0.9435 (t70) cc_final: 0.9191 (t0) REVERT: B 734 TYR cc_start: 0.7684 (m-80) cc_final: 0.7444 (m-80) REVERT: B 877 LEU cc_start: 0.8625 (tp) cc_final: 0.8386 (tt) REVERT: B 1172 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 1264 TYR cc_start: 0.7501 (t80) cc_final: 0.7090 (t80) REVERT: B 1315 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8604 (mtpp) REVERT: B 1446 ILE cc_start: 0.7954 (pt) cc_final: 0.7748 (pt) REVERT: C 151 MET cc_start: 0.6363 (tpt) cc_final: 0.5756 (tpp) REVERT: C 381 ASN cc_start: 0.9641 (t0) cc_final: 0.9363 (m-40) REVERT: C 385 PHE cc_start: 0.8965 (m-80) cc_final: 0.8714 (m-80) REVERT: C 409 ILE cc_start: 0.8402 (pt) cc_final: 0.8097 (tt) REVERT: C 456 LYS cc_start: 0.9409 (pttm) cc_final: 0.8735 (tptt) REVERT: C 460 HIS cc_start: 0.8310 (t70) cc_final: 0.7345 (t-90) REVERT: C 607 MET cc_start: 0.5945 (mtt) cc_final: 0.5531 (mtt) REVERT: C 655 TYR cc_start: 0.2341 (p90) cc_final: 0.1990 (p90) REVERT: C 673 MET cc_start: 0.3717 (mmp) cc_final: 0.2799 (mmm) REVERT: C 968 MET cc_start: 0.6176 (mmp) cc_final: 0.5750 (mmp) REVERT: C 985 TYR cc_start: 0.6017 (m-10) cc_final: 0.5506 (m-10) REVERT: C 1314 MET cc_start: 0.0259 (tmm) cc_final: 0.0026 (tmm) REVERT: C 1330 TYR cc_start: 0.9682 (p90) cc_final: 0.9421 (p90) REVERT: D 84 LEU cc_start: 0.6878 (mp) cc_final: 0.6402 (mt) REVERT: D 139 LYS cc_start: 0.9294 (tmtt) cc_final: 0.8903 (tmtt) REVERT: D 151 MET cc_start: 0.8463 (tpp) cc_final: 0.8174 (tpp) REVERT: D 173 ASN cc_start: 0.9457 (p0) cc_final: 0.8988 (p0) REVERT: D 183 LEU cc_start: 0.9367 (mp) cc_final: 0.9163 (mp) REVERT: D 221 VAL cc_start: 0.9416 (t) cc_final: 0.9103 (p) REVERT: D 254 TYR cc_start: 0.9292 (m-10) cc_final: 0.8993 (m-10) REVERT: D 321 HIS cc_start: 0.9023 (p-80) cc_final: 0.8692 (p-80) REVERT: D 333 VAL cc_start: 0.8262 (t) cc_final: 0.7795 (p) REVERT: D 381 ASN cc_start: 0.9516 (m110) cc_final: 0.9057 (t0) REVERT: D 385 PHE cc_start: 0.8968 (m-80) cc_final: 0.8518 (m-80) REVERT: D 407 PHE cc_start: 0.9023 (p90) cc_final: 0.8783 (p90) REVERT: D 425 TYR cc_start: 0.9199 (t80) cc_final: 0.8827 (t80) REVERT: D 441 HIS cc_start: 0.7920 (m-70) cc_final: 0.7704 (m-70) REVERT: D 479 HIS cc_start: 0.8783 (m90) cc_final: 0.8478 (m-70) REVERT: D 496 TYR cc_start: 0.8418 (m-80) cc_final: 0.8215 (m-10) REVERT: D 500 MET cc_start: 0.7841 (mtt) cc_final: 0.7612 (mmt) REVERT: D 505 ILE cc_start: 0.9722 (mm) cc_final: 0.8662 (mm) REVERT: D 520 MET cc_start: 0.6496 (ttt) cc_final: 0.6284 (ttt) REVERT: D 569 ASP cc_start: 0.8860 (t0) cc_final: 0.8496 (t0) REVERT: D 570 LEU cc_start: 0.8719 (pp) cc_final: 0.8509 (pp) REVERT: D 625 LYS cc_start: 0.8976 (pptt) cc_final: 0.8722 (ptmm) REVERT: D 673 MET cc_start: 0.8732 (tpt) cc_final: 0.8488 (tpp) REVERT: D 734 TYR cc_start: 0.7662 (m-80) cc_final: 0.7411 (m-80) REVERT: D 877 LEU cc_start: 0.8656 (tp) cc_final: 0.8418 (tt) REVERT: D 1164 LYS cc_start: 0.7182 (tptt) cc_final: 0.6951 (tptt) REVERT: D 1172 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8407 (mm-30) REVERT: D 1264 TYR cc_start: 0.7465 (t80) cc_final: 0.7075 (t80) REVERT: D 1315 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8593 (mtpp) REVERT: D 1331 ASN cc_start: 0.9236 (m-40) cc_final: 0.8852 (m-40) REVERT: D 1398 MET cc_start: 0.7954 (tmm) cc_final: 0.7686 (tpp) REVERT: D 1446 ILE cc_start: 0.7969 (pt) cc_final: 0.7717 (pt) outliers start: 5 outliers final: 3 residues processed: 673 average time/residue: 0.6063 time to fit residues: 671.5622 Evaluate side-chains 551 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 548 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 336 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 324 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 345 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 427 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 208 GLN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1281 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 ASN D 646 HIS D 854 GLN ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 45592 Z= 0.274 Angle : 0.851 12.798 61950 Z= 0.426 Chirality : 0.052 0.379 7198 Planarity : 0.006 0.071 7916 Dihedral : 7.921 59.562 6934 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.59 % Favored : 85.25 % Rotamer: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.10), residues: 5620 helix: -1.69 (0.17), residues: 732 sheet: -2.15 (0.12), residues: 1582 loop : -3.41 (0.09), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 741 HIS 0.012 0.002 HIS D 321 PHE 0.037 0.002 PHE B1049 TYR 0.033 0.002 TYR D1418 ARG 0.014 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 662 time to evaluate : 5.335 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 381 ASN cc_start: 0.9627 (t0) cc_final: 0.9351 (m-40) REVERT: A 456 LYS cc_start: 0.9440 (pttm) cc_final: 0.8814 (tptt) REVERT: A 460 HIS cc_start: 0.8240 (t70) cc_final: 0.7689 (t70) REVERT: A 607 MET cc_start: 0.6198 (mtt) cc_final: 0.5849 (mtt) REVERT: A 649 TYR cc_start: 0.8637 (m-10) cc_final: 0.7651 (t80) REVERT: A 655 TYR cc_start: 0.2107 (p90) cc_final: 0.1772 (p90) REVERT: A 673 MET cc_start: 0.4253 (mmp) cc_final: 0.3231 (mmm) REVERT: A 940 VAL cc_start: 0.1846 (t) cc_final: 0.1600 (m) REVERT: A 968 MET cc_start: 0.6330 (mmp) cc_final: 0.5807 (mmp) REVERT: A 1314 MET cc_start: 0.0423 (tmm) cc_final: -0.0008 (tmm) REVERT: A 1330 TYR cc_start: 0.9448 (p90) cc_final: 0.9169 (p90) REVERT: B 50 LEU cc_start: 0.9122 (mt) cc_final: 0.8260 (mt) REVERT: B 139 LYS cc_start: 0.9360 (tmtt) cc_final: 0.8960 (tmtt) REVERT: B 221 VAL cc_start: 0.9500 (t) cc_final: 0.9231 (p) REVERT: B 254 TYR cc_start: 0.9212 (m-10) cc_final: 0.8844 (m-10) REVERT: B 321 HIS cc_start: 0.8974 (p-80) cc_final: 0.8648 (p-80) REVERT: B 333 VAL cc_start: 0.8022 (t) cc_final: 0.7471 (p) REVERT: B 381 ASN cc_start: 0.9562 (m110) cc_final: 0.9187 (t0) REVERT: B 384 ILE cc_start: 0.9467 (pt) cc_final: 0.9237 (tp) REVERT: B 385 PHE cc_start: 0.8965 (m-80) cc_final: 0.8664 (m-80) REVERT: B 407 PHE cc_start: 0.9096 (p90) cc_final: 0.8854 (p90) REVERT: B 419 LEU cc_start: 0.8684 (mt) cc_final: 0.8259 (pp) REVERT: B 425 TYR cc_start: 0.9275 (t80) cc_final: 0.8896 (t80) REVERT: B 479 HIS cc_start: 0.8953 (m90) cc_final: 0.8629 (m90) REVERT: B 500 MET cc_start: 0.7717 (mmt) cc_final: 0.7157 (tpp) REVERT: B 502 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8269 (ptpt) REVERT: B 569 ASP cc_start: 0.9066 (t0) cc_final: 0.8670 (t0) REVERT: B 1038 ASN cc_start: 0.8246 (m-40) cc_final: 0.8010 (m-40) REVERT: B 1110 LEU cc_start: 0.9278 (tp) cc_final: 0.8557 (tp) REVERT: B 1208 MET cc_start: 0.8730 (ppp) cc_final: 0.8515 (ppp) REVERT: B 1264 TYR cc_start: 0.7579 (t80) cc_final: 0.7272 (t80) REVERT: B 1315 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8871 (mtpp) REVERT: B 1396 VAL cc_start: 0.8425 (t) cc_final: 0.8122 (t) REVERT: C 381 ASN cc_start: 0.9633 (t0) cc_final: 0.9366 (m-40) REVERT: C 456 LYS cc_start: 0.9457 (pttm) cc_final: 0.8851 (tptt) REVERT: C 460 HIS cc_start: 0.8253 (t70) cc_final: 0.7705 (t70) REVERT: C 607 MET cc_start: 0.6193 (mtt) cc_final: 0.5841 (mtt) REVERT: C 649 TYR cc_start: 0.8633 (m-10) cc_final: 0.7649 (t80) REVERT: C 655 TYR cc_start: 0.2099 (p90) cc_final: 0.1757 (p90) REVERT: C 673 MET cc_start: 0.4291 (mmp) cc_final: 0.3262 (mmm) REVERT: C 940 VAL cc_start: 0.1871 (t) cc_final: 0.1637 (m) REVERT: C 968 MET cc_start: 0.6242 (mmp) cc_final: 0.5691 (mmp) REVERT: C 1314 MET cc_start: 0.1005 (tmm) cc_final: 0.0341 (tmm) REVERT: D 50 LEU cc_start: 0.9146 (mt) cc_final: 0.8551 (mt) REVERT: D 84 LEU cc_start: 0.7140 (mp) cc_final: 0.6753 (mp) REVERT: D 139 LYS cc_start: 0.9346 (tmtt) cc_final: 0.8942 (tmtt) REVERT: D 151 MET cc_start: 0.8505 (tpp) cc_final: 0.8174 (tpp) REVERT: D 221 VAL cc_start: 0.9502 (t) cc_final: 0.9253 (p) REVERT: D 319 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8368 (mmmt) REVERT: D 381 ASN cc_start: 0.9547 (m110) cc_final: 0.9167 (t0) REVERT: D 385 PHE cc_start: 0.8994 (m-80) cc_final: 0.8513 (m-80) REVERT: D 407 PHE cc_start: 0.9103 (p90) cc_final: 0.8875 (p90) REVERT: D 419 LEU cc_start: 0.8478 (mt) cc_final: 0.8100 (pp) REVERT: D 425 TYR cc_start: 0.9217 (t80) cc_final: 0.8812 (t80) REVERT: D 479 HIS cc_start: 0.8964 (m90) cc_final: 0.8617 (m90) REVERT: D 496 TYR cc_start: 0.8478 (m-80) cc_final: 0.8275 (m-10) REVERT: D 505 ILE cc_start: 0.9717 (mm) cc_final: 0.8382 (mm) REVERT: D 569 ASP cc_start: 0.9060 (t0) cc_final: 0.8688 (t0) REVERT: D 625 LYS cc_start: 0.8937 (pptt) cc_final: 0.8733 (ptmm) REVERT: D 673 MET cc_start: 0.8982 (tpt) cc_final: 0.8683 (tpp) REVERT: D 1038 ASN cc_start: 0.8245 (m-40) cc_final: 0.8008 (m-40) REVERT: D 1110 LEU cc_start: 0.9280 (tp) cc_final: 0.8566 (tp) REVERT: D 1164 LYS cc_start: 0.7679 (tptt) cc_final: 0.7417 (tptt) REVERT: D 1208 MET cc_start: 0.8759 (ppp) cc_final: 0.8558 (ppp) REVERT: D 1264 TYR cc_start: 0.7601 (t80) cc_final: 0.7177 (t80) REVERT: D 1315 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8632 (mtpp) REVERT: D 1446 ILE cc_start: 0.8062 (pt) cc_final: 0.7830 (pt) outliers start: 3 outliers final: 2 residues processed: 665 average time/residue: 0.6114 time to fit residues: 666.5933 Evaluate side-chains 559 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 9.9990 chunk 520 optimal weight: 3.9990 chunk 475 optimal weight: 4.9990 chunk 506 optimal weight: 0.0970 chunk 304 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 397 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 457 optimal weight: 2.9990 chunk 479 optimal weight: 0.8980 chunk 504 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 843 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 GLN B1038 ASN B1051 GLN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN D1038 ASN ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45592 Z= 0.220 Angle : 0.807 14.505 61950 Z= 0.396 Chirality : 0.050 0.397 7198 Planarity : 0.006 0.069 7916 Dihedral : 7.915 59.446 6934 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.20 % Favored : 86.62 % Rotamer: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.10), residues: 5620 helix: -1.53 (0.18), residues: 724 sheet: -2.07 (0.12), residues: 1588 loop : -3.32 (0.09), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 741 HIS 0.015 0.001 HIS D 321 PHE 0.035 0.002 PHE D1049 TYR 0.037 0.002 TYR B1216 ARG 0.011 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 673 time to evaluate : 5.149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 381 ASN cc_start: 0.9602 (t0) cc_final: 0.9319 (m-40) REVERT: A 409 ILE cc_start: 0.8659 (pt) cc_final: 0.8338 (tt) REVERT: A 456 LYS cc_start: 0.9446 (pttm) cc_final: 0.8849 (tptt) REVERT: A 460 HIS cc_start: 0.8290 (t70) cc_final: 0.7746 (t70) REVERT: A 607 MET cc_start: 0.6175 (mtt) cc_final: 0.5803 (mtt) REVERT: A 649 TYR cc_start: 0.8621 (m-10) cc_final: 0.7639 (t80) REVERT: A 655 TYR cc_start: 0.2084 (p90) cc_final: 0.1806 (p90) REVERT: A 673 MET cc_start: 0.3996 (mmp) cc_final: 0.3142 (mmm) REVERT: A 798 MET cc_start: 0.4128 (tpt) cc_final: 0.3924 (tpt) REVERT: A 817 TYR cc_start: 0.5663 (m-10) cc_final: 0.5321 (m-80) REVERT: A 968 MET cc_start: 0.6156 (mmp) cc_final: 0.5617 (mmp) REVERT: A 1314 MET cc_start: 0.0928 (tmm) cc_final: 0.0317 (tmm) REVERT: A 1330 TYR cc_start: 0.9503 (p90) cc_final: 0.9216 (p90) REVERT: B 50 LEU cc_start: 0.8985 (mt) cc_final: 0.8257 (mt) REVERT: B 139 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9027 (tmtt) REVERT: B 221 VAL cc_start: 0.9468 (t) cc_final: 0.9155 (p) REVERT: B 223 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 254 TYR cc_start: 0.9204 (m-10) cc_final: 0.8802 (m-10) REVERT: B 318 MET cc_start: 0.8871 (tpt) cc_final: 0.8634 (tpp) REVERT: B 320 LEU cc_start: 0.9496 (mt) cc_final: 0.9094 (mt) REVERT: B 321 HIS cc_start: 0.8925 (p-80) cc_final: 0.8526 (p-80) REVERT: B 333 VAL cc_start: 0.8205 (t) cc_final: 0.7644 (p) REVERT: B 381 ASN cc_start: 0.9524 (m110) cc_final: 0.9084 (t0) REVERT: B 385 PHE cc_start: 0.8976 (m-80) cc_final: 0.8473 (m-80) REVERT: B 407 PHE cc_start: 0.9056 (p90) cc_final: 0.8781 (p90) REVERT: B 419 LEU cc_start: 0.8704 (mt) cc_final: 0.8327 (pp) REVERT: B 425 TYR cc_start: 0.9271 (t80) cc_final: 0.8902 (t80) REVERT: B 479 HIS cc_start: 0.9001 (m90) cc_final: 0.8692 (m90) REVERT: B 500 MET cc_start: 0.7525 (mmt) cc_final: 0.6648 (mmt) REVERT: B 502 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8032 (ptpt) REVERT: B 569 ASP cc_start: 0.8943 (t0) cc_final: 0.8567 (t0) REVERT: B 570 LEU cc_start: 0.8828 (pp) cc_final: 0.8619 (pp) REVERT: B 796 LEU cc_start: 0.9059 (pt) cc_final: 0.8669 (pt) REVERT: B 798 MET cc_start: 0.7916 (tmm) cc_final: 0.6734 (mmt) REVERT: B 877 LEU cc_start: 0.8602 (tp) cc_final: 0.8378 (tt) REVERT: B 1038 ASN cc_start: 0.8189 (m110) cc_final: 0.7911 (m-40) REVERT: B 1110 LEU cc_start: 0.9254 (tp) cc_final: 0.8819 (tp) REVERT: B 1152 TYR cc_start: 0.7401 (t80) cc_final: 0.7097 (t80) REVERT: B 1172 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 1264 TYR cc_start: 0.7344 (t80) cc_final: 0.6925 (t80) REVERT: B 1315 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8931 (mtpp) REVERT: B 1328 LEU cc_start: 0.8953 (tt) cc_final: 0.8609 (tt) REVERT: B 1330 TYR cc_start: 0.9038 (p90) cc_final: 0.8708 (p90) REVERT: B 1365 LEU cc_start: 0.9111 (mm) cc_final: 0.8907 (mm) REVERT: B 1446 ILE cc_start: 0.7949 (pt) cc_final: 0.7714 (pt) REVERT: C 28 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7128 (tptp) REVERT: C 151 MET cc_start: 0.7270 (tpp) cc_final: 0.6973 (tpp) REVERT: C 381 ASN cc_start: 0.9602 (t0) cc_final: 0.9324 (m-40) REVERT: C 385 PHE cc_start: 0.8908 (m-80) cc_final: 0.8662 (m-80) REVERT: C 409 ILE cc_start: 0.8656 (pt) cc_final: 0.8330 (tt) REVERT: C 456 LYS cc_start: 0.9464 (pttm) cc_final: 0.8865 (tptt) REVERT: C 460 HIS cc_start: 0.8272 (t70) cc_final: 0.7729 (t70) REVERT: C 607 MET cc_start: 0.6166 (mtt) cc_final: 0.5794 (mtt) REVERT: C 649 TYR cc_start: 0.8618 (m-10) cc_final: 0.7635 (t80) REVERT: C 655 TYR cc_start: 0.2068 (p90) cc_final: 0.1786 (p90) REVERT: C 673 MET cc_start: 0.4133 (mmp) cc_final: 0.3206 (mmm) REVERT: C 798 MET cc_start: 0.4171 (tpt) cc_final: 0.3966 (tpt) REVERT: C 817 TYR cc_start: 0.5624 (m-10) cc_final: 0.5276 (m-80) REVERT: C 968 MET cc_start: 0.6071 (mmp) cc_final: 0.5511 (mmp) REVERT: C 1314 MET cc_start: 0.1049 (tmm) cc_final: 0.0397 (tmm) REVERT: C 1330 TYR cc_start: 0.9588 (p90) cc_final: 0.9304 (p90) REVERT: D 50 LEU cc_start: 0.9073 (mt) cc_final: 0.8421 (mt) REVERT: D 84 LEU cc_start: 0.6911 (mp) cc_final: 0.6481 (mp) REVERT: D 139 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9027 (tmtt) REVERT: D 151 MET cc_start: 0.8568 (tpp) cc_final: 0.8256 (tpp) REVERT: D 169 ASP cc_start: 0.8627 (t0) cc_final: 0.8403 (t70) REVERT: D 221 VAL cc_start: 0.9470 (t) cc_final: 0.9155 (p) REVERT: D 223 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7884 (mm-30) REVERT: D 319 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8409 (mmmt) REVERT: D 321 HIS cc_start: 0.8911 (p-80) cc_final: 0.8133 (p90) REVERT: D 354 LYS cc_start: 0.8129 (tttt) cc_final: 0.7342 (tptt) REVERT: D 381 ASN cc_start: 0.9507 (m110) cc_final: 0.9065 (t0) REVERT: D 385 PHE cc_start: 0.8972 (m-80) cc_final: 0.8546 (m-80) REVERT: D 407 PHE cc_start: 0.9053 (p90) cc_final: 0.8767 (p90) REVERT: D 419 LEU cc_start: 0.8525 (mt) cc_final: 0.8187 (pp) REVERT: D 425 TYR cc_start: 0.9219 (t80) cc_final: 0.8811 (t80) REVERT: D 479 HIS cc_start: 0.8992 (m90) cc_final: 0.8667 (m90) REVERT: D 500 MET cc_start: 0.7646 (mmt) cc_final: 0.7009 (mmt) REVERT: D 505 ILE cc_start: 0.9378 (mm) cc_final: 0.9012 (mm) REVERT: D 569 ASP cc_start: 0.8924 (t0) cc_final: 0.8556 (t0) REVERT: D 625 LYS cc_start: 0.8972 (pptt) cc_final: 0.8765 (ptmm) REVERT: D 673 MET cc_start: 0.8815 (tpt) cc_final: 0.8574 (tpp) REVERT: D 796 LEU cc_start: 0.9049 (pt) cc_final: 0.8677 (pt) REVERT: D 798 MET cc_start: 0.7939 (tmm) cc_final: 0.6743 (mmt) REVERT: D 877 LEU cc_start: 0.8650 (tp) cc_final: 0.8365 (tt) REVERT: D 1038 ASN cc_start: 0.8154 (m110) cc_final: 0.7875 (m-40) REVERT: D 1110 LEU cc_start: 0.9265 (tp) cc_final: 0.8868 (tp) REVERT: D 1152 TYR cc_start: 0.7381 (t80) cc_final: 0.7133 (t80) REVERT: D 1164 LYS cc_start: 0.7439 (tptt) cc_final: 0.7152 (tptt) REVERT: D 1264 TYR cc_start: 0.7351 (t80) cc_final: 0.6906 (t80) REVERT: D 1315 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8910 (mtpp) REVERT: D 1328 LEU cc_start: 0.8983 (tt) cc_final: 0.8639 (tt) REVERT: D 1330 TYR cc_start: 0.9030 (p90) cc_final: 0.8730 (p90) REVERT: D 1396 VAL cc_start: 0.8754 (t) cc_final: 0.8482 (t) REVERT: D 1446 ILE cc_start: 0.8021 (pt) cc_final: 0.7752 (pt) outliers start: 2 outliers final: 2 residues processed: 675 average time/residue: 0.6061 time to fit residues: 671.1693 Evaluate side-chains 544 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 542 time to evaluate : 5.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 332 optimal weight: 10.0000 chunk 535 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 254 optimal weight: 0.0000 chunk 372 optimal weight: 0.0270 chunk 561 optimal weight: 3.9990 chunk 517 optimal weight: 0.7980 chunk 447 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 345 optimal weight: 30.0000 chunk 274 optimal weight: 0.7980 overall best weight: 0.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 ASN ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 HIS B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 ASN ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1233 ASN ** C1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 HIS D 983 ASN D 994 GLN D1009 ASN ** D1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1118 HIS D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45592 Z= 0.196 Angle : 0.788 15.942 61950 Z= 0.384 Chirality : 0.050 0.335 7198 Planarity : 0.006 0.073 7916 Dihedral : 7.676 59.749 6934 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.17 % Favored : 87.69 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.10), residues: 5620 helix: -1.45 (0.18), residues: 706 sheet: -1.91 (0.13), residues: 1606 loop : -3.22 (0.10), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 858 HIS 0.011 0.001 HIS D 321 PHE 0.035 0.001 PHE D1049 TYR 0.040 0.002 TYR B 985 ARG 0.021 0.001 ARG D 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11240 Ramachandran restraints generated. 5620 Oldfield, 0 Emsley, 5620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 678 time to evaluate : 5.269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASN cc_start: 0.9570 (t0) cc_final: 0.9311 (m-40) REVERT: A 385 PHE cc_start: 0.8901 (m-80) cc_final: 0.8664 (m-80) REVERT: A 409 ILE cc_start: 0.8646 (pt) cc_final: 0.8319 (tt) REVERT: A 456 LYS cc_start: 0.9437 (pttm) cc_final: 0.8839 (tptt) REVERT: A 460 HIS cc_start: 0.8323 (t70) cc_final: 0.7930 (t-90) REVERT: A 500 MET cc_start: 0.6441 (ptt) cc_final: 0.5060 (ttt) REVERT: A 607 MET cc_start: 0.6068 (mtt) cc_final: 0.5220 (ptp) REVERT: A 649 TYR cc_start: 0.8606 (m-10) cc_final: 0.7623 (t80) REVERT: A 673 MET cc_start: 0.3840 (mmp) cc_final: 0.2668 (mmm) REVERT: A 765 TRP cc_start: 0.7343 (m100) cc_final: 0.6829 (m100) REVERT: A 817 TYR cc_start: 0.5510 (m-10) cc_final: 0.5202 (m-80) REVERT: A 968 MET cc_start: 0.6133 (mmp) cc_final: 0.5628 (mmp) REVERT: A 985 TYR cc_start: 0.5968 (m-10) cc_final: 0.4873 (t80) REVERT: A 1314 MET cc_start: 0.0978 (tmm) cc_final: 0.0677 (tmm) REVERT: A 1330 TYR cc_start: 0.9455 (p90) cc_final: 0.9081 (p90) REVERT: B 50 LEU cc_start: 0.8933 (mt) cc_final: 0.8209 (mt) REVERT: B 139 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9052 (tmtt) REVERT: B 145 LYS cc_start: 0.8596 (mptt) cc_final: 0.8125 (mmtm) REVERT: B 151 MET cc_start: 0.8010 (tpp) cc_final: 0.7650 (tpp) REVERT: B 173 ASN cc_start: 0.9548 (p0) cc_final: 0.9315 (p0) REVERT: B 221 VAL cc_start: 0.9443 (t) cc_final: 0.9087 (p) REVERT: B 223 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 254 TYR cc_start: 0.9187 (m-10) cc_final: 0.8831 (m-10) REVERT: B 320 LEU cc_start: 0.9482 (mt) cc_final: 0.9076 (mt) REVERT: B 321 HIS cc_start: 0.8927 (p-80) cc_final: 0.8516 (p-80) REVERT: B 326 ILE cc_start: 0.8460 (pt) cc_final: 0.8253 (pt) REVERT: B 333 VAL cc_start: 0.8379 (t) cc_final: 0.8042 (t) REVERT: B 381 ASN cc_start: 0.9500 (m110) cc_final: 0.9093 (t0) REVERT: B 384 ILE cc_start: 0.9432 (pt) cc_final: 0.9085 (mm) REVERT: B 385 PHE cc_start: 0.8947 (m-80) cc_final: 0.8402 (m-80) REVERT: B 407 PHE cc_start: 0.8938 (p90) cc_final: 0.8697 (p90) REVERT: B 425 TYR cc_start: 0.9253 (t80) cc_final: 0.8867 (t80) REVERT: B 479 HIS cc_start: 0.8975 (m90) cc_final: 0.8696 (m-70) REVERT: B 502 LYS cc_start: 0.8722 (ptpt) cc_final: 0.8088 (ptpt) REVERT: B 541 LEU cc_start: 0.6810 (tt) cc_final: 0.6374 (tt) REVERT: B 569 ASP cc_start: 0.8765 (t0) cc_final: 0.8564 (t70) REVERT: B 796 LEU cc_start: 0.9000 (pt) cc_final: 0.7878 (pt) REVERT: B 798 MET cc_start: 0.7821 (tmm) cc_final: 0.6886 (mmt) REVERT: B 877 LEU cc_start: 0.8613 (tp) cc_final: 0.8308 (tt) REVERT: B 1038 ASN cc_start: 0.8057 (m110) cc_final: 0.7745 (m-40) REVERT: B 1110 LEU cc_start: 0.9220 (tp) cc_final: 0.8869 (tp) REVERT: B 1133 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8544 (mmtt) REVERT: B 1264 TYR cc_start: 0.7003 (t80) cc_final: 0.6684 (t80) REVERT: B 1315 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8918 (mtpp) REVERT: B 1330 TYR cc_start: 0.8842 (p90) cc_final: 0.8522 (p90) REVERT: C 28 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7227 (tptp) REVERT: C 151 MET cc_start: 0.7154 (tpp) cc_final: 0.6825 (tpp) REVERT: C 230 GLU cc_start: 0.8220 (mp0) cc_final: 0.7974 (mp0) REVERT: C 381 ASN cc_start: 0.9573 (t0) cc_final: 0.9316 (m-40) REVERT: C 385 PHE cc_start: 0.8898 (m-80) cc_final: 0.8667 (m-80) REVERT: C 409 ILE cc_start: 0.8643 (pt) cc_final: 0.8312 (tt) REVERT: C 456 LYS cc_start: 0.9466 (pttm) cc_final: 0.8895 (tptt) REVERT: C 460 HIS cc_start: 0.8352 (t70) cc_final: 0.7969 (t-90) REVERT: C 607 MET cc_start: 0.6053 (mtt) cc_final: 0.5204 (ptp) REVERT: C 649 TYR cc_start: 0.8602 (m-10) cc_final: 0.7619 (t80) REVERT: C 673 MET cc_start: 0.3954 (mmp) cc_final: 0.3067 (mmm) REVERT: C 765 TRP cc_start: 0.7337 (m100) cc_final: 0.6847 (m100) REVERT: C 968 MET cc_start: 0.6069 (mmp) cc_final: 0.5633 (mmp) REVERT: C 985 TYR cc_start: 0.5969 (m-10) cc_final: 0.4917 (t80) REVERT: C 1314 MET cc_start: 0.0979 (tmm) cc_final: 0.0342 (tmm) REVERT: C 1330 TYR cc_start: 0.9564 (p90) cc_final: 0.9274 (p90) REVERT: D 50 LEU cc_start: 0.9059 (mt) cc_final: 0.8403 (mt) REVERT: D 139 LYS cc_start: 0.9321 (tmtt) cc_final: 0.9004 (tmtt) REVERT: D 145 LYS cc_start: 0.8454 (mptt) cc_final: 0.8119 (mmtm) REVERT: D 151 MET cc_start: 0.8596 (tpp) cc_final: 0.8355 (tpp) REVERT: D 173 ASN cc_start: 0.9528 (p0) cc_final: 0.9306 (p0) REVERT: D 221 VAL cc_start: 0.9440 (t) cc_final: 0.9084 (p) REVERT: D 223 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7828 (mm-30) REVERT: D 319 LYS cc_start: 0.8677 (mmpt) cc_final: 0.8246 (mmmt) REVERT: D 354 LYS cc_start: 0.8094 (tttt) cc_final: 0.7293 (tptt) REVERT: D 381 ASN cc_start: 0.9480 (m110) cc_final: 0.9039 (t0) REVERT: D 407 PHE cc_start: 0.8928 (p90) cc_final: 0.8674 (p90) REVERT: D 425 TYR cc_start: 0.9210 (t80) cc_final: 0.8802 (t80) REVERT: D 479 HIS cc_start: 0.8983 (m90) cc_final: 0.8683 (m-70) REVERT: D 496 TYR cc_start: 0.8424 (m-10) cc_final: 0.7562 (m-10) REVERT: D 500 MET cc_start: 0.7703 (mmt) cc_final: 0.6892 (mmt) REVERT: D 505 ILE cc_start: 0.9481 (mm) cc_final: 0.9107 (mm) REVERT: D 569 ASP cc_start: 0.8708 (t0) cc_final: 0.8500 (t70) REVERT: D 673 MET cc_start: 0.8869 (tpt) cc_final: 0.8581 (tpp) REVERT: D 796 LEU cc_start: 0.8970 (pt) cc_final: 0.7979 (pt) REVERT: D 798 MET cc_start: 0.7821 (tmm) cc_final: 0.6880 (mmt) REVERT: D 877 LEU cc_start: 0.8659 (tp) cc_final: 0.8369 (tt) REVERT: D 1038 ASN cc_start: 0.8058 (m110) cc_final: 0.7783 (m-40) REVERT: D 1110 LEU cc_start: 0.9226 (tp) cc_final: 0.8876 (tp) REVERT: D 1164 LYS cc_start: 0.7182 (tptt) cc_final: 0.6918 (tptt) REVERT: D 1264 TYR cc_start: 0.7067 (t80) cc_final: 0.6736 (t80) REVERT: D 1315 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8928 (mtpp) REVERT: D 1337 GLU cc_start: 0.9016 (pm20) cc_final: 0.8806 (pm20) REVERT: D 1446 ILE cc_start: 0.7821 (pt) cc_final: 0.7502 (pt) outliers start: 3 outliers final: 2 residues processed: 681 average time/residue: 0.6175 time to fit residues: 691.2044 Evaluate side-chains 537 residues out of total 4944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 535 time to evaluate : 5.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 355 optimal weight: 0.0370 chunk 476 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 412 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 448 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 82 optimal weight: 0.0070 overall best weight: 1.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 HIS B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1118 HIS D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** 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 = 0.4873 r_free = 0.4873 target = 0.177592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.155880 restraints weight = 294567.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.158501 restraints weight = 174070.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.159500 restraints weight = 101418.147| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45592 Z= 0.206 Angle : 0.771 14.019 61950 Z= 0.379 Chirality : 0.049 0.325 7198 Planarity : 0.006 0.074 7916 Dihedral : 7.581 59.865 6934 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.78 % Favored : 87.05 % Rotamer: Outliers : 0.04 % Allowed : 0.63 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.10), residues: 5620 helix: -1.38 (0.18), residues: 706 sheet: -1.78 (0.13), residues: 1596 loop : -3.22 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 741 HIS 0.007 0.001 HIS B 321 PHE 0.035 0.002 PHE A 669 TYR 0.031 0.002 TYR D 985 ARG 0.007 0.001 ARG B 147 =============================================================================== Job complete usr+sys time: 11857.19 seconds wall clock time: 219 minutes 17.78 seconds (13157.78 seconds total)