Starting phenix.real_space_refine on Tue Jul 7 05:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_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 { model { file = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7l_12747/07_2026/7o7l_12747.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 5 Restraints were copied for chains: C, D, H, I, J Time building chain proxies: 32.04, per 1000 atoms: 0.72 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=46, 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 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.04 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.04 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.10 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.04 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.05 Simple disulfide: pdb=" SG CYS C1352 " - pdb=" SG CYS C1467 " distance=2.04 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.04 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.04 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.04 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.05 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.01 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.04 Simple disulfide: pdb=" SG CYS D1352 " - pdb=" SG CYS D1467 " distance=2.03 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: 4.05 Conformation dependent library (CDL) restraints added in 2.3 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: 1.11 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: 6.31 Time building geometry restraints manager: 5.34 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 - 17.86: 23766 17.86 - 35.72: 2818 35.72 - 53.58: 510 53.58 - 71.44: 108 71.44 - 89.30: 58 Dihedral angle restraints: 27260 sinusoidal: 10802 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 27257 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: 2.03 - 2.60: 1182 2.60 - 3.18: 44200 3.18 - 3.75: 72806 3.75 - 4.33: 97981 4.33 - 4.90: 147940 Nonbonded interactions: 364109 Sorted by model distance: 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=" OG SER B 773 " pdb=" OD1 ASP B 775 " model vdw 2.033 3.040 nonbonded pdb=" OG SER D 773 " pdb=" OD1 ASP D 775 " model vdw 2.033 3.040 nonbonded pdb=" O LYS B1236 " pdb=" OG1 THR B1239 " model vdw 2.034 3.040 ... (remaining 364104 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 60.690 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.413 45680 Z= 0.438 Angle : 1.256 30.966 62168 Z= 0.651 Chirality : 0.083 1.852 7198 Planarity : 0.020 0.308 7916 Dihedral : 16.102 89.303 16514 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.47 (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 ARG 0.013 0.001 ARG D 147 TYR 0.036 0.003 TYR B1418 PHE 0.050 0.003 PHE D1057 TRP 0.016 0.002 TRP A1183 HIS 0.012 0.002 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.36 (45592) covalent geometry : angle 1.16060 / 0.63 (61950) SS BOND : bond 0.01768 / 1.48 ( 46) SS BOND : angle 3.21086 / 2.06 ( 92) hydrogen bonds : bond 0.26563 / 17.38 ( 384) hydrogen bonds : angle 10.43976 / 7.16 ( 1152) link_ALPHA1-6 : bond 0.00059 / 0.03 ( 2) link_ALPHA1-6 : angle 0.28836 / 0.16 ( 6) link_BETA1-4 : bond 0.00960 / 0.72 ( 10) link_BETA1-4 : angle 4.32164 / 3.28 ( 30) link_NAG-ASN : bond 0.19505 / 15.11 ( 30) link_NAG-ASN : angle 12.07287 / 8.76 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.399 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: A 281 GLU cc_start: -0.7410 (OUTLIER) cc_final: -0.7751 (mt-10) REVERT: A 381 ASN cc_start: 0.9673 (t0) cc_final: 0.9460 (m-40) REVERT: A 460 HIS cc_start: 0.6586 (t-170) cc_final: 0.4354 (t-170) REVERT: A 607 MET cc_start: 0.5343 (mtt) cc_final: 0.4976 (mtt) REVERT: A 985 TYR cc_start: 0.5907 (m-10) cc_final: 0.5221 (m-10) outliers start: 9 outliers final: 1 residues processed: 171 average time/residue: 0.1316 time to fit residues: 30.4439 Evaluate side-chains 102 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.407 Evaluate side-chains 324 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 321 time to evaluate : 0.348 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: B 197 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 200 GLN cc_start: 0.8019 (tt0) cc_final: 0.7745 (tm-30) REVERT: B 318 MET cc_start: 0.9232 (ttp) cc_final: 0.8980 (ttm) REVERT: B 333 VAL cc_start: 0.7683 (t) cc_final: 0.7386 (p) REVERT: B 347 ILE cc_start: 0.1532 (mm) cc_final: 0.0440 (mm) REVERT: B 381 ASN cc_start: 0.9420 (m110) cc_final: 0.9097 (t0) REVERT: B 428 ARG cc_start: 0.8928 (ptp90) cc_final: 0.8210 (ttp80) REVERT: B 500 MET cc_start: 0.7877 (ttm) cc_final: 0.6943 (ttm) REVERT: B 520 MET cc_start: 0.3654 (ttt) cc_final: 0.3144 (ttt) REVERT: B 539 ARG cc_start: 0.7376 (mtt-85) cc_final: 0.6958 (mtt180) REVERT: B 569 ASP cc_start: 0.8579 (t0) cc_final: 0.8357 (t0) REVERT: B 735 PHE cc_start: 0.9269 (m-80) cc_final: 0.9015 (m-80) REVERT: B 840 GLU cc_start: 0.7372 (pm20) cc_final: 0.6547 (tp30) REVERT: B 877 LEU cc_start: 0.8833 (tt) cc_final: 0.8554 (mm) REVERT: B 916 PHE cc_start: 0.8737 (m-80) cc_final: 0.8393 (m-80) REVERT: B 933 LEU cc_start: 0.9172 (mp) cc_final: 0.7691 (mp) REVERT: B 1047 LYS cc_start: 0.8284 (ptpt) cc_final: 0.7508 (pttp) REVERT: B 1152 TYR cc_start: 0.7503 (t80) cc_final: 0.7215 (t80) REVERT: B 1172 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7879 (mm-30) REVERT: B 1312 TYR cc_start: 0.8946 (m-80) cc_final: 0.8611 (m-80) REVERT: B 1330 TYR cc_start: 0.9009 (p90) cc_final: 0.8539 (p90) REVERT: B 1331 ASN cc_start: 0.8731 (m110) cc_final: 0.8479 (m-40) REVERT: B 1390 ILE cc_start: 0.9627 (tt) cc_final: 0.9281 (tp) REVERT: B 1446 ILE cc_start: 0.8342 (pt) cc_final: 0.8032 (pt) outliers start: 3 outliers final: 1 residues processed: 324 average time/residue: 0.1211 time to fit residues: 53.5566 Evaluate side-chains 222 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.410 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.0870 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS A 460 HIS ** 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** A1242 GLN A1259 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 168 GLN B 182 GLN B 460 HIS B 644 ASN ** 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** ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 ASN B1259 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.153163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.135704 restraints weight = 101112.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.136861 restraints weight = 81801.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.137666 restraints weight = 68731.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.138474 restraints weight = 60632.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.139380 restraints weight = 54368.914| |-----------------------------------------------------------------------------| r_work (final): 0.4506 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084742 restraints weight = 47350.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087704 restraints weight = 35822.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.090134 restraints weight = 28579.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.092146 restraints weight = 23613.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.093758 restraints weight = 20051.646| |-----------------------------------------------------------------------------| r_work (final): 0.3811 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.053893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051568 restraints weight = 386.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052167 restraints weight = 124.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052583 restraints weight = 66.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.052748 restraints weight = 45.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.052892 restraints weight = 38.905| |-----------------------------------------------------------------------------| r_work (final): 0.2759 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074765 restraints weight = 342.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075661 restraints weight = 170.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076146 restraints weight = 104.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076606 restraints weight = 73.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076858 restraints weight = 52.262| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.061415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058305 restraints weight = 263.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.059240 restraints weight = 141.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.059784 restraints weight = 94.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.060135 restraints weight = 68.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.060373 restraints weight = 52.640| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 45680 Z= 0.181 Angle : 1.064 55.834 62168 Z= 0.533 Chirality : 0.056 0.635 7198 Planarity : 0.006 0.079 7916 Dihedral : 7.775 36.402 6022 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.45 % Favored : 86.16 % Rotamer: Outliers : 0.40 % Allowed : 8.09 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.09), residues: 5620 helix: -2.88 (0.15), residues: 708 sheet: -2.72 (0.12), residues: 1524 loop : -3.78 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 313 TYR 0.032 0.002 TYR C1418 PHE 0.043 0.002 PHE D 452 TRP 0.029 0.002 TRP C1183 HIS 0.012 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (45592) covalent geometry : angle 1.03817 / 0.53 (61950) SS BOND : bond 0.00694 / 0.41 ( 46) SS BOND : angle 1.73830 / 1.25 ( 92) hydrogen bonds : bond 0.07829 / 5.25 ( 384) hydrogen bonds : angle 7.73059 / 5.32 ( 1152) link_ALPHA1-6 : bond 0.01061 / 0.53 ( 2) link_ALPHA1-6 : angle 1.37378 / 0.80 ( 6) link_BETA1-4 : bond 0.00973 / 0.69 ( 10) link_BETA1-4 : angle 2.70816 / 2.06 ( 30) link_NAG-ASN : bond 0.01105 / 0.73 ( 30) link_NAG-ASN : angle 5.88171 / 3.84 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.439 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: C 230 GLU cc_start: 0.7668 (mp0) cc_final: 0.7401 (mp0) REVERT: C 270 ARG cc_start: 0.2013 (mtp180) cc_final: 0.0368 (mmp80) REVERT: C 381 ASN cc_start: 0.9637 (t0) cc_final: 0.9387 (m-40) REVERT: C 385 PHE cc_start: 0.8839 (m-80) cc_final: 0.8423 (m-80) REVERT: C 460 HIS cc_start: 0.7258 (t-170) cc_final: 0.6582 (t-170) REVERT: C 607 MET cc_start: 0.3838 (mtt) cc_final: 0.3184 (mtt) REVERT: C 648 VAL cc_start: 0.6751 (OUTLIER) cc_final: 0.6419 (t) REVERT: C 916 PHE cc_start: 0.8110 (m-10) cc_final: 0.7779 (m-10) REVERT: C 968 MET cc_start: 0.5733 (mmp) cc_final: 0.5362 (mmm) REVERT: C 985 TYR cc_start: 0.6021 (m-10) cc_final: 0.5175 (m-10) REVERT: C 1259 HIS cc_start: 0.9503 (t-90) cc_final: 0.9252 (t-90) REVERT: C 1311 GLU cc_start: 0.8589 (pm20) cc_final: 0.8259 (pm20) REVERT: C 1330 TYR cc_start: 0.9571 (p90) cc_final: 0.9173 (p90) outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.1153 time to fit residues: 22.6495 Evaluate side-chains 99 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.420 Evaluate side-chains 288 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 283 time to evaluate : 0.429 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: D 121 MET cc_start: 0.7592 (mmp) cc_final: 0.7093 (mpp) REVERT: D 145 LYS cc_start: 0.8402 (mptt) cc_final: 0.8111 (mmtm) REVERT: D 177 GLN cc_start: 0.8511 (tt0) cc_final: 0.8309 (tm-30) REVERT: D 194 LEU cc_start: 0.9125 (mt) cc_final: 0.8856 (mt) REVERT: D 197 GLU cc_start: 0.8611 (tm-30) cc_final: 0.7918 (pp20) REVERT: D 200 GLN cc_start: 0.8190 (tt0) cc_final: 0.7972 (tm-30) REVERT: D 333 VAL cc_start: 0.7685 (t) cc_final: 0.6863 (t) REVERT: D 381 ASN cc_start: 0.9462 (m110) cc_final: 0.9085 (t0) REVERT: D 415 MET cc_start: 0.7750 (mmp) cc_final: 0.7548 (mmp) REVERT: D 428 ARG cc_start: 0.9168 (ptp90) cc_final: 0.8564 (ttp80) REVERT: D 734 TYR cc_start: 0.8083 (m-80) cc_final: 0.7862 (m-80) REVERT: D 735 PHE cc_start: 0.9308 (m-80) cc_final: 0.8989 (m-80) REVERT: D 840 GLU cc_start: 0.7400 (pm20) cc_final: 0.6560 (tp30) REVERT: D 916 PHE cc_start: 0.8780 (m-80) cc_final: 0.8456 (m-80) REVERT: D 977 MET cc_start: 0.6873 (mmp) cc_final: 0.6519 (mmp) REVERT: D 1121 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9142 (m) REVERT: D 1152 TYR cc_start: 0.7634 (t80) cc_final: 0.7131 (t80) REVERT: D 1208 MET cc_start: 0.8758 (ptm) cc_final: 0.8556 (ptm) REVERT: D 1248 PHE cc_start: 0.8080 (t80) cc_final: 0.7609 (t80) REVERT: D 1279 THR cc_start: 0.9259 (p) cc_final: 0.8959 (p) REVERT: D 1312 TYR cc_start: 0.9171 (m-80) cc_final: 0.8875 (m-80) REVERT: D 1314 MET cc_start: 0.9359 (mmp) cc_final: 0.9016 (mmp) REVERT: D 1330 TYR cc_start: 0.9074 (p90) cc_final: 0.8650 (p90) REVERT: D 1331 ASN cc_start: 0.8571 (m110) cc_final: 0.7983 (m-40) REVERT: D 1436 ASP cc_start: 0.7230 (m-30) cc_final: 0.6903 (m-30) REVERT: D 1446 ILE cc_start: 0.8337 (pt) cc_final: 0.8091 (pt) outliers start: 5 outliers final: 2 residues processed: 287 average time/residue: 0.1216 time to fit residues: 48.0821 Evaluate side-chains 215 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 0.404 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 504 optimal weight: 4.9990 chunk 319 optimal weight: 0.0980 chunk 522 optimal weight: 0.1980 chunk 284 optimal weight: 0.2980 chunk 242 optimal weight: 6.9990 chunk 491 optimal weight: 0.0870 chunk 151 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 chunk 259 optimal weight: 3.9990 chunk 525 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 177 GLN C 279 HIS C 302 GLN C 327 GLN C 511 HIS C 646 HIS C1038 ASN C1179 ASN C1242 GLN ** C1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 168 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS D 511 HIS D 644 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN D 994 GLN ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1179 ASN D1242 GLN D1259 HIS D1301 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.136897 restraints weight = 100212.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.138048 restraints weight = 83116.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.138902 restraints weight = 69674.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.139680 restraints weight = 61347.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.140373 restraints weight = 54760.904| |-----------------------------------------------------------------------------| r_work (final): 0.4502 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089135 restraints weight = 44840.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092326 restraints weight = 33434.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.094865 restraints weight = 26254.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.096922 restraints weight = 21457.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.098606 restraints weight = 18071.840| |-----------------------------------------------------------------------------| r_work (final): 0.3866 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.057890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.055036 restraints weight = 334.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.055834 restraints weight = 103.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.056381 restraints weight = 51.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.056695 restraints weight = 31.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.056809 restraints weight = 22.105| |-----------------------------------------------------------------------------| r_work (final): 0.2829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.072223 restraints weight = 335.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072939 restraints weight = 112.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073274 restraints weight = 49.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073566 restraints weight = 27.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073642 restraints weight = 13.366| |-----------------------------------------------------------------------------| r_work (final): 0.3047 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.052920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.048824 restraints weight = 248.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.049735 restraints weight = 159.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.050268 restraints weight = 119.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.050648 restraints weight = 95.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.050932 restraints weight = 79.928| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 45680 Z= 0.159 Angle : 0.884 14.231 62168 Z= 0.428 Chirality : 0.052 0.295 7198 Planarity : 0.006 0.075 7916 Dihedral : 7.165 30.903 6022 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.06 % Favored : 86.62 % Rotamer: Outliers : 0.08 % Allowed : 6.63 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.10), residues: 5620 helix: -2.46 (0.16), residues: 736 sheet: -2.48 (0.12), residues: 1566 loop : -3.59 (0.09), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.033 0.002 TYR D1007 PHE 0.032 0.002 PHE B1049 TRP 0.018 0.002 TRP C1183 HIS 0.017 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (45592) covalent geometry : angle 0.86791 / 0.42 (61950) SS BOND : bond 0.00645 / 0.38 ( 46) SS BOND : angle 1.63150 / 1.15 ( 92) hydrogen bonds : bond 0.06861 / 4.59 ( 384) hydrogen bonds : angle 7.18289 / 4.98 ( 1152) link_ALPHA1-6 : bond 0.00418 / 0.21 ( 2) link_ALPHA1-6 : angle 1.42528 / 0.82 ( 6) link_BETA1-4 : bond 0.00599 / 0.43 ( 10) link_BETA1-4 : angle 2.14790 / 1.47 ( 30) link_NAG-ASN : bond 0.01433 / 0.95 ( 30) link_NAG-ASN : angle 4.11312 / 2.83 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.429 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: A 183 LEU cc_start: 0.8300 (mt) cc_final: 0.8069 (mt) REVERT: A 270 ARG cc_start: 0.1705 (mtp180) cc_final: 0.0801 (mmm160) REVERT: A 305 LYS cc_start: 0.8677 (mppt) cc_final: 0.8049 (mppt) REVERT: A 318 MET cc_start: 0.4398 (mtt) cc_final: 0.3800 (mtt) REVERT: A 381 ASN cc_start: 0.9536 (t0) cc_final: 0.9326 (m-40) REVERT: A 385 PHE cc_start: 0.8661 (m-80) cc_final: 0.8336 (m-80) REVERT: A 456 LYS cc_start: 0.9300 (pttm) cc_final: 0.8579 (tptt) REVERT: A 460 HIS cc_start: 0.7407 (t-170) cc_final: 0.6902 (t-170) REVERT: A 520 MET cc_start: 0.8083 (tmm) cc_final: 0.7879 (tpt) REVERT: A 607 MET cc_start: 0.3751 (mtt) cc_final: 0.3119 (mtt) REVERT: A 655 TYR cc_start: 0.3633 (p90) cc_final: 0.1131 (m-10) REVERT: A 673 MET cc_start: 0.2418 (mmp) cc_final: 0.1790 (mmm) REVERT: A 916 PHE cc_start: 0.8302 (m-10) cc_final: 0.8058 (m-10) REVERT: A 985 TYR cc_start: 0.5874 (m-10) cc_final: 0.5463 (m-10) REVERT: A 1330 TYR cc_start: 0.9541 (p90) cc_final: 0.9080 (p90) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1203 time to fit residues: 22.0503 Evaluate side-chains 95 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.422 Evaluate side-chains 272 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.405 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: D 121 MET cc_start: 0.7514 (mmp) cc_final: 0.7148 (mpp) REVERT: D 194 LEU cc_start: 0.9231 (mt) cc_final: 0.8992 (mt) REVERT: D 197 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7918 (pp20) REVERT: D 221 VAL cc_start: 0.9355 (t) cc_final: 0.8906 (p) REVERT: D 254 TYR cc_start: 0.9258 (m-10) cc_final: 0.8985 (m-10) REVERT: D 321 HIS cc_start: 0.9105 (p-80) cc_final: 0.8834 (p-80) REVERT: D 333 VAL cc_start: 0.7708 (t) cc_final: 0.7030 (t) REVERT: D 365 PHE cc_start: 0.9007 (p90) cc_final: 0.8714 (p90) REVERT: D 381 ASN cc_start: 0.9497 (m110) cc_final: 0.9025 (t0) REVERT: D 422 ARG cc_start: 0.6883 (mmt180) cc_final: 0.6378 (mtp180) REVERT: D 441 HIS cc_start: 0.8508 (m-70) cc_final: 0.8163 (m-70) REVERT: D 500 MET cc_start: 0.7488 (mtt) cc_final: 0.5883 (mtt) REVERT: D 557 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8822 (mmtp) REVERT: D 586 ARG cc_start: 0.8849 (ttt180) cc_final: 0.8295 (tpt-90) REVERT: D 673 MET cc_start: 0.8212 (tpt) cc_final: 0.8006 (tpt) REVERT: D 735 PHE cc_start: 0.9239 (m-80) cc_final: 0.8946 (m-80) REVERT: D 840 GLU cc_start: 0.7298 (pm20) cc_final: 0.6342 (tp30) REVERT: D 916 PHE cc_start: 0.8591 (m-80) cc_final: 0.8369 (m-80) REVERT: D 933 LEU cc_start: 0.9003 (mp) cc_final: 0.7216 (mp) REVERT: D 977 MET cc_start: 0.6804 (mmp) cc_final: 0.6477 (mmp) REVERT: D 1007 TYR cc_start: 0.8814 (m-80) cc_final: 0.8499 (m-80) REVERT: D 1101 LEU cc_start: 0.9143 (mm) cc_final: 0.8711 (pp) REVERT: D 1104 TYR cc_start: 0.8389 (m-10) cc_final: 0.8027 (m-10) REVERT: D 1152 TYR cc_start: 0.7765 (t80) cc_final: 0.7341 (t80) REVERT: D 1164 LYS cc_start: 0.7288 (tptt) cc_final: 0.7080 (tptt) REVERT: D 1213 LEU cc_start: 0.9483 (tp) cc_final: 0.9270 (tp) REVERT: D 1248 PHE cc_start: 0.7969 (t80) cc_final: 0.7492 (t80) REVERT: D 1281 GLN cc_start: 0.8393 (pm20) cc_final: 0.8182 (pm20) REVERT: D 1297 ARG cc_start: 0.8937 (tmm-80) cc_final: 0.8693 (tmm-80) REVERT: D 1298 LEU cc_start: 0.8678 (pt) cc_final: 0.8377 (tt) REVERT: D 1312 TYR cc_start: 0.9092 (m-80) cc_final: 0.8760 (m-80) REVERT: D 1314 MET cc_start: 0.9170 (mmp) cc_final: 0.8864 (mmp) REVERT: D 1393 LYS cc_start: 0.9168 (tptp) cc_final: 0.8927 (tptp) REVERT: D 1436 ASP cc_start: 0.7293 (m-30) cc_final: 0.6876 (m-30) REVERT: D 1446 ILE cc_start: 0.8285 (pt) cc_final: 0.8015 (pt) outliers start: 2 outliers final: 1 residues processed: 272 average time/residue: 0.1150 time to fit residues: 43.3881 Evaluate side-chains 207 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.408 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 221 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 164 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 335 optimal weight: 0.0470 chunk 411 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 177 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 overall best weight: 0.7456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 85 HIS A 177 GLN A 232 GLN A 279 HIS A 302 GLN A 327 GLN A 511 HIS A 646 HIS A1089 ASN A1179 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 ASN D 142 GLN D 182 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 562 ASN D 693 GLN D 938 ASN ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.137515 restraints weight = 98575.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.138591 restraints weight = 80055.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.139419 restraints weight = 67178.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.140162 restraints weight = 59561.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.140442 restraints weight = 53730.482| |-----------------------------------------------------------------------------| r_work (final): 0.4551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.116508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086750 restraints weight = 44950.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.089985 restraints weight = 33585.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.092619 restraints weight = 26590.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.094717 restraints weight = 21865.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.096398 restraints weight = 18530.796| |-----------------------------------------------------------------------------| r_work (final): 0.3852 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.057934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.055056 restraints weight = 330.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.055848 restraints weight = 109.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.056321 restraints weight = 56.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.056645 restraints weight = 35.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.056837 restraints weight = 25.589| |-----------------------------------------------------------------------------| r_work (final): 0.2826 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072138 restraints weight = 341.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072789 restraints weight = 101.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073184 restraints weight = 44.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073365 restraints weight = 21.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073518 restraints weight = 13.761| |-----------------------------------------------------------------------------| r_work (final): 0.3062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.051420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.048826 restraints weight = 305.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.049558 restraints weight = 167.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.049981 restraints weight = 119.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.050254 restraints weight = 90.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.050540 restraints weight = 72.063| |-----------------------------------------------------------------------------| r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45680 Z= 0.147 Angle : 0.851 17.244 62168 Z= 0.408 Chirality : 0.051 0.340 7198 Planarity : 0.006 0.071 7916 Dihedral : 6.791 29.434 6022 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.10 % Favored : 87.54 % Rotamer: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.10), residues: 5620 helix: -2.20 (0.17), residues: 724 sheet: -2.23 (0.13), residues: 1524 loop : -3.47 (0.09), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 804 TYR 0.027 0.002 TYR A1018 PHE 0.023 0.002 PHE B1049 TRP 0.022 0.002 TRP B1040 HIS 0.013 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (45592) covalent geometry : angle 0.82535 / 0.40 (61950) SS BOND : bond 0.00680 / 0.41 ( 46) SS BOND : angle 1.54326 / 1.09 ( 92) hydrogen bonds : bond 0.06205 / 4.16 ( 384) hydrogen bonds : angle 6.82714 / 4.73 ( 1152) link_ALPHA1-6 : bond 0.00418 / 0.21 ( 2) link_ALPHA1-6 : angle 1.33211 / 0.77 ( 6) link_BETA1-4 : bond 0.00612 / 0.42 ( 10) link_BETA1-4 : angle 2.11844 / 1.36 ( 30) link_NAG-ASN : bond 0.01196 / 0.69 ( 30) link_NAG-ASN : angle 5.23270 / 3.26 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.421 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: A 151 MET cc_start: 0.6558 (tpt) cc_final: 0.6058 (tpt) REVERT: A 231 VAL cc_start: 0.5994 (t) cc_final: 0.5493 (t) REVERT: A 305 LYS cc_start: 0.8667 (mppt) cc_final: 0.8055 (mppt) REVERT: A 381 ASN cc_start: 0.9609 (t0) cc_final: 0.9317 (m-40) REVERT: A 385 PHE cc_start: 0.8804 (m-80) cc_final: 0.8438 (m-80) REVERT: A 409 ILE cc_start: 0.8048 (pt) cc_final: 0.7794 (tt) REVERT: A 456 LYS cc_start: 0.9352 (pttm) cc_final: 0.8617 (tptt) REVERT: A 460 HIS cc_start: 0.7487 (t-170) cc_final: 0.6947 (t-170) REVERT: A 607 MET cc_start: 0.3778 (mtt) cc_final: 0.3161 (mtt) REVERT: A 655 TYR cc_start: 0.3434 (p90) cc_final: 0.1126 (m-10) REVERT: A 673 MET cc_start: 0.2476 (mmp) cc_final: 0.1760 (mmm) REVERT: A 1330 TYR cc_start: 0.9565 (p90) cc_final: 0.9180 (p90) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.1278 time to fit residues: 22.8164 Evaluate side-chains 88 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.431 Evaluate side-chains 255 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.400 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: D 32 MET cc_start: 0.7828 (ttp) cc_final: 0.7423 (ttp) REVERT: D 101 MET cc_start: 0.1781 (ptm) cc_final: 0.0728 (ttp) REVERT: D 121 MET cc_start: 0.7470 (mmp) cc_final: 0.6971 (mpp) REVERT: D 132 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8550 (tm-30) REVERT: D 151 MET cc_start: 0.8591 (tpp) cc_final: 0.8360 (tpp) REVERT: D 175 ILE cc_start: 0.9549 (tp) cc_final: 0.9343 (tp) REVERT: D 319 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8451 (mmmt) REVERT: D 321 HIS cc_start: 0.9104 (p-80) cc_final: 0.8644 (p-80) REVERT: D 365 PHE cc_start: 0.8997 (p90) cc_final: 0.8646 (p90) REVERT: D 381 ASN cc_start: 0.9516 (m110) cc_final: 0.9065 (t0) REVERT: D 422 ARG cc_start: 0.7564 (tpp80) cc_final: 0.6947 (mtp180) REVERT: D 464 MET cc_start: 0.8183 (mmp) cc_final: 0.7925 (mmt) REVERT: D 476 VAL cc_start: 0.8752 (t) cc_final: 0.8436 (t) REVERT: D 500 MET cc_start: 0.7611 (mtt) cc_final: 0.6882 (mtt) REVERT: D 557 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8776 (mmtp) REVERT: D 586 ARG cc_start: 0.8857 (ttt180) cc_final: 0.8317 (tpt-90) REVERT: D 735 PHE cc_start: 0.9264 (m-80) cc_final: 0.8965 (m-80) REVERT: D 795 GLU cc_start: 0.9168 (tp30) cc_final: 0.8745 (tm-30) REVERT: D 916 PHE cc_start: 0.8536 (m-80) cc_final: 0.8336 (m-80) REVERT: D 933 LEU cc_start: 0.8879 (mp) cc_final: 0.7332 (mp) REVERT: D 938 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7288 (t0) REVERT: D 977 MET cc_start: 0.6796 (mmp) cc_final: 0.6523 (mmp) REVERT: D 1003 LYS cc_start: 0.7591 (tptp) cc_final: 0.7163 (tptp) REVERT: D 1007 TYR cc_start: 0.8697 (m-80) cc_final: 0.8208 (m-80) REVERT: D 1152 TYR cc_start: 0.7944 (t80) cc_final: 0.7583 (t80) REVERT: D 1164 LYS cc_start: 0.7406 (tptt) cc_final: 0.7196 (tptt) REVERT: D 1208 MET cc_start: 0.8475 (ppp) cc_final: 0.8125 (ppp) REVERT: D 1209 THR cc_start: 0.8804 (m) cc_final: 0.8358 (m) REVERT: D 1213 LEU cc_start: 0.9450 (tp) cc_final: 0.9173 (tp) REVERT: D 1248 PHE cc_start: 0.8091 (t80) cc_final: 0.7590 (t80) REVERT: D 1264 TYR cc_start: 0.7937 (t80) cc_final: 0.7586 (t80) REVERT: D 1279 THR cc_start: 0.9301 (p) cc_final: 0.8888 (p) REVERT: D 1314 MET cc_start: 0.8833 (mmp) cc_final: 0.8544 (mmp) REVERT: D 1315 LYS cc_start: 0.9345 (mmpt) cc_final: 0.9000 (mmmt) REVERT: D 1378 MET cc_start: 0.6414 (mtm) cc_final: 0.6040 (mtm) REVERT: D 1436 ASP cc_start: 0.7418 (m-30) cc_final: 0.6983 (m-30) outliers start: 2 outliers final: 0 residues processed: 254 average time/residue: 0.1123 time to fit residues: 40.0001 Evaluate side-chains 207 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.439 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 3 optimal weight: 6.9990 chunk 447 optimal weight: 0.0030 chunk 259 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 262 optimal weight: 0.0170 chunk 106 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 535 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.8034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN A 263 HIS ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 358 HIS ** 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 ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.154069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.135809 restraints weight = 99499.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.137014 restraints weight = 81461.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.137949 restraints weight = 68327.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.138715 restraints weight = 60191.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.139262 restraints weight = 53955.307| |-----------------------------------------------------------------------------| r_work (final): 0.4497 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.113213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.084920 restraints weight = 44156.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.087950 restraints weight = 33392.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.090292 restraints weight = 26684.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.092180 restraints weight = 22212.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.093701 restraints weight = 19015.305| |-----------------------------------------------------------------------------| r_work (final): 0.3817 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.057291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.054722 restraints weight = 410.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.055426 restraints weight = 125.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.055836 restraints weight = 66.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.056081 restraints weight = 43.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.056219 restraints weight = 31.782| |-----------------------------------------------------------------------------| r_work (final): 0.2837 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072574 restraints weight = 376.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072977 restraints weight = 72.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073110 restraints weight = 22.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073175 restraints weight = 7.382 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073197 restraints weight = 2.516 | |-----------------------------------------------------------------------------| r_work (final): 0.3040 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.051980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.048820 restraints weight = 351.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.049950 restraints weight = 151.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.050528 restraints weight = 96.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.050822 restraints weight = 70.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.051038 restraints weight = 55.082| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45680 Z= 0.147 Angle : 0.819 17.127 62168 Z= 0.397 Chirality : 0.050 0.326 7198 Planarity : 0.006 0.070 7916 Dihedral : 6.532 32.321 6022 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.81 % Favored : 86.94 % Rotamer: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.10), residues: 5620 helix: -1.94 (0.18), residues: 716 sheet: -2.11 (0.13), residues: 1564 loop : -3.36 (0.09), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 270 TYR 0.031 0.002 TYR B1216 PHE 0.020 0.002 PHE D1049 TRP 0.017 0.002 TRP B 741 HIS 0.009 0.001 HIS C1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (45592) covalent geometry : angle 0.79693 / 0.39 (61950) SS BOND : bond 0.00576 / 0.35 ( 46) SS BOND : angle 1.40218 / 0.96 ( 92) hydrogen bonds : bond 0.06130 / 4.14 ( 384) hydrogen bonds : angle 6.60714 / 4.57 ( 1152) link_ALPHA1-6 : bond 0.00196 / 0.10 ( 2) link_ALPHA1-6 : angle 1.17100 / 0.67 ( 6) link_BETA1-4 : bond 0.00493 / 0.35 ( 10) link_BETA1-4 : angle 1.92128 / 1.29 ( 30) link_NAG-ASN : bond 0.01135 / 0.64 ( 30) link_NAG-ASN : angle 4.83367 / 3.02 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.419 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: C 151 MET cc_start: 0.6369 (tpt) cc_final: 0.5598 (tpp) REVERT: C 183 LEU cc_start: 0.8741 (mt) cc_final: 0.8464 (mt) REVERT: C 305 LYS cc_start: 0.8643 (mppt) cc_final: 0.7937 (mppt) REVERT: C 385 PHE cc_start: 0.8043 (m-80) cc_final: 0.7722 (m-80) REVERT: C 456 LYS cc_start: 0.9450 (pttm) cc_final: 0.8657 (tptt) REVERT: C 464 MET cc_start: 0.7513 (tmm) cc_final: 0.7272 (tmm) REVERT: C 607 MET cc_start: 0.2625 (mtt) cc_final: 0.1918 (mtt) REVERT: C 647 ASN cc_start: 0.7269 (p0) cc_final: 0.5835 (p0) REVERT: C 655 TYR cc_start: 0.3152 (p90) cc_final: 0.1064 (m-10) REVERT: C 673 MET cc_start: 0.2462 (mmp) cc_final: 0.1539 (mmm) REVERT: C 966 LEU cc_start: 0.8162 (tp) cc_final: 0.7956 (mp) REVERT: C 968 MET cc_start: 0.5617 (mmp) cc_final: 0.5189 (mmp) REVERT: C 1330 TYR cc_start: 0.9585 (p90) cc_final: 0.9041 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1098 time to fit residues: 18.1987 Evaluate side-chains 82 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.484 Evaluate side-chains 247 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.492 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: D 32 MET cc_start: 0.7937 (ttp) cc_final: 0.7615 (ttp) REVERT: D 101 MET cc_start: 0.2415 (ptm) cc_final: 0.1306 (ttp) REVERT: D 121 MET cc_start: 0.7653 (mmp) cc_final: 0.7178 (mpp) REVERT: D 151 MET cc_start: 0.8536 (tpp) cc_final: 0.8275 (tpp) REVERT: D 183 LEU cc_start: 0.9553 (mp) cc_final: 0.9339 (mp) REVERT: D 223 GLU cc_start: 0.8850 (tp30) cc_final: 0.8340 (tp30) REVERT: D 321 HIS cc_start: 0.9134 (p-80) cc_final: 0.8622 (p-80) REVERT: D 365 PHE cc_start: 0.9130 (p90) cc_final: 0.8803 (p90) REVERT: D 373 ASP cc_start: 0.8095 (t0) cc_final: 0.7883 (t70) REVERT: D 381 ASN cc_start: 0.9529 (m110) cc_final: 0.9115 (t0) REVERT: D 384 ILE cc_start: 0.9463 (pt) cc_final: 0.9261 (tp) REVERT: D 422 ARG cc_start: 0.7661 (tpp80) cc_final: 0.6764 (mtp180) REVERT: D 464 MET cc_start: 0.8066 (mmp) cc_final: 0.7795 (mmt) REVERT: D 476 VAL cc_start: 0.8814 (t) cc_final: 0.8549 (t) REVERT: D 500 MET cc_start: 0.7900 (mtt) cc_final: 0.7216 (mtt) REVERT: D 502 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8325 (ptmt) REVERT: D 539 ARG cc_start: 0.6325 (mtt180) cc_final: 0.4648 (mtt180) REVERT: D 557 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8877 (mmtp) REVERT: D 735 PHE cc_start: 0.9283 (m-80) cc_final: 0.8988 (m-80) REVERT: D 916 PHE cc_start: 0.8747 (m-80) cc_final: 0.8459 (m-80) REVERT: D 933 LEU cc_start: 0.8923 (mp) cc_final: 0.7588 (mp) REVERT: D 977 MET cc_start: 0.7013 (mmp) cc_final: 0.6734 (mmp) REVERT: D 1003 LYS cc_start: 0.7831 (tptp) cc_final: 0.7342 (tptp) REVERT: D 1007 TYR cc_start: 0.8719 (m-80) cc_final: 0.8234 (m-80) REVERT: D 1137 GLU cc_start: 0.7342 (tp30) cc_final: 0.7121 (tp30) REVERT: D 1152 TYR cc_start: 0.8130 (t80) cc_final: 0.7729 (t80) REVERT: D 1208 MET cc_start: 0.8536 (ppp) cc_final: 0.8037 (ppp) REVERT: D 1209 THR cc_start: 0.8962 (m) cc_final: 0.8556 (m) REVERT: D 1213 LEU cc_start: 0.9439 (tp) cc_final: 0.9198 (tp) REVERT: D 1248 PHE cc_start: 0.8128 (t80) cc_final: 0.7595 (t80) REVERT: D 1313 SER cc_start: 0.9022 (p) cc_final: 0.8815 (t) REVERT: D 1314 MET cc_start: 0.8623 (mmp) cc_final: 0.8304 (mmp) REVERT: D 1315 LYS cc_start: 0.9329 (mmpt) cc_final: 0.8928 (mmmt) REVERT: D 1331 ASN cc_start: 0.9229 (m-40) cc_final: 0.8933 (m-40) REVERT: D 1429 LEU cc_start: 0.9009 (pt) cc_final: 0.8806 (pt) REVERT: D 1436 ASP cc_start: 0.7541 (m-30) cc_final: 0.7096 (m-30) outliers start: 1 outliers final: 1 residues processed: 247 average time/residue: 0.1116 time to fit residues: 38.9770 Evaluate side-chains 197 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.406 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 182 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 522 optimal weight: 0.0370 chunk 73 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 319 optimal weight: 2.9990 chunk 408 optimal weight: 0.0060 chunk 245 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 460 HIS C 917 ASN ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN C1259 HIS C1325 GLN D 132 GLN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 ASN D 994 GLN D1118 HIS D1123 ASN D1296 ASN ** D1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1331 ASN ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.155381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.137353 restraints weight = 97418.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.138436 restraints weight = 80875.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.139554 restraints weight = 67308.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.140110 restraints weight = 59105.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.140125 restraints weight = 53601.432| |-----------------------------------------------------------------------------| r_work (final): 0.4546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.115960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.087153 restraints weight = 44804.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.090232 restraints weight = 33998.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.092701 restraints weight = 27142.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.094701 restraints weight = 22493.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.096308 restraints weight = 19195.116| |-----------------------------------------------------------------------------| r_work (final): 0.3847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.052691 restraints weight = 293.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.053325 restraints weight = 102.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053807 restraints weight = 56.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.054121 restraints weight = 37.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.054255 restraints weight = 27.005| |-----------------------------------------------------------------------------| r_work (final): 0.2750 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.076798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076194 restraints weight = 348.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076478 restraints weight = 58.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076639 restraints weight = 18.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076689 restraints weight = 5.088 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076705 restraints weight = 2.002 | |-----------------------------------------------------------------------------| r_work (final): 0.3150 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.050288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 15)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.046628 restraints weight = 310.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.047743 restraints weight = 160.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.048381 restraints weight = 107.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.048882 restraints weight = 77.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.049230 restraints weight = 54.182| |-----------------------------------------------------------------------------| r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45680 Z= 0.133 Angle : 0.804 17.756 62168 Z= 0.387 Chirality : 0.050 0.370 7198 Planarity : 0.005 0.069 7916 Dihedral : 6.310 29.283 6022 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.81 % Favored : 87.97 % Rotamer: Outliers : 0.12 % Allowed : 3.28 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.10), residues: 5620 helix: -1.70 (0.18), residues: 716 sheet: -1.93 (0.13), residues: 1518 loop : -3.31 (0.09), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 270 TYR 0.043 0.002 TYR A 985 PHE 0.023 0.002 PHE A1044 TRP 0.018 0.002 TRP B 858 HIS 0.010 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (45592) covalent geometry : angle 0.77890 / 0.38 (61950) SS BOND : bond 0.00506 / 0.30 ( 46) SS BOND : angle 1.36904 / 0.97 ( 92) hydrogen bonds : bond 0.05800 / 3.91 ( 384) hydrogen bonds : angle 6.41731 / 4.44 ( 1152) link_ALPHA1-6 : bond 0.00341 / 0.17 ( 2) link_ALPHA1-6 : angle 1.40124 / 0.81 ( 6) link_BETA1-4 : bond 0.00584 / 0.40 ( 10) link_BETA1-4 : angle 2.00001 / 1.28 ( 30) link_NAG-ASN : bond 0.00963 / 0.54 ( 30) link_NAG-ASN : angle 5.10705 / 3.18 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.393 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: A 151 MET cc_start: 0.6280 (tpt) cc_final: 0.5480 (tpp) REVERT: A 183 LEU cc_start: 0.8143 (mt) cc_final: 0.7901 (mt) REVERT: A 305 LYS cc_start: 0.8732 (mppt) cc_final: 0.8171 (mppt) REVERT: A 385 PHE cc_start: 0.8859 (m-80) cc_final: 0.8586 (m-80) REVERT: A 456 LYS cc_start: 0.9421 (pttm) cc_final: 0.8708 (tptt) REVERT: A 460 HIS cc_start: 0.8216 (t-170) cc_final: 0.7597 (t-170) REVERT: A 607 MET cc_start: 0.4131 (mtt) cc_final: 0.3579 (mtt) REVERT: A 647 ASN cc_start: 0.7170 (p0) cc_final: 0.5944 (p0) REVERT: A 655 TYR cc_start: 0.3394 (p90) cc_final: 0.1398 (m-10) REVERT: A 673 MET cc_start: 0.2914 (mmp) cc_final: 0.2026 (mmm) REVERT: A 966 LEU cc_start: 0.8510 (tp) cc_final: 0.8270 (mp) REVERT: A 968 MET cc_start: 0.6086 (mmp) cc_final: 0.5757 (mmp) REVERT: A 1330 TYR cc_start: 0.9628 (p90) cc_final: 0.9177 (p90) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1156 time to fit residues: 18.1599 Evaluate side-chains 79 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.441 Evaluate side-chains 252 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 249 time to evaluate : 0.394 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: D 101 MET cc_start: 0.3417 (ptm) cc_final: 0.3114 (ptm) REVERT: D 121 MET cc_start: 0.7426 (mmp) cc_final: 0.7003 (mpp) REVERT: D 151 MET cc_start: 0.8522 (tpp) cc_final: 0.8269 (tpp) REVERT: D 183 LEU cc_start: 0.9484 (mp) cc_final: 0.9257 (mp) REVERT: D 223 GLU cc_start: 0.8745 (tp30) cc_final: 0.8250 (tp30) REVERT: D 321 HIS cc_start: 0.9106 (p-80) cc_final: 0.8579 (p-80) REVERT: D 365 PHE cc_start: 0.9074 (p90) cc_final: 0.8735 (p90) REVERT: D 373 ASP cc_start: 0.8155 (t0) cc_final: 0.7926 (t70) REVERT: D 381 ASN cc_start: 0.9495 (m110) cc_final: 0.9077 (t0) REVERT: D 384 ILE cc_start: 0.9376 (pt) cc_final: 0.9103 (mm) REVERT: D 464 MET cc_start: 0.7999 (mmp) cc_final: 0.7714 (mmt) REVERT: D 496 TYR cc_start: 0.8151 (m-80) cc_final: 0.7944 (m-10) REVERT: D 500 MET cc_start: 0.7597 (mtt) cc_final: 0.7066 (mtt) REVERT: D 502 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8364 (ptmt) REVERT: D 539 ARG cc_start: 0.6685 (mtt180) cc_final: 0.4791 (mtt180) REVERT: D 557 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8777 (mmtp) REVERT: D 586 ARG cc_start: 0.8878 (ttt180) cc_final: 0.8338 (tpt-90) REVERT: D 796 LEU cc_start: 0.9217 (pt) cc_final: 0.8621 (pt) REVERT: D 798 MET cc_start: 0.7903 (tmm) cc_final: 0.6092 (mmt) REVERT: D 880 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8387 (pp30) REVERT: D 916 PHE cc_start: 0.8566 (m-80) cc_final: 0.8328 (m-80) REVERT: D 933 LEU cc_start: 0.8758 (mp) cc_final: 0.7449 (mp) REVERT: D 1003 LYS cc_start: 0.7693 (tptp) cc_final: 0.7123 (tptp) REVERT: D 1007 TYR cc_start: 0.8688 (m-80) cc_final: 0.8123 (m-80) REVERT: D 1126 PHE cc_start: 0.9142 (m-10) cc_final: 0.8929 (m-10) REVERT: D 1152 TYR cc_start: 0.8029 (t80) cc_final: 0.7725 (t80) REVERT: D 1164 LYS cc_start: 0.7538 (tptt) cc_final: 0.7303 (tptt) REVERT: D 1208 MET cc_start: 0.8490 (ppp) cc_final: 0.8132 (ppp) REVERT: D 1209 THR cc_start: 0.8792 (m) cc_final: 0.8501 (m) REVERT: D 1248 PHE cc_start: 0.7908 (t80) cc_final: 0.7362 (t80) REVERT: D 1264 TYR cc_start: 0.7714 (t80) cc_final: 0.7429 (t80) REVERT: D 1279 THR cc_start: 0.9143 (p) cc_final: 0.8756 (p) REVERT: D 1314 MET cc_start: 0.8417 (mmp) cc_final: 0.8202 (mmp) REVERT: D 1315 LYS cc_start: 0.9322 (mmpt) cc_final: 0.8928 (mmmt) REVERT: D 1436 ASP cc_start: 0.7481 (m-30) cc_final: 0.7032 (m-30) outliers start: 3 outliers final: 1 residues processed: 252 average time/residue: 0.1052 time to fit residues: 37.8678 Evaluate side-chains 189 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.430 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 281 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 345 optimal weight: 8.9990 chunk 427 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 254 optimal weight: 0.0370 chunk 494 optimal weight: 0.5980 chunk 420 optimal weight: 0.0000 chunk 256 optimal weight: 4.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A 917 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN A1259 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS D 938 ASN D 994 GLN D1118 HIS ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1325 GLN ** D1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.155762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.137651 restraints weight = 96855.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.138812 restraints weight = 78607.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.139531 restraints weight = 67551.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.140312 restraints weight = 59954.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.140321 restraints weight = 54066.294| |-----------------------------------------------------------------------------| r_work (final): 0.4520 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.116585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.087317 restraints weight = 43779.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.090532 restraints weight = 32746.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.093087 restraints weight = 25944.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.095132 restraints weight = 21360.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.096751 restraints weight = 18156.024| |-----------------------------------------------------------------------------| r_work (final): 0.3880 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.055945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053376 restraints weight = 296.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.054044 restraints weight = 96.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.054571 restraints weight = 52.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.054828 restraints weight = 31.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.054828 restraints weight = 21.794| |-----------------------------------------------------------------------------| r_work (final): 0.2794 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077574 restraints weight = 397.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077782 restraints weight = 63.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.078127 restraints weight = 24.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078124 restraints weight = 4.633 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078137 restraints weight = 3.152 | |-----------------------------------------------------------------------------| r_work (final): 0.3179 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.045313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.041769 restraints weight = 275.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.042749 restraints weight = 160.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.043288 restraints weight = 114.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.043688 restraints weight = 88.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.043951 restraints weight = 71.827| |-----------------------------------------------------------------------------| r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45680 Z= 0.130 Angle : 0.785 18.093 62168 Z= 0.379 Chirality : 0.048 0.375 7198 Planarity : 0.005 0.071 7916 Dihedral : 6.132 29.545 6022 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.78 % Favored : 88.01 % Rotamer: Outliers : 0.12 % Allowed : 1.98 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.10), residues: 5620 helix: -1.68 (0.18), residues: 724 sheet: -1.85 (0.13), residues: 1546 loop : -3.25 (0.09), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 270 TYR 0.030 0.002 TYR B1216 PHE 0.031 0.002 PHE B 524 TRP 0.019 0.001 TRP D 858 HIS 0.007 0.001 HIS C1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (45592) covalent geometry : angle 0.76128 / 0.37 (61950) SS BOND : bond 0.00493 / 0.26 ( 46) SS BOND : angle 1.40103 / 0.99 ( 92) hydrogen bonds : bond 0.05677 / 3.81 ( 384) hydrogen bonds : angle 6.29850 / 4.31 ( 1152) link_ALPHA1-6 : bond 0.00396 / 0.20 ( 2) link_ALPHA1-6 : angle 1.43330 / 0.83 ( 6) link_BETA1-4 : bond 0.00555 / 0.39 ( 10) link_BETA1-4 : angle 1.92765 / 1.21 ( 30) link_NAG-ASN : bond 0.00940 / 0.54 ( 30) link_NAG-ASN : angle 4.86303 / 3.01 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.430 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: A 151 MET cc_start: 0.5560 (tpt) cc_final: 0.4495 (tpp) REVERT: A 183 LEU cc_start: 0.8726 (mt) cc_final: 0.8501 (mt) REVERT: A 305 LYS cc_start: 0.8611 (mppt) cc_final: 0.7891 (tppt) REVERT: A 385 PHE cc_start: 0.7976 (m-80) cc_final: 0.7756 (m-80) REVERT: A 456 LYS cc_start: 0.9460 (pttm) cc_final: 0.8704 (tptt) REVERT: A 607 MET cc_start: 0.2446 (mtt) cc_final: 0.1920 (mtt) REVERT: A 647 ASN cc_start: 0.7161 (p0) cc_final: 0.5626 (p0) REVERT: A 655 TYR cc_start: 0.3363 (p90) cc_final: 0.1370 (m-10) REVERT: A 673 MET cc_start: 0.2610 (mmp) cc_final: 0.1200 (mmm) REVERT: A 985 TYR cc_start: 0.6898 (m-80) cc_final: 0.6366 (m-80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1138 time to fit residues: 17.2668 Evaluate side-chains 82 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.425 Evaluate side-chains 241 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.431 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: D 32 MET cc_start: 0.7953 (ttp) cc_final: 0.7385 (ttp) REVERT: D 121 MET cc_start: 0.7453 (mmp) cc_final: 0.6961 (mpp) REVERT: D 146 PHE cc_start: 0.9404 (p90) cc_final: 0.9180 (p90) REVERT: D 151 MET cc_start: 0.8442 (tpp) cc_final: 0.8220 (tpp) REVERT: D 183 LEU cc_start: 0.9393 (mp) cc_final: 0.9170 (mp) REVERT: D 221 VAL cc_start: 0.9510 (t) cc_final: 0.8666 (p) REVERT: D 321 HIS cc_start: 0.9094 (p-80) cc_final: 0.8500 (p-80) REVERT: D 365 PHE cc_start: 0.8983 (p90) cc_final: 0.8572 (p90) REVERT: D 373 ASP cc_start: 0.8099 (t0) cc_final: 0.7889 (t70) REVERT: D 381 ASN cc_start: 0.9504 (m110) cc_final: 0.9040 (t0) REVERT: D 384 ILE cc_start: 0.9405 (pt) cc_final: 0.9162 (mm) REVERT: D 422 ARG cc_start: 0.6308 (tpp80) cc_final: 0.5803 (mtp180) REVERT: D 460 HIS cc_start: 0.8630 (t-90) cc_final: 0.8349 (t-90) REVERT: D 464 MET cc_start: 0.8034 (mmp) cc_final: 0.7758 (mmt) REVERT: D 476 VAL cc_start: 0.8670 (t) cc_final: 0.8126 (t) REVERT: D 496 TYR cc_start: 0.8151 (m-80) cc_final: 0.7923 (m-10) REVERT: D 500 MET cc_start: 0.7619 (mtt) cc_final: 0.7175 (mtt) REVERT: D 502 LYS cc_start: 0.8650 (ptpt) cc_final: 0.8333 (ptmt) REVERT: D 520 MET cc_start: 0.5940 (ttt) cc_final: 0.5640 (ttt) REVERT: D 557 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8778 (mmtp) REVERT: D 607 MET cc_start: 0.6001 (ttp) cc_final: 0.5733 (ttp) REVERT: D 796 LEU cc_start: 0.9196 (pt) cc_final: 0.8541 (pt) REVERT: D 798 MET cc_start: 0.7668 (tmm) cc_final: 0.6299 (mmt) REVERT: D 930 GLU cc_start: 0.8682 (tp30) cc_final: 0.8423 (mp0) REVERT: D 931 LEU cc_start: 0.8936 (tp) cc_final: 0.8627 (tp) REVERT: D 933 LEU cc_start: 0.8709 (mp) cc_final: 0.7294 (mp) REVERT: D 1003 LYS cc_start: 0.7633 (tptp) cc_final: 0.7039 (tptp) REVERT: D 1007 TYR cc_start: 0.8651 (m-80) cc_final: 0.8078 (m-80) REVERT: D 1126 PHE cc_start: 0.9115 (m-10) cc_final: 0.8729 (m-10) REVERT: D 1152 TYR cc_start: 0.7940 (t80) cc_final: 0.7692 (t80) REVERT: D 1208 MET cc_start: 0.8531 (ppp) cc_final: 0.8111 (ppp) REVERT: D 1209 THR cc_start: 0.8724 (m) cc_final: 0.8415 (m) REVERT: D 1264 TYR cc_start: 0.7414 (t80) cc_final: 0.7182 (t80) REVERT: D 1279 THR cc_start: 0.9135 (p) cc_final: 0.8818 (p) REVERT: D 1315 LYS cc_start: 0.9295 (mmpt) cc_final: 0.8891 (mmmt) REVERT: D 1325 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: D 1436 ASP cc_start: 0.7515 (m-30) cc_final: 0.7069 (m-30) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.1042 time to fit residues: 35.8917 Evaluate side-chains 187 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.419 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 26 optimal weight: 0.3980 chunk 288 optimal weight: 0.0070 chunk 70 optimal weight: 0.0470 chunk 7 optimal weight: 0.0980 chunk 410 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 528 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 535 optimal weight: 2.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 ASN D 994 GLN D1118 HIS ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.156638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.138214 restraints weight = 95804.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.139621 restraints weight = 79429.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.140361 restraints weight = 67379.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.141351 restraints weight = 59794.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.141351 restraints weight = 52205.618| |-----------------------------------------------------------------------------| r_work (final): 0.4527 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.118601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.088872 restraints weight = 43125.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.092173 restraints weight = 32238.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.094732 restraints weight = 25505.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.096836 restraints weight = 21062.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.098485 restraints weight = 17890.878| |-----------------------------------------------------------------------------| r_work (final): 0.3895 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.054430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.052318 restraints weight = 355.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052866 restraints weight = 112.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053267 restraints weight = 58.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.053535 restraints weight = 35.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.053585 restraints weight = 24.598| |-----------------------------------------------------------------------------| r_work (final): 0.2774 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076523 restraints weight = 307.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076698 restraints weight = 45.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076884 restraints weight = 20.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076896 restraints weight = 4.673 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076908 restraints weight = 1.145 | |-----------------------------------------------------------------------------| r_work (final): 0.3138 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.044922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.041387 restraints weight = 290.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.042448 restraints weight = 166.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.043082 restraints weight = 115.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2343 r_free = 0.2343 target = 0.043492 restraints weight = 86.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.043794 restraints weight = 67.215| |-----------------------------------------------------------------------------| r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45680 Z= 0.129 Angle : 0.787 18.129 62168 Z= 0.376 Chirality : 0.049 0.375 7198 Planarity : 0.005 0.071 7916 Dihedral : 5.988 28.214 6022 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.53 % Favored : 88.29 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.10), residues: 5620 helix: -1.55 (0.18), residues: 714 sheet: -1.65 (0.13), residues: 1528 loop : -3.16 (0.09), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1297 TYR 0.029 0.002 TYR B1216 PHE 0.036 0.002 PHE D 524 TRP 0.020 0.001 TRP B 858 HIS 0.008 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (45592) covalent geometry : angle 0.76026 / 0.37 (61950) SS BOND : bond 0.00478 / 0.28 ( 46) SS BOND : angle 1.29501 / 0.90 ( 92) hydrogen bonds : bond 0.05632 / 3.75 ( 384) hydrogen bonds : angle 6.07514 / 4.18 ( 1152) link_ALPHA1-6 : bond 0.00383 / 0.19 ( 2) link_ALPHA1-6 : angle 1.41823 / 0.82 ( 6) link_BETA1-4 : bond 0.00559 / 0.40 ( 10) link_BETA1-4 : angle 1.90638 / 1.17 ( 30) link_NAG-ASN : bond 0.01035 / 0.65 ( 30) link_NAG-ASN : angle 5.19954 / 3.21 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.443 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: A 151 MET cc_start: 0.5529 (tpt) cc_final: 0.4428 (tpp) REVERT: A 183 LEU cc_start: 0.8738 (mt) cc_final: 0.8492 (mt) REVERT: A 305 LYS cc_start: 0.8568 (mppt) cc_final: 0.7851 (tppt) REVERT: A 318 MET cc_start: 0.5491 (ttm) cc_final: 0.5258 (ttm) REVERT: A 456 LYS cc_start: 0.9475 (pttm) cc_final: 0.8789 (tptt) REVERT: A 607 MET cc_start: 0.2668 (mtt) cc_final: 0.2093 (mtt) REVERT: A 647 ASN cc_start: 0.6937 (p0) cc_final: 0.5500 (p0) REVERT: A 655 TYR cc_start: 0.3261 (p90) cc_final: 0.1295 (m-10) REVERT: A 673 MET cc_start: 0.2667 (mmp) cc_final: 0.1253 (mmm) REVERT: A 968 MET cc_start: 0.4611 (mmp) cc_final: 0.4094 (mmp) REVERT: A 985 TYR cc_start: 0.6660 (m-80) cc_final: 0.6085 (m-80) REVERT: A 1314 MET cc_start: -0.0463 (tmm) cc_final: -0.1803 (tmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1113 time to fit residues: 17.7720 Evaluate side-chains 78 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.390 Evaluate side-chains 229 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.404 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: B 32 MET cc_start: 0.7978 (ttp) cc_final: 0.7567 (ttp) REVERT: B 121 MET cc_start: 0.7462 (mmp) cc_final: 0.7060 (mpp) REVERT: B 146 PHE cc_start: 0.9398 (p90) cc_final: 0.9122 (p90) REVERT: B 183 LEU cc_start: 0.9494 (mp) cc_final: 0.9259 (mp) REVERT: B 223 GLU cc_start: 0.9243 (tp30) cc_final: 0.8757 (tp30) REVERT: B 254 TYR cc_start: 0.9108 (m-10) cc_final: 0.8867 (m-10) REVERT: B 321 HIS cc_start: 0.9108 (p-80) cc_final: 0.8495 (p-80) REVERT: B 365 PHE cc_start: 0.9107 (p90) cc_final: 0.8778 (p90) REVERT: B 381 ASN cc_start: 0.9502 (m110) cc_final: 0.9047 (t0) REVERT: B 422 ARG cc_start: 0.6386 (tpp80) cc_final: 0.5750 (mtp180) REVERT: B 464 MET cc_start: 0.7875 (mmp) cc_final: 0.7632 (mmt) REVERT: B 500 MET cc_start: 0.7589 (mtt) cc_final: 0.7194 (mtt) REVERT: B 502 LYS cc_start: 0.8692 (ptpt) cc_final: 0.8374 (ptmt) REVERT: B 557 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8651 (mmtp) REVERT: B 796 LEU cc_start: 0.9182 (pt) cc_final: 0.8920 (pt) REVERT: B 798 MET cc_start: 0.7973 (tmm) cc_final: 0.6507 (mmt) REVERT: B 916 PHE cc_start: 0.8111 (m-80) cc_final: 0.7755 (m-80) REVERT: B 930 GLU cc_start: 0.8790 (tp30) cc_final: 0.8544 (mp0) REVERT: B 931 LEU cc_start: 0.9057 (tp) cc_final: 0.8640 (tp) REVERT: B 1003 LYS cc_start: 0.7500 (tptp) cc_final: 0.6992 (tptp) REVERT: B 1007 TYR cc_start: 0.8715 (m-80) cc_final: 0.8146 (m-80) REVERT: B 1126 PHE cc_start: 0.9085 (m-10) cc_final: 0.8740 (m-10) REVERT: B 1152 TYR cc_start: 0.8213 (t80) cc_final: 0.7830 (t80) REVERT: B 1208 MET cc_start: 0.8553 (ppp) cc_final: 0.8158 (ppp) REVERT: B 1279 THR cc_start: 0.9240 (p) cc_final: 0.8949 (p) REVERT: B 1315 LYS cc_start: 0.9366 (mmpt) cc_final: 0.9028 (mmmt) REVERT: B 1330 TYR cc_start: 0.8895 (p90) cc_final: 0.8589 (p90) REVERT: B 1393 LYS cc_start: 0.9185 (tptp) cc_final: 0.8957 (tptp) REVERT: B 1436 ASP cc_start: 0.7500 (m-30) cc_final: 0.7042 (m-30) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1026 time to fit residues: 33.8861 Evaluate side-chains 184 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.427 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 154 optimal weight: 3.9990 chunk 455 optimal weight: 0.0030 chunk 108 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 345 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 425 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 overall best weight: 1.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 460 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN B 967 GLN B 994 GLN B1062 HIS B1118 HIS B1123 ASN B1143 HIS ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.135470 restraints weight = 96977.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.136960 restraints weight = 78987.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.137737 restraints weight = 66647.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.138700 restraints weight = 59661.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.138700 restraints weight = 51470.682| |-----------------------------------------------------------------------------| r_work (final): 0.4517 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.113252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.084265 restraints weight = 44739.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087415 restraints weight = 33536.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089883 restraints weight = 26603.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.091862 restraints weight = 21999.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.093450 restraints weight = 18755.079| |-----------------------------------------------------------------------------| r_work (final): 0.3819 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.051344 restraints weight = 319.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.051980 restraints weight = 117.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.052397 restraints weight = 59.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.052695 restraints weight = 33.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.052807 restraints weight = 22.069| |-----------------------------------------------------------------------------| r_work (final): 0.2744 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075139 restraints weight = 343.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075269 restraints weight = 48.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075449 restraints weight = 23.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075496 restraints weight = 6.654 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075496 restraints weight = 1.852 | |-----------------------------------------------------------------------------| r_work (final): 0.3076 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.042177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.038162 restraints weight = 255.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.039266 restraints weight = 133.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.039926 restraints weight = 92.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.040374 restraints weight = 69.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.040682 restraints weight = 55.777| |-----------------------------------------------------------------------------| r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45680 Z= 0.139 Angle : 0.775 18.372 62168 Z= 0.374 Chirality : 0.048 0.361 7198 Planarity : 0.005 0.070 7916 Dihedral : 5.918 27.928 6022 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.32 % Favored : 88.51 % Rotamer: Outliers : 0.16 % Allowed : 1.21 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.10), residues: 5620 helix: -1.46 (0.18), residues: 718 sheet: -1.64 (0.13), residues: 1582 loop : -3.15 (0.09), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1297 TYR 0.026 0.002 TYR D1216 PHE 0.021 0.002 PHE D 309 TRP 0.021 0.002 TRP B 741 HIS 0.008 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (45592) covalent geometry : angle 0.74874 / 0.37 (61950) SS BOND : bond 0.00459 / 0.27 ( 46) SS BOND : angle 1.08455 / 0.73 ( 92) hydrogen bonds : bond 0.05519 / 3.69 ( 384) hydrogen bonds : angle 6.18106 / 4.20 ( 1152) link_ALPHA1-6 : bond 0.00289 / 0.14 ( 2) link_ALPHA1-6 : angle 1.55028 / 0.89 ( 6) link_BETA1-4 : bond 0.00560 / 0.39 ( 10) link_BETA1-4 : angle 1.86580 / 1.18 ( 30) link_NAG-ASN : bond 0.00999 / 0.61 ( 30) link_NAG-ASN : angle 5.17139 / 3.18 ( 90) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.429 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: C 151 MET cc_start: 0.6338 (tpt) cc_final: 0.5334 (tpp) REVERT: C 183 LEU cc_start: 0.8408 (mt) cc_final: 0.8193 (mt) REVERT: C 305 LYS cc_start: 0.8786 (mppt) cc_final: 0.8230 (tppt) REVERT: C 359 PHE cc_start: 0.8623 (t80) cc_final: 0.8327 (t80) REVERT: C 450 LEU cc_start: 0.7987 (tp) cc_final: 0.7768 (tp) REVERT: C 456 LYS cc_start: 0.9482 (pttm) cc_final: 0.8867 (tptt) REVERT: C 460 HIS cc_start: 0.8487 (t-170) cc_final: 0.7965 (t-170) REVERT: C 607 MET cc_start: 0.3967 (mtt) cc_final: 0.3497 (mtt) REVERT: C 655 TYR cc_start: 0.3114 (p90) cc_final: 0.1160 (m-10) REVERT: C 673 MET cc_start: 0.3159 (mmp) cc_final: 0.2421 (mmm) REVERT: C 968 MET cc_start: 0.5368 (mmp) cc_final: 0.4916 (mmp) REVERT: C 985 TYR cc_start: 0.6583 (m-80) cc_final: 0.6027 (m-80) REVERT: C 1314 MET cc_start: -0.0653 (tmm) cc_final: -0.0985 (tmm) REVERT: C 1330 TYR cc_start: 0.9656 (p90) cc_final: 0.9204 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1177 time to fit residues: 16.9522 Evaluate side-chains 77 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.423 Evaluate side-chains 226 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.432 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: B 32 MET cc_start: 0.8130 (ttp) cc_final: 0.7631 (ttp) REVERT: B 121 MET cc_start: 0.7562 (mmp) cc_final: 0.7186 (mpp) REVERT: B 146 PHE cc_start: 0.9426 (p90) cc_final: 0.9165 (p90) REVERT: B 321 HIS cc_start: 0.9084 (p-80) cc_final: 0.8672 (p-80) REVERT: B 354 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7569 (tptt) REVERT: B 365 PHE cc_start: 0.9065 (p90) cc_final: 0.8735 (p90) REVERT: B 381 ASN cc_start: 0.9493 (m110) cc_final: 0.9012 (t0) REVERT: B 422 ARG cc_start: 0.6635 (tpp80) cc_final: 0.6112 (tpp-160) REVERT: B 441 HIS cc_start: 0.8405 (m-70) cc_final: 0.7905 (m-70) REVERT: B 460 HIS cc_start: 0.8908 (t-90) cc_final: 0.8611 (t-90) REVERT: B 496 TYR cc_start: 0.8421 (m-10) cc_final: 0.7967 (m-80) REVERT: B 500 MET cc_start: 0.7777 (mtt) cc_final: 0.7554 (mmt) REVERT: B 502 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8315 (ptmt) REVERT: B 557 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8820 (mptt) REVERT: B 586 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8373 (tpt-90) REVERT: B 672 ASP cc_start: 0.9246 (t0) cc_final: 0.8892 (t0) REVERT: B 796 LEU cc_start: 0.9292 (pt) cc_final: 0.8873 (pt) REVERT: B 798 MET cc_start: 0.8102 (tmm) cc_final: 0.6888 (mmt) REVERT: B 916 PHE cc_start: 0.8475 (m-80) cc_final: 0.8126 (m-80) REVERT: B 1003 LYS cc_start: 0.7670 (tptp) cc_final: 0.6982 (tptp) REVERT: B 1007 TYR cc_start: 0.8811 (m-80) cc_final: 0.8100 (m-80) REVERT: B 1110 LEU cc_start: 0.9118 (tp) cc_final: 0.8483 (tp) REVERT: B 1126 PHE cc_start: 0.9121 (m-10) cc_final: 0.8743 (m-10) REVERT: B 1152 TYR cc_start: 0.8171 (t80) cc_final: 0.7868 (t80) REVERT: B 1208 MET cc_start: 0.8475 (ppp) cc_final: 0.8179 (ppp) REVERT: B 1248 PHE cc_start: 0.8042 (t80) cc_final: 0.7623 (t80) REVERT: B 1279 THR cc_start: 0.9251 (p) cc_final: 0.8914 (p) REVERT: B 1314 MET cc_start: 0.8676 (mmp) cc_final: 0.8349 (mmm) REVERT: B 1315 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8990 (mmmt) REVERT: B 1330 TYR cc_start: 0.8923 (p90) cc_final: 0.8639 (p90) REVERT: B 1398 MET cc_start: 0.8006 (ptm) cc_final: 0.7404 (ppp) REVERT: B 1436 ASP cc_start: 0.7649 (m-30) cc_final: 0.7181 (m-30) outliers start: 4 outliers final: 2 residues processed: 225 average time/residue: 0.1013 time to fit residues: 32.8025 Evaluate side-chains 187 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.408 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 484 optimal weight: 9.9990 chunk 179 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 359 optimal weight: 1.9990 chunk 475 optimal weight: 0.1980 chunk 175 optimal weight: 8.9990 chunk 418 optimal weight: 2.9990 chunk 367 optimal weight: 0.0980 chunk 413 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 938 ASN B 983 ASN B 994 GLN B1118 HIS B1143 HIS ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 460 HIS C1015 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.155504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.137000 restraints weight = 97059.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.137986 restraints weight = 80056.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.138945 restraints weight = 67670.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.139663 restraints weight = 59487.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.140508 restraints weight = 53706.163| |-----------------------------------------------------------------------------| r_work (final): 0.4546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.087190 restraints weight = 44472.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.090258 restraints weight = 33853.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.092692 restraints weight = 27126.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.094649 restraints weight = 22497.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096157 restraints weight = 19240.845| |-----------------------------------------------------------------------------| r_work (final): 0.3865 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.053787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.051932 restraints weight = 326.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.052602 restraints weight = 99.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.052947 restraints weight = 43.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053216 restraints weight = 24.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.053355 restraints weight = 15.770| |-----------------------------------------------------------------------------| r_work (final): 0.2747 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075852 restraints weight = 312.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076103 restraints weight = 41.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076226 restraints weight = 13.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076247 restraints weight = 3.048 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076244 restraints weight = 0.720 | |-----------------------------------------------------------------------------| r_work (final): 0.3084 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.043102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.039131 restraints weight = 289.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.040389 restraints weight = 142.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.041184 restraints weight = 95.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.041586 restraints weight = 71.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.041879 restraints weight = 56.661| |-----------------------------------------------------------------------------| r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45680 Z= 0.124 Angle : 0.776 18.373 62168 Z= 0.368 Chirality : 0.048 0.365 7198 Planarity : 0.005 0.072 7916 Dihedral : 5.841 30.025 6022 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.10 % Favored : 88.68 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.10), residues: 5620 helix: -1.44 (0.18), residues: 732 sheet: -1.53 (0.13), residues: 1544 loop : -3.12 (0.09), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1297 TYR 0.030 0.001 TYR D1216 PHE 0.041 0.001 PHE D1049 TRP 0.022 0.002 TRP A 436 HIS 0.013 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (45592) covalent geometry : angle 0.74981 / 0.36 (61950) SS BOND : bond 0.00418 / 0.24 ( 46) SS BOND : angle 1.11824 / 0.77 ( 92) hydrogen bonds : bond 0.05338 / 3.59 ( 384) hydrogen bonds : angle 5.98639 / 4.13 ( 1152) link_ALPHA1-6 : bond 0.00369 / 0.19 ( 2) link_ALPHA1-6 : angle 1.40233 / 0.81 ( 6) link_BETA1-4 : bond 0.00540 / 0.37 ( 10) link_BETA1-4 : angle 1.85057 / 1.13 ( 30) link_NAG-ASN : bond 0.01022 / 0.63 ( 30) link_NAG-ASN : angle 5.15910 / 3.17 ( 90) ********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.413 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: A 305 LYS cc_start: 0.8767 (mppt) cc_final: 0.8216 (tppt) REVERT: A 359 PHE cc_start: 0.8704 (t80) cc_final: 0.8356 (t80) REVERT: A 450 LEU cc_start: 0.7868 (tp) cc_final: 0.7593 (tp) REVERT: A 456 LYS cc_start: 0.9514 (pttm) cc_final: 0.8907 (tptt) REVERT: A 460 HIS cc_start: 0.8643 (t-170) cc_final: 0.8114 (t-170) REVERT: A 607 MET cc_start: 0.4217 (mtt) cc_final: 0.3726 (mtt) REVERT: A 655 TYR cc_start: 0.2742 (p90) cc_final: 0.0913 (m-10) REVERT: A 673 MET cc_start: 0.2956 (mmp) cc_final: 0.2322 (mmm) REVERT: A 968 MET cc_start: 0.5293 (mmp) cc_final: 0.4845 (mmp) REVERT: A 985 TYR cc_start: 0.6412 (m-80) cc_final: 0.5859 (m-80) REVERT: A 1314 MET cc_start: -0.0323 (tmm) cc_final: -0.1357 (tmm) REVERT: A 1330 TYR cc_start: 0.9703 (p90) cc_final: 0.9434 (p90) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1113 time to fit residues: 16.2917 Evaluate side-chains 78 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.351 Evaluate side-chains 224 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.459 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: D 32 MET cc_start: 0.8079 (ttp) cc_final: 0.7854 (ttp) REVERT: D 121 MET cc_start: 0.7569 (mmp) cc_final: 0.7328 (mpp) REVERT: D 146 PHE cc_start: 0.9424 (p90) cc_final: 0.9126 (p90) REVERT: D 183 LEU cc_start: 0.9435 (mp) cc_final: 0.9203 (mp) REVERT: D 254 TYR cc_start: 0.9126 (m-10) cc_final: 0.8806 (m-80) REVERT: D 321 HIS cc_start: 0.8732 (p-80) cc_final: 0.8303 (p-80) REVERT: D 365 PHE cc_start: 0.9065 (p90) cc_final: 0.8734 (p90) REVERT: D 381 ASN cc_start: 0.9472 (m110) cc_final: 0.8984 (t0) REVERT: D 422 ARG cc_start: 0.6472 (tpp80) cc_final: 0.5990 (tpp-160) REVERT: D 441 HIS cc_start: 0.8485 (m-70) cc_final: 0.7941 (m-70) REVERT: D 460 HIS cc_start: 0.8896 (t-90) cc_final: 0.8597 (t-90) REVERT: D 502 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8390 (ptmt) REVERT: D 557 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8719 (mptt) REVERT: D 672 ASP cc_start: 0.9226 (t0) cc_final: 0.8913 (t0) REVERT: D 673 MET cc_start: 0.8687 (tpt) cc_final: 0.8341 (tpp) REVERT: D 796 LEU cc_start: 0.9253 (pt) cc_final: 0.8850 (pt) REVERT: D 798 MET cc_start: 0.8130 (tmm) cc_final: 0.6938 (mmt) REVERT: D 815 LEU cc_start: 0.8957 (mm) cc_final: 0.8726 (mt) REVERT: D 916 PHE cc_start: 0.8491 (m-80) cc_final: 0.8252 (m-80) REVERT: D 931 LEU cc_start: 0.9069 (tp) cc_final: 0.8780 (tp) REVERT: D 933 LEU cc_start: 0.8733 (mp) cc_final: 0.7984 (mp) REVERT: D 983 ASN cc_start: 0.8720 (m110) cc_final: 0.8359 (m110) REVERT: D 1003 LYS cc_start: 0.7610 (tptp) cc_final: 0.7000 (tptp) REVERT: D 1007 TYR cc_start: 0.8817 (m-80) cc_final: 0.8216 (m-80) REVERT: D 1110 LEU cc_start: 0.9107 (tp) cc_final: 0.8804 (tp) REVERT: D 1126 PHE cc_start: 0.9110 (m-10) cc_final: 0.8750 (m-10) REVERT: D 1152 TYR cc_start: 0.8219 (t80) cc_final: 0.7710 (t80) REVERT: D 1208 MET cc_start: 0.8571 (ppp) cc_final: 0.8291 (ppp) REVERT: D 1264 TYR cc_start: 0.7412 (t80) cc_final: 0.6964 (t80) REVERT: D 1279 THR cc_start: 0.9205 (p) cc_final: 0.8953 (p) REVERT: D 1315 LYS cc_start: 0.9343 (mmpt) cc_final: 0.9024 (mmmt) REVERT: D 1398 MET cc_start: 0.7921 (ptm) cc_final: 0.7225 (ppp) REVERT: D 1436 ASP cc_start: 0.7713 (m-30) cc_final: 0.7218 (m-30) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.1010 time to fit residues: 32.5723 Evaluate side-chains 184 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.394 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 198 optimal weight: 0.0050 chunk 418 optimal weight: 0.0070 chunk 78 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 359 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 429 optimal weight: 10.0000 chunk 112 optimal weight: 0.0770 chunk 269 optimal weight: 0.0470 chunk 329 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.6270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 460 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN D 938 ASN D 983 ASN D 994 GLN D1118 HIS D1325 GLN D1331 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.155513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.136987 restraints weight = 96781.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.138253 restraints weight = 79491.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.139142 restraints weight = 67067.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.140035 restraints weight = 59201.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.140559 restraints weight = 52774.585| |-----------------------------------------------------------------------------| r_work (final): 0.4508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.116312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.087669 restraints weight = 43415.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.090710 restraints weight = 33163.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.093122 restraints weight = 26639.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095085 restraints weight = 22190.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.096660 restraints weight = 19006.893| |-----------------------------------------------------------------------------| r_work (final): 0.3875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.054341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.052557 restraints weight = 665.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052886 restraints weight = 251.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.053162 restraints weight = 157.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053282 restraints weight = 114.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053282 restraints weight = 96.289| |-----------------------------------------------------------------------------| r_work (final): 0.2831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077889 restraints weight = 365.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077900 restraints weight = 11.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077888 restraints weight = 0.423 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077888 restraints weight = 0.148 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077888 restraints weight = 0.147 | |-----------------------------------------------------------------------------| r_work (final): 0.3147 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.042789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.038374 restraints weight = 306.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.039461 restraints weight = 158.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.040228 restraints weight = 113.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.040681 restraints weight = 88.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.040937 restraints weight = 78.536| |-----------------------------------------------------------------------------| r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 45680 Z= 0.124 Angle : 0.762 18.099 62168 Z= 0.362 Chirality : 0.048 0.360 7198 Planarity : 0.005 0.071 7916 Dihedral : 5.687 29.586 6022 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.96 % Favored : 88.90 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.10), residues: 5620 helix: -1.29 (0.18), residues: 732 sheet: -1.57 (0.13), residues: 1582 loop : -3.06 (0.10), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 895 TYR 0.029 0.001 TYR B1216 PHE 0.039 0.001 PHE D1049 TRP 0.024 0.002 TRP B 741 HIS 0.009 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (45592) covalent geometry : angle 0.73614 / 0.36 (61950) SS BOND : bond 0.00412 / 0.24 ( 46) SS BOND : angle 1.05560 / 0.69 ( 92) hydrogen bonds : bond 0.05190 / 3.49 ( 384) hydrogen bonds : angle 5.89338 / 4.07 ( 1152) link_ALPHA1-6 : bond 0.00020 / 0.01 ( 2) link_ALPHA1-6 : angle 1.24812 / 0.72 ( 6) link_BETA1-4 : bond 0.00494 / 0.29 ( 10) link_BETA1-4 : angle 1.83486 / 1.14 ( 30) link_NAG-ASN : bond 0.00997 / 0.63 ( 30) link_NAG-ASN : angle 5.03452 / 3.10 ( 90) =============================================================================== Job complete usr+sys time: 5477.17 seconds wall clock time: 97 minutes 22.77 seconds (5842.77 seconds total)