Starting phenix.real_space_refine on Sat Mar 7 13:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7l_12747/03_2026/7o7l_12747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7l_12747/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7l_12747/03_2026/7o7l_12747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7l_12747/03_2026/7o7l_12747.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7l_12747/03_2026/7o7l_12747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7l_12747/03_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44614 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11004 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 74, 'TRANS': 1335} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: C, D, H, I, J Time building chain proxies: 29.49, per 1000 atoms: 0.66 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: 3.47 Conformation dependent library (CDL) restraints added in 2.2 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: 0.75 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: 5.60 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 13390 1.34 - 1.48: 12514 1.48 - 1.63: 19404 1.63 - 1.78: 10 1.78 - 1.92: 274 Bond restraints: 45592 Sorted by residual: bond pdb=" CA SER B1372 " pdb=" CB SER B1372 " ideal model delta sigma weight residual 1.530 1.482 0.049 9.80e-03 1.04e+04 2.45e+01 bond pdb=" CA SER D1372 " pdb=" CB SER D1372 " ideal model delta sigma weight residual 1.530 1.482 0.049 9.80e-03 1.04e+04 2.45e+01 bond pdb=" C LYS C 271 " pdb=" O LYS C 271 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.10e-02 8.26e+03 1.79e+01 bond pdb=" C LYS A 271 " pdb=" O LYS A 271 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.10e-02 8.26e+03 1.79e+01 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.22e-02 6.72e+03 1.48e+01 ... (remaining 45587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 61206 4.05 - 8.10: 692 8.10 - 12.14: 34 12.14 - 16.19: 14 16.19 - 20.24: 4 Bond angle restraints: 61950 Sorted by residual: angle pdb=" N ALA D 391 " pdb=" CA ALA D 391 " pdb=" C ALA D 391 " ideal model delta sigma weight residual 114.12 98.01 16.11 1.39e+00 5.18e-01 1.34e+02 angle pdb=" N ALA B 391 " pdb=" CA ALA B 391 " pdb=" C ALA B 391 " ideal model delta sigma weight residual 114.12 98.01 16.11 1.39e+00 5.18e-01 1.34e+02 angle pdb=" N PRO A 845 " pdb=" CA PRO A 845 " pdb=" C PRO A 845 " ideal model delta sigma weight residual 111.26 93.43 17.83 1.63e+00 3.76e-01 1.20e+02 angle pdb=" N PRO C 845 " pdb=" CA PRO C 845 " pdb=" C PRO C 845 " ideal model delta sigma weight residual 111.26 93.43 17.83 1.63e+00 3.76e-01 1.20e+02 angle pdb=" N SER B 801 " pdb=" CA SER B 801 " pdb=" C SER B 801 " ideal model delta sigma weight residual 108.96 92.95 16.01 1.59e+00 3.96e-01 1.01e+02 ... (remaining 61945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 25528 21.46 - 42.92: 2204 42.92 - 64.38: 326 64.38 - 85.84: 92 85.84 - 107.30: 22 Dihedral angle restraints: 28172 sinusoidal: 11714 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 28169 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: 0.08 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: 2.830 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: 0.060 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 55.320 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 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 : 16.568 107.301 17426 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 covalent geometry : bond 0.00756 (45592) covalent geometry : angle 1.16060 (61950) SS BOND : bond 0.01768 ( 46) SS BOND : angle 3.21086 ( 92) hydrogen bonds : bond 0.26563 ( 384) hydrogen bonds : angle 10.43976 ( 1152) link_ALPHA1-6 : bond 0.00059 ( 2) link_ALPHA1-6 : angle 0.28836 ( 6) link_BETA1-4 : bond 0.00960 ( 10) link_BETA1-4 : angle 4.32164 ( 30) link_NAG-ASN : bond 0.19505 ( 30) link_NAG-ASN : angle 12.07287 ( 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 : 0.438 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: 0.1296 time to fit residues: 29.7848 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 : 0.382 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 : 0.425 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: 0.1201 time to fit residues: 52.7954 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 : 0.391 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: 0.0011 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 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=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... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS D 168 GLN D 182 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS D 644 ASN ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1179 ASN D1259 HIS Total number of N/Q/H flips: 9 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.153314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.135828 restraints weight = 100038.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.137119 restraints weight = 82642.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.138049 restraints weight = 67752.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.138926 restraints weight = 59169.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.139258 restraints weight = 53481.566| |-----------------------------------------------------------------------------| r_work (final): 0.4502 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084731 restraints weight = 47276.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087713 restraints weight = 35790.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.090146 restraints weight = 28493.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.092117 restraints weight = 23557.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.093705 restraints weight = 20054.465| |-----------------------------------------------------------------------------| r_work (final): 0.3810 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.053831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.051343 restraints weight = 382.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051971 restraints weight = 138.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052395 restraints weight = 79.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.052582 restraints weight = 54.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.052774 restraints weight = 44.617| |-----------------------------------------------------------------------------| r_work (final): 0.2756 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076454 restraints weight = 355.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077407 restraints weight = 139.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077909 restraints weight = 60.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078176 restraints weight = 30.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078306 restraints weight = 13.707| |-----------------------------------------------------------------------------| r_work (final): 0.3086 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.054507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.051653 restraints weight = 289.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.052321 restraints weight = 171.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.052726 restraints weight = 123.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.052957 restraints weight = 97.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.053084 restraints weight = 80.118| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45680 Z= 0.184 Angle : 1.058 56.073 62168 Z= 0.531 Chirality : 0.056 0.772 7198 Planarity : 0.006 0.079 7916 Dihedral : 9.757 69.988 6934 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.42 % Favored : 86.19 % Rotamer: Outliers : 0.36 % Allowed : 8.09 % Favored : 91.55 % 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: -2.89 (0.15), residues: 712 sheet: -2.71 (0.12), residues: 1520 loop : -3.79 (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 B 321 Details of bonding type rmsd covalent geometry : bond 0.00401 (45592) covalent geometry : angle 1.03218 (61950) SS BOND : bond 0.00720 ( 46) SS BOND : angle 1.71183 ( 92) hydrogen bonds : bond 0.07828 ( 384) hydrogen bonds : angle 7.71245 ( 1152) link_ALPHA1-6 : bond 0.01032 ( 2) link_ALPHA1-6 : angle 1.78005 ( 6) link_BETA1-4 : bond 0.01353 ( 10) link_BETA1-4 : angle 3.25923 ( 30) link_NAG-ASN : bond 0.01072 ( 30) link_NAG-ASN : angle 5.73643 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8432 Ramachandran restraints generated. 4216 Oldfield, 0 Emsley, 4216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8432 Ramachandran restraints generated. 4216 Oldfield, 0 Emsley, 4216 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 : 0.341 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: A 230 GLU cc_start: 0.7604 (mp0) cc_final: 0.7363 (mp0) REVERT: A 270 ARG cc_start: 0.1926 (mtp180) cc_final: 0.0263 (mmp80) REVERT: A 381 ASN cc_start: 0.9605 (t0) cc_final: 0.9357 (m-40) REVERT: A 385 PHE cc_start: 0.8781 (m-80) cc_final: 0.8350 (m-80) REVERT: A 460 HIS cc_start: 0.7233 (t-90) cc_final: 0.6639 (t-170) REVERT: A 607 MET cc_start: 0.3680 (mtt) cc_final: 0.3020 (mtt) REVERT: A 648 VAL cc_start: 0.6692 (OUTLIER) cc_final: 0.6350 (t) REVERT: A 916 PHE cc_start: 0.8097 (m-10) cc_final: 0.7751 (m-10) REVERT: A 968 MET cc_start: 0.5677 (mmp) cc_final: 0.5304 (mmm) REVERT: A 985 TYR cc_start: 0.5978 (m-10) cc_final: 0.5505 (m-10) REVERT: A 1311 GLU cc_start: 0.8617 (pm20) cc_final: 0.8281 (pm20) REVERT: A 1330 TYR cc_start: 0.9562 (p90) cc_final: 0.9146 (p90) outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.1104 time to fit residues: 21.5254 Evaluate side-chains 101 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.431 Evaluate side-chains 286 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.414 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: 0.7587 (mmp) cc_final: 0.7086 (mpp) REVERT: D 145 LYS cc_start: 0.8403 (mptt) cc_final: 0.8107 (mmtm) REVERT: D 194 LEU cc_start: 0.9138 (mt) cc_final: 0.8866 (mt) REVERT: D 197 GLU cc_start: 0.8610 (tm-30) cc_final: 0.7916 (pp20) REVERT: D 200 GLN cc_start: 0.8203 (tt0) cc_final: 0.7974 (tm-30) REVERT: D 333 VAL cc_start: 0.7660 (t) cc_final: 0.6843 (t) REVERT: D 381 ASN cc_start: 0.9463 (m110) cc_final: 0.9082 (t0) REVERT: D 415 MET cc_start: 0.7761 (mmp) cc_final: 0.7550 (mmp) REVERT: D 428 ARG cc_start: 0.9159 (ptp90) cc_final: 0.8549 (ttp80) REVERT: D 625 LYS cc_start: 0.8559 (pptt) cc_final: 0.8335 (ptmm) REVERT: D 734 TYR cc_start: 0.8079 (m-80) cc_final: 0.7860 (m-80) REVERT: D 735 PHE cc_start: 0.9308 (m-80) cc_final: 0.8990 (m-80) REVERT: D 840 GLU cc_start: 0.7415 (pm20) cc_final: 0.6556 (tp30) REVERT: D 916 PHE cc_start: 0.8768 (m-80) cc_final: 0.8456 (m-80) REVERT: D 977 MET cc_start: 0.6865 (mmp) cc_final: 0.6503 (mmp) REVERT: D 1121 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9136 (m) REVERT: D 1152 TYR cc_start: 0.7626 (t80) cc_final: 0.7128 (t80) REVERT: D 1248 PHE cc_start: 0.8091 (t80) cc_final: 0.7620 (t80) REVERT: D 1279 THR cc_start: 0.9256 (p) cc_final: 0.8965 (p) REVERT: D 1292 VAL cc_start: 0.9490 (t) cc_final: 0.9279 (t) REVERT: D 1312 TYR cc_start: 0.9153 (m-80) cc_final: 0.8865 (m-80) REVERT: D 1314 MET cc_start: 0.9345 (mmp) cc_final: 0.8998 (mmp) REVERT: D 1330 TYR cc_start: 0.9067 (p90) cc_final: 0.8644 (p90) REVERT: D 1331 ASN cc_start: 0.8571 (m110) cc_final: 0.7977 (m-40) REVERT: D 1436 ASP cc_start: 0.7250 (m-30) cc_final: 0.6917 (m-30) REVERT: D 1446 ILE cc_start: 0.8322 (pt) cc_final: 0.8073 (pt) outliers start: 4 outliers final: 2 residues processed: 286 average time/residue: 0.1129 time to fit residues: 44.1613 Evaluate side-chains 208 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.395 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: 0.0018 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: 0.0013 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 ------------------------------------------------------------------------------- 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: 0.0010 chunk 319 optimal weight: 40.0000 chunk 522 optimal weight: 30.0000 chunk 284 optimal weight: 0.0770 chunk 242 optimal weight: 7.9990 chunk 491 optimal weight: 20.0000 chunk 151 optimal weight: 0.0770 chunk 72 optimal weight: 40.0000 chunk 259 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 125 optimal weight: 0.1980 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 177 GLN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 460 HIS A 511 HIS A 646 HIS A1179 ASN A1187 GLN Total number of N/Q/H flips: 8 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 511 HIS ** D 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN ** D1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1242 GLN D1301 GLN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.153785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.135744 restraints weight = 101095.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.136926 restraints weight = 82151.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.137799 restraints weight = 69021.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.138658 restraints weight = 60898.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.139094 restraints weight = 55122.106| |-----------------------------------------------------------------------------| r_work (final): 0.4507 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.116108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.088113 restraints weight = 44538.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091267 restraints weight = 33061.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.093806 restraints weight = 25950.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.095870 restraints weight = 21171.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097546 restraints weight = 17792.487| |-----------------------------------------------------------------------------| r_work (final): 0.3840 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052715 restraints weight = 414.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.053297 restraints weight = 141.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053587 restraints weight = 73.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.054016 restraints weight = 53.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054208 restraints weight = 37.799| |-----------------------------------------------------------------------------| r_work (final): 0.2829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.073643 restraints weight = 413.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.074234 restraints weight = 123.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074530 restraints weight = 50.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074694 restraints weight = 22.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074709 restraints weight = 11.351| |-----------------------------------------------------------------------------| r_work (final): 0.2955 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.058202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.054004 restraints weight = 233.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.055020 restraints weight = 142.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.055702 restraints weight = 101.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.056138 restraints weight = 78.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.056439 restraints weight = 63.466| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45680 Z= 0.160 Angle : 0.887 14.293 62168 Z= 0.428 Chirality : 0.056 1.255 7198 Planarity : 0.006 0.075 7916 Dihedral : 8.631 57.317 6934 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.23 % Favored : 85.37 % Rotamer: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z 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: -4.61 (0.10), residues: 5620 helix: -2.49 (0.16), residues: 720 sheet: -2.48 (0.12), residues: 1536 loop : -3.65 (0.09), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 338 TYR 0.033 0.002 TYR D1007 PHE 0.033 0.002 PHE B1049 TRP 0.021 0.002 TRP A1183 HIS 0.016 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00347 (45592) covalent geometry : angle 0.86452 (61950) SS BOND : bond 0.00620 ( 46) SS BOND : angle 1.68270 ( 92) hydrogen bonds : bond 0.06820 ( 384) hydrogen bonds : angle 7.21610 ( 1152) link_ALPHA1-6 : bond 0.00300 ( 2) link_ALPHA1-6 : angle 1.61578 ( 6) link_BETA1-4 : bond 0.00469 ( 10) link_BETA1-4 : angle 2.73211 ( 30) link_NAG-ASN : bond 0.01251 ( 30) link_NAG-ASN : angle 4.85368 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8432 Ramachandran restraints generated. 4216 Oldfield, 0 Emsley, 4216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8432 Ramachandran restraints generated. 4216 Oldfield, 0 Emsley, 4216 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: 0 poor density : 127 time to evaluate : 0.450 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: A 151 MET cc_start: 0.6838 (tpp) cc_final: 0.6214 (tpp) REVERT: A 183 LEU cc_start: 0.8681 (mt) cc_final: 0.8358 (mt) REVERT: A 270 ARG cc_start: 0.0979 (mtp180) cc_final: -0.0001 (mmm160) REVERT: A 305 LYS cc_start: 0.8600 (mppt) cc_final: 0.7839 (mppt) REVERT: A 318 MET cc_start: 0.3520 (mtt) cc_final: 0.2966 (mtt) REVERT: A 385 PHE cc_start: 0.8117 (m-80) cc_final: 0.7794 (m-80) REVERT: A 456 LYS cc_start: 0.9298 (pttm) cc_final: 0.8542 (tptt) REVERT: A 460 HIS cc_start: 0.7527 (t70) cc_final: 0.7000 (t-170) REVERT: A 607 MET cc_start: 0.2841 (mtt) cc_final: 0.2141 (mtt) REVERT: A 655 TYR cc_start: 0.3430 (p90) cc_final: 0.0860 (m-10) REVERT: A 673 MET cc_start: 0.2341 (mmp) cc_final: 0.1794 (mmm) REVERT: A 916 PHE cc_start: 0.8325 (m-10) cc_final: 0.8060 (m-10) REVERT: A 985 TYR cc_start: 0.5823 (m-10) cc_final: 0.5199 (m-10) REVERT: A 1330 TYR cc_start: 0.9512 (p90) cc_final: 0.8979 (p90) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1165 time to fit residues: 20.6984 Evaluate side-chains 94 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.380 Evaluate side-chains 271 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.382 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: D 121 MET cc_start: 0.7543 (mmp) cc_final: 0.7158 (mpp) REVERT: D 132 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8363 (tm-30) REVERT: D 145 LYS cc_start: 0.8343 (mptt) cc_final: 0.8041 (mmtm) REVERT: D 183 LEU cc_start: 0.9443 (mt) cc_final: 0.9227 (mt) REVERT: D 184 GLU cc_start: 0.8728 (pp20) cc_final: 0.8340 (pm20) REVERT: D 194 LEU cc_start: 0.9246 (mt) cc_final: 0.9004 (mt) REVERT: D 197 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7882 (pp20) REVERT: D 221 VAL cc_start: 0.9359 (t) cc_final: 0.8917 (p) REVERT: D 254 TYR cc_start: 0.9256 (m-10) cc_final: 0.9000 (m-10) REVERT: D 321 HIS cc_start: 0.9081 (p-80) cc_final: 0.8805 (p-80) REVERT: D 333 VAL cc_start: 0.7716 (t) cc_final: 0.7055 (t) REVERT: D 381 ASN cc_start: 0.9522 (m110) cc_final: 0.9089 (t0) REVERT: D 422 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6636 (mtp180) REVERT: D 441 HIS cc_start: 0.8518 (m-70) cc_final: 0.8133 (m-70) REVERT: D 500 MET cc_start: 0.7615 (mtt) cc_final: 0.5937 (mtt) REVERT: D 557 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8915 (mmtp) REVERT: D 586 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8300 (tpt-90) REVERT: D 624 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8778 (tp30) REVERT: D 625 LYS cc_start: 0.8853 (pptt) cc_final: 0.8408 (ptmm) REVERT: D 673 MET cc_start: 0.8306 (tpt) cc_final: 0.8084 (tpt) REVERT: D 735 PHE cc_start: 0.9257 (m-80) cc_final: 0.8957 (m-80) REVERT: D 840 GLU cc_start: 0.7392 (pm20) cc_final: 0.6317 (tp30) REVERT: D 916 PHE cc_start: 0.8666 (m-80) cc_final: 0.8368 (m-80) REVERT: D 933 LEU cc_start: 0.9005 (mp) cc_final: 0.7201 (mp) REVERT: D 977 MET cc_start: 0.6902 (mmp) cc_final: 0.6565 (mmp) REVERT: D 1007 TYR cc_start: 0.8858 (m-80) cc_final: 0.8488 (m-80) REVERT: D 1104 TYR cc_start: 0.8323 (m-10) cc_final: 0.8043 (m-10) REVERT: D 1152 TYR cc_start: 0.7766 (t80) cc_final: 0.7316 (t80) REVERT: D 1164 LYS cc_start: 0.7477 (tptt) cc_final: 0.7257 (tptt) REVERT: D 1208 MET cc_start: 0.8477 (ppp) cc_final: 0.8265 (ppp) REVERT: D 1213 LEU cc_start: 0.9478 (tp) cc_final: 0.9235 (tp) REVERT: D 1248 PHE cc_start: 0.8055 (t80) cc_final: 0.7567 (t80) REVERT: D 1297 ARG cc_start: 0.8943 (tmm-80) cc_final: 0.8695 (tmm-80) REVERT: D 1298 LEU cc_start: 0.8672 (pt) cc_final: 0.8365 (tt) REVERT: D 1312 TYR cc_start: 0.9118 (m-80) cc_final: 0.8750 (m-80) REVERT: D 1314 MET cc_start: 0.9200 (mmp) cc_final: 0.8834 (mmp) REVERT: D 1393 LYS cc_start: 0.9178 (tptp) cc_final: 0.8941 (tptp) REVERT: D 1446 ILE cc_start: 0.8303 (pt) cc_final: 0.8049 (pt) outliers start: 2 outliers final: 1 residues processed: 271 average time/residue: 0.1136 time to fit residues: 42.6430 Evaluate side-chains 211 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.392 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 : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 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: 7.9990 chunk 120 optimal weight: 0.5980 chunk 180 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 335 optimal weight: 0.7980 chunk 411 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 369 optimal weight: 0.0970 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 917 ASN C1089 ASN ** C1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 GLN C1403 ASN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN B 938 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.153856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.135921 restraints weight = 99023.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.136951 restraints weight = 80679.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.137950 restraints weight = 70751.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.138540 restraints weight = 60432.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.138912 restraints weight = 55082.743| |-----------------------------------------------------------------------------| r_work (final): 0.4484 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.085416 restraints weight = 45043.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.088472 restraints weight = 33928.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.090923 restraints weight = 26977.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092918 restraints weight = 22251.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.094539 restraints weight = 18925.225| |-----------------------------------------------------------------------------| r_work (final): 0.3826 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.054988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.052400 restraints weight = 363.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.053452 restraints weight = 133.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053843 restraints weight = 55.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.054080 restraints weight = 31.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.054326 restraints weight = 24.250| |-----------------------------------------------------------------------------| r_work (final): 0.2786 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074858 restraints weight = 445.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075380 restraints weight = 118.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075630 restraints weight = 48.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075630 restraints weight = 26.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075630 restraints weight = 26.216| |-----------------------------------------------------------------------------| r_work (final): 0.3015 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.054488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.049984 restraints weight = 253.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.051132 restraints weight = 149.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.051683 restraints weight = 107.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.052123 restraints weight = 88.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.052452 restraints weight = 72.714| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45680 Z= 0.146 Angle : 0.822 12.605 62168 Z= 0.398 Chirality : 0.050 0.350 7198 Planarity : 0.006 0.071 7916 Dihedral : 8.006 58.662 6934 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.49 % Favored : 86.12 % Rotamer: Outliers : 0.16 % Allowed : 5.66 % Favored : 94.17 % 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: -4.45 (0.10), residues: 5620 helix: -2.32 (0.17), residues: 712 sheet: -2.36 (0.13), residues: 1516 loop : -3.56 (0.09), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 853 TYR 0.028 0.002 TYR D1216 PHE 0.025 0.002 PHE D1049 TRP 0.016 0.002 TRP A1183 HIS 0.015 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00314 (45592) covalent geometry : angle 0.80448 (61950) SS BOND : bond 0.00571 ( 46) SS BOND : angle 1.57036 ( 92) hydrogen bonds : bond 0.06194 ( 384) hydrogen bonds : angle 6.87092 ( 1152) link_ALPHA1-6 : bond 0.00410 ( 2) link_ALPHA1-6 : angle 1.54081 ( 6) link_BETA1-4 : bond 0.00807 ( 10) link_BETA1-4 : angle 2.63703 ( 30) link_NAG-ASN : bond 0.00984 ( 30) link_NAG-ASN : angle 4.09839 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.479 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: C 151 MET cc_start: 0.6883 (tpp) cc_final: 0.6434 (tpp) REVERT: C 305 LYS cc_start: 0.8702 (mppt) cc_final: 0.8145 (mppt) REVERT: C 318 MET cc_start: 0.4486 (mtt) cc_final: 0.3981 (mtt) REVERT: C 385 PHE cc_start: 0.8898 (m-80) cc_final: 0.8564 (m-80) REVERT: C 409 ILE cc_start: 0.8188 (pt) cc_final: 0.7930 (tt) REVERT: C 456 LYS cc_start: 0.9369 (pttm) cc_final: 0.8625 (tptt) REVERT: C 460 HIS cc_start: 0.7885 (t70) cc_final: 0.6920 (t-170) REVERT: C 607 MET cc_start: 0.4448 (mtt) cc_final: 0.3884 (mtt) REVERT: C 655 TYR cc_start: 0.3527 (p90) cc_final: 0.1178 (m-10) REVERT: C 673 MET cc_start: 0.2480 (mmp) cc_final: 0.1874 (mmm) REVERT: C 986 VAL cc_start: 0.6362 (m) cc_final: 0.6077 (m) REVERT: C 987 LEU cc_start: 0.8305 (tt) cc_final: 0.8066 (mt) REVERT: C 1330 TYR cc_start: 0.9612 (p90) cc_final: 0.9248 (p90) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.1196 time to fit residues: 20.7015 Evaluate side-chains 90 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.305 Evaluate side-chains 258 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 0.366 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: B 121 MET cc_start: 0.7619 (mmp) cc_final: 0.7169 (mpp) REVERT: B 151 MET cc_start: 0.8686 (tpp) cc_final: 0.8450 (tpp) REVERT: B 197 GLU cc_start: 0.8655 (tm-30) cc_final: 0.7951 (pp20) REVERT: B 221 VAL cc_start: 0.9417 (t) cc_final: 0.8928 (p) REVERT: B 223 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8464 (mm-30) REVERT: B 321 HIS cc_start: 0.9094 (p-80) cc_final: 0.8636 (p-80) REVERT: B 365 PHE cc_start: 0.8899 (p90) cc_final: 0.8640 (p90) REVERT: B 381 ASN cc_start: 0.9543 (m110) cc_final: 0.9132 (t0) REVERT: B 385 PHE cc_start: 0.9039 (m-80) cc_final: 0.8614 (m-80) REVERT: B 464 MET cc_start: 0.8275 (mmp) cc_final: 0.8054 (mmt) REVERT: B 500 MET cc_start: 0.7681 (mtt) cc_final: 0.6976 (mtt) REVERT: B 557 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8858 (mmtp) REVERT: B 586 ARG cc_start: 0.8881 (ttt180) cc_final: 0.8316 (tpt-90) REVERT: B 625 LYS cc_start: 0.8850 (pptt) cc_final: 0.8494 (ptmm) REVERT: B 735 PHE cc_start: 0.9277 (m-80) cc_final: 0.8993 (m-80) REVERT: B 916 PHE cc_start: 0.8593 (m-80) cc_final: 0.8385 (m-80) REVERT: B 933 LEU cc_start: 0.8952 (mp) cc_final: 0.7341 (mp) REVERT: B 938 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7247 (t0) REVERT: B 977 MET cc_start: 0.6954 (mmp) cc_final: 0.6629 (mmp) REVERT: B 1003 LYS cc_start: 0.7756 (tptp) cc_final: 0.7346 (tptp) REVERT: B 1007 TYR cc_start: 0.8767 (m-80) cc_final: 0.8262 (m-80) REVERT: B 1152 TYR cc_start: 0.8010 (t80) cc_final: 0.7600 (t80) REVERT: B 1208 MET cc_start: 0.8584 (ppp) cc_final: 0.7952 (ppp) REVERT: B 1209 THR cc_start: 0.8860 (m) cc_final: 0.8326 (m) REVERT: B 1213 LEU cc_start: 0.9478 (tp) cc_final: 0.9196 (tp) REVERT: B 1248 PHE cc_start: 0.8155 (t80) cc_final: 0.7618 (t80) REVERT: B 1264 TYR cc_start: 0.7894 (t80) cc_final: 0.7606 (t80) REVERT: B 1279 THR cc_start: 0.9269 (p) cc_final: 0.8686 (p) REVERT: B 1281 GLN cc_start: 0.8410 (pm20) cc_final: 0.7439 (pm20) REVERT: B 1297 ARG cc_start: 0.8975 (tmm-80) cc_final: 0.8751 (tmm-80) REVERT: B 1298 LEU cc_start: 0.8824 (pt) cc_final: 0.8456 (tt) REVERT: B 1312 TYR cc_start: 0.9024 (m-80) cc_final: 0.8675 (m-80) REVERT: B 1314 MET cc_start: 0.9115 (mmp) cc_final: 0.8499 (mmp) REVERT: B 1315 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8823 (mmtm) REVERT: B 1331 ASN cc_start: 0.8849 (m-40) cc_final: 0.8636 (m-40) REVERT: B 1436 ASP cc_start: 0.7523 (m-30) cc_final: 0.6994 (m-30) outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 0.1157 time to fit residues: 41.3877 Evaluate side-chains 206 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.402 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 3 optimal weight: 5.9990 chunk 447 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 535 optimal weight: 0.0020 chunk 90 optimal weight: 9.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN A1301 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS B 938 ASN ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN B1171 ASN B1220 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1425 GLN ** B1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.150456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.131694 restraints weight = 98064.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.133008 restraints weight = 78742.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.133782 restraints weight = 66049.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.134646 restraints weight = 58583.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.135379 restraints weight = 53087.407| |-----------------------------------------------------------------------------| r_work (final): 0.4440 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078768 restraints weight = 47703.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.081550 restraints weight = 36373.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083714 restraints weight = 29226.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.085444 restraints weight = 24361.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.086840 restraints weight = 20915.362| |-----------------------------------------------------------------------------| r_work (final): 0.3698 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.049930 restraints weight = 466.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.050657 restraints weight = 139.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051084 restraints weight = 61.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051271 restraints weight = 33.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.051453 restraints weight = 23.807| |-----------------------------------------------------------------------------| r_work (final): 0.2750 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077160 restraints weight = 547.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077583 restraints weight = 140.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077888 restraints weight = 68.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078021 restraints weight = 41.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078162 restraints weight = 25.402| |-----------------------------------------------------------------------------| r_work (final): 0.3082 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.048311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.043007 restraints weight = 268.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.044427 restraints weight = 144.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.045227 restraints weight = 100.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.045762 restraints weight = 77.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.046123 restraints weight = 62.442| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45680 Z= 0.186 Angle : 0.825 14.688 62168 Z= 0.405 Chirality : 0.050 0.318 7198 Planarity : 0.006 0.086 7916 Dihedral : 7.637 59.976 6934 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 1.57 % Allowed : 16.12 % Favored : 82.31 % Rotamer: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % 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: -4.80 (0.09), residues: 5620 helix: -2.62 (0.16), residues: 700 sheet: -2.67 (0.12), residues: 1596 loop : -3.75 (0.09), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 270 TYR 0.036 0.002 TYR A 985 PHE 0.025 0.002 PHE D 808 TRP 0.014 0.002 TRP B 858 HIS 0.012 0.002 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00398 (45592) covalent geometry : angle 0.81197 (61950) SS BOND : bond 0.00654 ( 46) SS BOND : angle 1.40682 ( 92) hydrogen bonds : bond 0.06009 ( 384) hydrogen bonds : angle 6.96089 ( 1152) link_ALPHA1-6 : bond 0.00260 ( 2) link_ALPHA1-6 : angle 1.55705 ( 6) link_BETA1-4 : bond 0.00644 ( 10) link_BETA1-4 : angle 2.38771 ( 30) link_NAG-ASN : bond 0.00875 ( 30) link_NAG-ASN : angle 3.48913 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 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 : 0.413 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6040 (tpp) cc_final: 0.5540 (tpp) REVERT: A 183 LEU cc_start: 0.8831 (mt) cc_final: 0.8538 (mt) REVERT: A 230 GLU cc_start: 0.7314 (mp0) cc_final: 0.7066 (mp0) REVERT: A 385 PHE cc_start: 0.8300 (m-80) cc_final: 0.7949 (m-80) REVERT: A 456 LYS cc_start: 0.9512 (pttm) cc_final: 0.8741 (tptt) REVERT: A 460 HIS cc_start: 0.7554 (t70) cc_final: 0.7080 (t-90) REVERT: A 607 MET cc_start: 0.3192 (mtt) cc_final: 0.2457 (mtt) REVERT: A 655 TYR cc_start: 0.3375 (p90) cc_final: 0.1184 (m-10) REVERT: A 673 MET cc_start: 0.2591 (mmp) cc_final: 0.1591 (mmm) REVERT: A 985 TYR cc_start: 0.6520 (m-10) cc_final: 0.5889 (m-80) REVERT: A 986 VAL cc_start: 0.6677 (m) cc_final: 0.6377 (m) REVERT: A 987 LEU cc_start: 0.8300 (tt) cc_final: 0.8048 (mt) REVERT: A 1330 TYR cc_start: 0.9621 (p90) cc_final: 0.9194 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1177 time to fit residues: 19.0409 Evaluate side-chains 87 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.349 Evaluate side-chains 242 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.411 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: B 121 MET cc_start: 0.7963 (mmp) cc_final: 0.7592 (mpp) REVERT: B 132 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 151 MET cc_start: 0.8632 (tpp) cc_final: 0.8322 (tpp) REVERT: B 197 GLU cc_start: 0.8694 (tm-30) cc_final: 0.7980 (pp20) REVERT: B 221 VAL cc_start: 0.9466 (t) cc_final: 0.9001 (p) REVERT: B 254 TYR cc_start: 0.9238 (m-10) cc_final: 0.8962 (m-10) REVERT: B 321 HIS cc_start: 0.9131 (p-80) cc_final: 0.8545 (p-80) REVERT: B 373 ASP cc_start: 0.8242 (t0) cc_final: 0.8025 (t70) REVERT: B 381 ASN cc_start: 0.9567 (m110) cc_final: 0.9207 (t0) REVERT: B 384 ILE cc_start: 0.9532 (pt) cc_final: 0.9270 (tp) REVERT: B 385 PHE cc_start: 0.9049 (m-80) cc_final: 0.8697 (m-80) REVERT: B 464 MET cc_start: 0.8531 (mmp) cc_final: 0.8321 (mmt) REVERT: B 557 LYS cc_start: 0.9349 (mtpt) cc_final: 0.9089 (mptt) REVERT: B 569 ASP cc_start: 0.9189 (t0) cc_final: 0.8925 (t0) REVERT: B 570 LEU cc_start: 0.8909 (pp) cc_final: 0.8657 (pp) REVERT: B 735 PHE cc_start: 0.9358 (m-80) cc_final: 0.9024 (m-80) REVERT: B 916 PHE cc_start: 0.8956 (m-80) cc_final: 0.8734 (m-80) REVERT: B 933 LEU cc_start: 0.9047 (mp) cc_final: 0.8403 (mp) REVERT: B 1003 LYS cc_start: 0.7975 (tptp) cc_final: 0.7311 (tptp) REVERT: B 1007 TYR cc_start: 0.8930 (m-80) cc_final: 0.8300 (m-80) REVERT: B 1152 TYR cc_start: 0.8047 (t80) cc_final: 0.7659 (t80) REVERT: B 1208 MET cc_start: 0.8933 (ppp) cc_final: 0.8490 (ppp) REVERT: B 1216 TYR cc_start: 0.8474 (m-80) cc_final: 0.8203 (m-80) REVERT: B 1248 PHE cc_start: 0.8426 (t80) cc_final: 0.7976 (t80) REVERT: B 1279 THR cc_start: 0.9326 (p) cc_final: 0.8772 (p) REVERT: B 1293 ASP cc_start: 0.9134 (m-30) cc_final: 0.8879 (m-30) REVERT: B 1314 MET cc_start: 0.9102 (mmp) cc_final: 0.8398 (mmp) REVERT: B 1315 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8902 (mmtm) REVERT: B 1328 LEU cc_start: 0.9059 (tt) cc_final: 0.8720 (tt) REVERT: B 1330 TYR cc_start: 0.9294 (p90) cc_final: 0.9071 (p90) REVERT: B 1331 ASN cc_start: 0.9060 (m-40) cc_final: 0.8628 (m-40) outliers start: 1 outliers final: 1 residues processed: 242 average time/residue: 0.1178 time to fit residues: 39.3715 Evaluate side-chains 199 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.347 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: 0.0011 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 182 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 280 optimal weight: 0.0030 chunk 341 optimal weight: 0.5980 chunk 522 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 108 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 chunk 408 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 ASN ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1118 HIS D1123 ASN D1179 ASN ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.153094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.134633 restraints weight = 97762.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.135754 restraints weight = 80463.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.136648 restraints weight = 67792.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.137501 restraints weight = 59343.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.137709 restraints weight = 53105.938| |-----------------------------------------------------------------------------| r_work (final): 0.4494 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.112198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083338 restraints weight = 44587.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.086557 restraints weight = 33175.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.089118 restraints weight = 26160.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.091161 restraints weight = 21464.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.092819 restraints weight = 18170.069| |-----------------------------------------------------------------------------| r_work (final): 0.3812 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.052999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.050776 restraints weight = 386.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051292 restraints weight = 140.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051592 restraints weight = 86.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051948 restraints weight = 59.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.052227 restraints weight = 40.033| |-----------------------------------------------------------------------------| r_work (final): 0.2759 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075202 restraints weight = 523.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075861 restraints weight = 158.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076004 restraints weight = 56.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076177 restraints weight = 31.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076176 restraints weight = 11.664| |-----------------------------------------------------------------------------| r_work (final): 0.3061 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.045929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.040386 restraints weight = 238.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.041613 restraints weight = 151.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.042343 restraints weight = 112.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.042857 restraints weight = 90.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.043278 restraints weight = 75.521| |-----------------------------------------------------------------------------| r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45680 Z= 0.132 Angle : 0.768 17.337 62168 Z= 0.369 Chirality : 0.049 0.345 7198 Planarity : 0.006 0.072 7916 Dihedral : 7.302 59.651 6934 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.89 % Allowed : 15.23 % Favored : 83.88 % Rotamer: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % 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: -4.66 (0.09), residues: 5620 helix: -2.63 (0.16), residues: 728 sheet: -2.56 (0.12), residues: 1572 loop : -3.63 (0.09), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1297 TYR 0.030 0.002 TYR D1216 PHE 0.022 0.002 PHE B 524 TRP 0.048 0.002 TRP B 741 HIS 0.011 0.001 HIS B1182 Details of bonding type rmsd covalent geometry : bond 0.00295 (45592) covalent geometry : angle 0.75646 (61950) SS BOND : bond 0.00549 ( 46) SS BOND : angle 1.35490 ( 92) hydrogen bonds : bond 0.05524 ( 384) hydrogen bonds : angle 6.58433 ( 1152) link_ALPHA1-6 : bond 0.00248 ( 2) link_ALPHA1-6 : angle 1.50565 ( 6) link_BETA1-4 : bond 0.00694 ( 10) link_BETA1-4 : angle 2.31315 ( 30) link_NAG-ASN : bond 0.00690 ( 30) link_NAG-ASN : angle 3.13882 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 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: 0.6720 (tpp) cc_final: 0.6358 (tpp) REVERT: A 183 LEU cc_start: 0.8376 (mt) cc_final: 0.8125 (mt) REVERT: A 385 PHE cc_start: 0.8854 (m-80) cc_final: 0.8623 (m-80) REVERT: A 456 LYS cc_start: 0.9477 (pttm) cc_final: 0.8751 (tptt) REVERT: A 460 HIS cc_start: 0.7877 (t70) cc_final: 0.7066 (t-90) REVERT: A 607 MET cc_start: 0.4247 (mtt) cc_final: 0.3702 (mtt) REVERT: A 655 TYR cc_start: 0.3381 (p90) cc_final: 0.1382 (m-10) REVERT: A 673 MET cc_start: 0.3061 (mmp) cc_final: 0.1805 (mmm) REVERT: A 968 MET cc_start: 0.6408 (mmp) cc_final: 0.5924 (mmp) REVERT: A 1330 TYR cc_start: 0.9664 (p90) cc_final: 0.9326 (p90) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1101 time to fit residues: 17.6079 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 : 0.399 Evaluate side-chains 244 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.397 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: D 50 LEU cc_start: 0.8989 (mt) cc_final: 0.8460 (mp) REVERT: D 101 MET cc_start: 0.3890 (ptm) cc_final: 0.3462 (ptm) REVERT: D 121 MET cc_start: 0.7720 (mmp) cc_final: 0.7326 (mpp) REVERT: D 151 MET cc_start: 0.8629 (tpp) cc_final: 0.8334 (tpp) REVERT: D 188 LYS cc_start: 0.9539 (tmtt) cc_final: 0.9222 (tptp) REVERT: D 189 GLN cc_start: 0.9549 (pm20) cc_final: 0.9036 (tt0) REVERT: D 221 VAL cc_start: 0.9492 (t) cc_final: 0.8881 (p) REVERT: D 237 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7873 (mmmt) REVERT: D 254 TYR cc_start: 0.9230 (m-10) cc_final: 0.8955 (m-10) REVERT: D 321 HIS cc_start: 0.9145 (p-80) cc_final: 0.8594 (p-80) REVERT: D 365 PHE cc_start: 0.9084 (p90) cc_final: 0.8769 (p90) REVERT: D 373 ASP cc_start: 0.8224 (t0) cc_final: 0.7983 (t70) REVERT: D 381 ASN cc_start: 0.9560 (m110) cc_final: 0.9154 (t0) REVERT: D 384 ILE cc_start: 0.9509 (pt) cc_final: 0.9240 (tp) REVERT: D 385 PHE cc_start: 0.8956 (m-80) cc_final: 0.8565 (m-80) REVERT: D 422 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6973 (tpp-160) REVERT: D 441 HIS cc_start: 0.8644 (m170) cc_final: 0.8282 (m-70) REVERT: D 557 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8892 (mptt) REVERT: D 625 LYS cc_start: 0.9098 (pptt) cc_final: 0.8879 (ptmm) REVERT: D 672 ASP cc_start: 0.9158 (t0) cc_final: 0.8867 (t0) REVERT: D 735 PHE cc_start: 0.9305 (m-80) cc_final: 0.9093 (m-10) REVERT: D 977 MET cc_start: 0.7205 (mmp) cc_final: 0.6924 (mmp) REVERT: D 1003 LYS cc_start: 0.7883 (tptp) cc_final: 0.7263 (tptp) REVERT: D 1007 TYR cc_start: 0.8879 (m-80) cc_final: 0.8317 (m-80) REVERT: D 1152 TYR cc_start: 0.7961 (t80) cc_final: 0.7625 (t80) REVERT: D 1164 LYS cc_start: 0.7708 (tptt) cc_final: 0.7465 (tptt) REVERT: D 1208 MET cc_start: 0.8751 (ppp) cc_final: 0.8075 (ppp) REVERT: D 1209 THR cc_start: 0.8736 (m) cc_final: 0.8297 (m) REVERT: D 1248 PHE cc_start: 0.8081 (t80) cc_final: 0.7588 (t80) REVERT: D 1264 TYR cc_start: 0.7760 (t80) cc_final: 0.7504 (t80) REVERT: D 1279 THR cc_start: 0.9383 (p) cc_final: 0.9057 (p) REVERT: D 1281 GLN cc_start: 0.8612 (pm20) cc_final: 0.7856 (pm20) REVERT: D 1314 MET cc_start: 0.9092 (mmp) cc_final: 0.8585 (mmp) REVERT: D 1315 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8865 (mmtm) REVERT: D 1398 MET cc_start: 0.8047 (tmm) cc_final: 0.7842 (tpp) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 0.1119 time to fit residues: 38.0919 Evaluate side-chains 203 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.385 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 : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 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: 7.9990 chunk 40 optimal weight: 0.0470 chunk 345 optimal weight: 10.0000 chunk 427 optimal weight: 0.8980 chunk 189 optimal weight: 0.0060 chunk 204 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 494 optimal weight: 9.9990 chunk 420 optimal weight: 0.0370 chunk 256 optimal weight: 9.9990 overall best weight: 1.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 ASN D 994 GLN ** D1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1118 HIS D1123 ASN D1143 HIS D1296 ASN ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.151783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.133115 restraints weight = 97608.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.134343 restraints weight = 79836.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.134343 restraints weight = 67268.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.134343 restraints weight = 67264.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.134343 restraints weight = 67264.513| |-----------------------------------------------------------------------------| r_work (final): 0.4405 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081102 restraints weight = 46721.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.084035 restraints weight = 35272.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086333 restraints weight = 28164.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.088231 restraints weight = 23416.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.089735 restraints weight = 20013.369| |-----------------------------------------------------------------------------| r_work (final): 0.3758 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.052759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050770 restraints weight = 395.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051468 restraints weight = 128.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051775 restraints weight = 60.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.052114 restraints weight = 37.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052236 restraints weight = 24.023| |-----------------------------------------------------------------------------| r_work (final): 0.2752 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075190 restraints weight = 526.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075318 restraints weight = 61.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075378 restraints weight = 22.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075409 restraints weight = 12.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075409 restraints weight = 8.520 | |-----------------------------------------------------------------------------| r_work (final): 0.3088 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.042607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.037103 restraints weight = 214.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.038142 restraints weight = 139.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.038868 restraints weight = 106.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.039357 restraints weight = 86.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.039985 restraints weight = 73.349| |-----------------------------------------------------------------------------| r_work (final): 0.2301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.5578 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= 0.135 Angle : 0.757 15.742 62168 Z= 0.365 Chirality : 0.048 0.335 7198 Planarity : 0.006 0.068 7916 Dihedral : 7.237 59.834 6934 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 1.25 % Allowed : 15.73 % Favored : 83.02 % Rotamer: Outliers : 0.12 % Allowed : 1.46 % Favored : 98.42 % 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: -4.66 (0.09), residues: 5620 helix: -2.59 (0.16), residues: 740 sheet: -2.59 (0.12), residues: 1582 loop : -3.63 (0.09), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 147 TYR 0.026 0.002 TYR B1216 PHE 0.024 0.002 PHE D1044 TRP 0.020 0.002 TRP D 741 HIS 0.008 0.001 HIS B1182 Details of bonding type rmsd covalent geometry : bond 0.00296 (45592) covalent geometry : angle 0.73945 (61950) SS BOND : bond 0.00523 ( 46) SS BOND : angle 1.34224 ( 92) hydrogen bonds : bond 0.05479 ( 384) hydrogen bonds : angle 6.52420 ( 1152) link_ALPHA1-6 : bond 0.00088 ( 2) link_ALPHA1-6 : angle 1.44086 ( 6) link_BETA1-4 : bond 0.00777 ( 10) link_BETA1-4 : angle 2.34176 ( 30) link_NAG-ASN : bond 0.00647 ( 30) link_NAG-ASN : angle 3.93218 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 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 : 0.419 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: A 151 MET cc_start: 0.6488 (tpp) cc_final: 0.6175 (tpp) REVERT: A 183 LEU cc_start: 0.8645 (mt) cc_final: 0.8312 (mt) REVERT: A 385 PHE cc_start: 0.8299 (m-80) cc_final: 0.7995 (m-80) REVERT: A 456 LYS cc_start: 0.9543 (pttm) cc_final: 0.8836 (tptt) REVERT: A 460 HIS cc_start: 0.7587 (t70) cc_final: 0.7262 (t70) REVERT: A 607 MET cc_start: 0.3348 (mtt) cc_final: 0.2756 (mtt) REVERT: A 655 TYR cc_start: 0.3362 (p90) cc_final: 0.1475 (m-10) REVERT: A 673 MET cc_start: 0.3158 (mmp) cc_final: 0.2087 (mmm) REVERT: A 1330 TYR cc_start: 0.9640 (p90) cc_final: 0.9216 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1144 time to fit residues: 16.6186 Evaluate side-chains 80 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.270 Evaluate side-chains 236 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.407 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: D 50 LEU cc_start: 0.8970 (mt) cc_final: 0.8586 (mt) REVERT: D 101 MET cc_start: 0.3520 (ptm) cc_final: 0.3252 (ptm) REVERT: D 121 MET cc_start: 0.7754 (mmp) cc_final: 0.7403 (mpp) REVERT: D 132 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 151 MET cc_start: 0.8589 (tpp) cc_final: 0.8269 (tpp) REVERT: D 221 VAL cc_start: 0.9497 (t) cc_final: 0.8858 (p) REVERT: D 254 TYR cc_start: 0.9247 (m-10) cc_final: 0.9007 (m-10) REVERT: D 321 HIS cc_start: 0.9102 (p-80) cc_final: 0.8534 (p-80) REVERT: D 353 VAL cc_start: 0.8945 (t) cc_final: 0.8401 (t) REVERT: D 373 ASP cc_start: 0.8135 (t0) cc_final: 0.7898 (t70) REVERT: D 381 ASN cc_start: 0.9574 (m110) cc_final: 0.9213 (t0) REVERT: D 384 ILE cc_start: 0.9501 (pt) cc_final: 0.9238 (tp) REVERT: D 385 PHE cc_start: 0.8991 (m-80) cc_final: 0.8617 (m-80) REVERT: D 500 MET cc_start: 0.7835 (mtt) cc_final: 0.7331 (mtt) REVERT: D 557 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8968 (mptt) REVERT: D 672 ASP cc_start: 0.9275 (t0) cc_final: 0.8971 (t0) REVERT: D 735 PHE cc_start: 0.9355 (m-80) cc_final: 0.9110 (m-10) REVERT: D 741 TRP cc_start: 0.7990 (t-100) cc_final: 0.7472 (t-100) REVERT: D 1003 LYS cc_start: 0.8122 (tptp) cc_final: 0.7404 (tptp) REVERT: D 1007 TYR cc_start: 0.8908 (m-80) cc_final: 0.8388 (m-80) REVERT: D 1110 LEU cc_start: 0.9187 (tp) cc_final: 0.8677 (tp) REVERT: D 1152 TYR cc_start: 0.7962 (t80) cc_final: 0.7493 (t80) REVERT: D 1208 MET cc_start: 0.8628 (ppp) cc_final: 0.8185 (ppp) REVERT: D 1209 THR cc_start: 0.8720 (m) cc_final: 0.8422 (m) REVERT: D 1248 PHE cc_start: 0.8212 (t80) cc_final: 0.7774 (t80) REVERT: D 1264 TYR cc_start: 0.7649 (t80) cc_final: 0.7449 (t80) REVERT: D 1314 MET cc_start: 0.8988 (mmp) cc_final: 0.8654 (mmm) REVERT: D 1315 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8718 (mmmm) REVERT: D 1398 MET cc_start: 0.8050 (tmm) cc_final: 0.7846 (tpp) outliers start: 3 outliers final: 2 residues processed: 235 average time/residue: 0.1113 time to fit residues: 36.6243 Evaluate side-chains 190 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.395 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: 0.0021 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 26 optimal weight: 0.0070 chunk 288 optimal weight: 7.9990 chunk 70 optimal weight: 0.0270 chunk 7 optimal weight: 0.0270 chunk 410 optimal weight: 0.0870 chunk 231 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 chunk 528 optimal weight: 0.3980 chunk 162 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 535 optimal weight: 0.0970 overall best weight: 0.0490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1281 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS D1118 HIS D1123 ASN ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.153746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.135135 restraints weight = 96152.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.136459 restraints weight = 78906.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.137152 restraints weight = 67120.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.137970 restraints weight = 59507.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.137970 restraints weight = 53278.959| |-----------------------------------------------------------------------------| r_work (final): 0.4491 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.113835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.084620 restraints weight = 46315.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.087748 restraints weight = 35054.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.090230 restraints weight = 28047.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.092200 restraints weight = 23286.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.093787 restraints weight = 19906.146| |-----------------------------------------------------------------------------| r_work (final): 0.3821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.053340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.050891 restraints weight = 377.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.051430 restraints weight = 138.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051735 restraints weight = 84.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.052180 restraints weight = 60.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052443 restraints weight = 36.190| |-----------------------------------------------------------------------------| r_work (final): 0.2736 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072540 restraints weight = 437.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072674 restraints weight = 48.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072679 restraints weight = 11.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072678 restraints weight = 11.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072677 restraints weight = 9.236 | |-----------------------------------------------------------------------------| r_work (final): 0.3041 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.042004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.036717 restraints weight = 260.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.037916 restraints weight = 149.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.038623 restraints weight = 111.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.039100 restraints weight = 90.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.039453 restraints weight = 76.774| |-----------------------------------------------------------------------------| r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45680 Z= 0.126 Angle : 0.753 15.700 62168 Z= 0.360 Chirality : 0.048 0.347 7198 Planarity : 0.006 0.072 7916 Dihedral : 7.179 59.820 6934 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.70 % Favored : 84.16 % Rotamer: Outliers : 0.08 % Allowed : 1.54 % Favored : 98.38 % 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: -4.62 (0.09), residues: 5620 helix: -2.73 (0.15), residues: 722 sheet: -2.55 (0.12), residues: 1582 loop : -3.57 (0.09), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 147 TYR 0.032 0.002 TYR B1216 PHE 0.029 0.002 PHE D1049 TRP 0.020 0.002 TRP B 858 HIS 0.010 0.001 HIS D1182 Details of bonding type rmsd covalent geometry : bond 0.00277 (45592) covalent geometry : angle 0.73912 (61950) SS BOND : bond 0.00635 ( 46) SS BOND : angle 1.12199 ( 92) hydrogen bonds : bond 0.05365 ( 384) hydrogen bonds : angle 6.42712 ( 1152) link_ALPHA1-6 : bond 0.00397 ( 2) link_ALPHA1-6 : angle 1.55912 ( 6) link_BETA1-4 : bond 0.00706 ( 10) link_BETA1-4 : angle 2.25319 ( 30) link_NAG-ASN : bond 0.00655 ( 30) link_NAG-ASN : angle 3.58917 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.416 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: A 151 MET cc_start: 0.6896 (tpp) cc_final: 0.6483 (tpp) REVERT: A 456 LYS cc_start: 0.9539 (pttm) cc_final: 0.8874 (tptt) REVERT: A 460 HIS cc_start: 0.7873 (t70) cc_final: 0.7342 (t70) REVERT: A 607 MET cc_start: 0.4102 (mtt) cc_final: 0.3552 (mtt) REVERT: A 655 TYR cc_start: 0.2937 (p90) cc_final: 0.1340 (m-10) REVERT: A 673 MET cc_start: 0.3185 (mmp) cc_final: 0.2579 (mmm) REVERT: A 1330 TYR cc_start: 0.9656 (p90) cc_final: 0.9223 (p90) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1144 time to fit residues: 17.5864 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 : 0.379 Evaluate side-chains 236 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.412 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: D 50 LEU cc_start: 0.8854 (mt) cc_final: 0.8454 (mt) REVERT: D 101 MET cc_start: 0.3592 (ptm) cc_final: 0.3357 (ptm) REVERT: D 151 MET cc_start: 0.8608 (tpp) cc_final: 0.8331 (tpp) REVERT: D 221 VAL cc_start: 0.9429 (t) cc_final: 0.8763 (p) REVERT: D 321 HIS cc_start: 0.9104 (p-80) cc_final: 0.8541 (p-80) REVERT: D 381 ASN cc_start: 0.9545 (m110) cc_final: 0.9191 (t0) REVERT: D 384 ILE cc_start: 0.9442 (pt) cc_final: 0.9184 (tp) REVERT: D 385 PHE cc_start: 0.8931 (m-80) cc_final: 0.8528 (m-80) REVERT: D 422 ARG cc_start: 0.7320 (tpp80) cc_final: 0.6978 (tpp-160) REVERT: D 441 HIS cc_start: 0.8621 (m170) cc_final: 0.8298 (m-70) REVERT: D 500 MET cc_start: 0.8006 (mtt) cc_final: 0.6355 (mtt) REVERT: D 557 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8761 (mptt) REVERT: D 672 ASP cc_start: 0.9193 (t0) cc_final: 0.8881 (t0) REVERT: D 673 MET cc_start: 0.8675 (tpt) cc_final: 0.8020 (tpt) REVERT: D 798 MET cc_start: 0.8606 (tmm) cc_final: 0.8294 (tpt) REVERT: D 1003 LYS cc_start: 0.7743 (tptp) cc_final: 0.7084 (tptp) REVERT: D 1007 TYR cc_start: 0.8867 (m-80) cc_final: 0.8331 (m-80) REVERT: D 1110 LEU cc_start: 0.9116 (tp) cc_final: 0.8641 (tp) REVERT: D 1126 PHE cc_start: 0.9154 (m-10) cc_final: 0.8804 (m-10) REVERT: D 1152 TYR cc_start: 0.8062 (t80) cc_final: 0.7494 (t80) REVERT: D 1208 MET cc_start: 0.8508 (ppp) cc_final: 0.8152 (ppp) REVERT: D 1209 THR cc_start: 0.8605 (m) cc_final: 0.8246 (m) REVERT: D 1248 PHE cc_start: 0.8053 (t80) cc_final: 0.7601 (t80) REVERT: D 1264 TYR cc_start: 0.7318 (t80) cc_final: 0.7059 (t80) REVERT: D 1279 THR cc_start: 0.9284 (p) cc_final: 0.9062 (p) REVERT: D 1281 GLN cc_start: 0.8738 (pm20) cc_final: 0.8181 (pm20) REVERT: D 1314 MET cc_start: 0.9057 (mmp) cc_final: 0.8554 (mmp) REVERT: D 1315 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8843 (mmtm) REVERT: D 1331 ASN cc_start: 0.9019 (m-40) cc_final: 0.8813 (m-40) REVERT: D 1398 MET cc_start: 0.8172 (tmm) cc_final: 0.7929 (tpp) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.1088 time to fit residues: 36.1959 Evaluate side-chains 185 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.429 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 154 optimal weight: 3.9990 chunk 455 optimal weight: 0.0010 chunk 108 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 345 optimal weight: 9.9990 chunk 465 optimal weight: 0.0570 chunk 16 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 425 optimal weight: 0.0010 chunk 343 optimal weight: 0.0030 overall best weight: 0.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS D 460 HIS ** D 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1377 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.154425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.136203 restraints weight = 95432.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.137311 restraints weight = 77281.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.138251 restraints weight = 65784.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.138973 restraints weight = 58161.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.139192 restraints weight = 52389.402| |-----------------------------------------------------------------------------| r_work (final): 0.4502 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.114556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.085907 restraints weight = 45912.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.088921 restraints weight = 34985.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091364 restraints weight = 28111.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.093289 restraints weight = 23411.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.094824 restraints weight = 20081.118| |-----------------------------------------------------------------------------| r_work (final): 0.3838 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.053088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.050912 restraints weight = 315.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.051380 restraints weight = 117.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.052006 restraints weight = 70.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.052182 restraints weight = 35.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.052182 restraints weight = 25.309| |-----------------------------------------------------------------------------| r_work (final): 0.2730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071034 restraints weight = 500.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071080 restraints weight = 33.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071081 restraints weight = 16.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071081 restraints weight = 8.888 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071081 restraints weight = 8.888 | |-----------------------------------------------------------------------------| r_work (final): 0.3003 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.040792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.035932 restraints weight = 275.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.036723 restraints weight = 179.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.037229 restraints weight = 143.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.037571 restraints weight = 122.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.037759 restraints weight = 110.340| |-----------------------------------------------------------------------------| r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45680 Z= 0.121 Angle : 0.731 14.973 62168 Z= 0.348 Chirality : 0.047 0.345 7198 Planarity : 0.006 0.073 7916 Dihedral : 7.167 59.597 6934 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 1.32 % Allowed : 14.41 % Favored : 84.27 % Rotamer: Outliers : 0.04 % Allowed : 0.93 % Favored : 99.03 % 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: -4.56 (0.09), residues: 5620 helix: -2.71 (0.15), residues: 734 sheet: -2.48 (0.12), residues: 1616 loop : -3.54 (0.09), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 338 TYR 0.030 0.002 TYR C 272 PHE 0.020 0.001 PHE D 524 TRP 0.019 0.001 TRP D 858 HIS 0.009 0.001 HIS B1182 Details of bonding type rmsd covalent geometry : bond 0.00266 (45592) covalent geometry : angle 0.71278 (61950) SS BOND : bond 0.00563 ( 46) SS BOND : angle 0.92754 ( 92) hydrogen bonds : bond 0.05143 ( 384) hydrogen bonds : angle 6.24874 ( 1152) link_ALPHA1-6 : bond 0.00224 ( 2) link_ALPHA1-6 : angle 1.45347 ( 6) link_BETA1-4 : bond 0.00713 ( 10) link_BETA1-4 : angle 2.23078 ( 30) link_NAG-ASN : bond 0.00719 ( 30) link_NAG-ASN : angle 4.11185 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.379 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: A 151 MET cc_start: 0.6561 (tpp) cc_final: 0.6315 (tpp) REVERT: A 183 LEU cc_start: 0.8667 (mt) cc_final: 0.8330 (mt) REVERT: A 456 LYS cc_start: 0.9520 (pttm) cc_final: 0.8863 (tptt) REVERT: A 460 HIS cc_start: 0.7506 (t70) cc_final: 0.7238 (t70) REVERT: A 607 MET cc_start: 0.2821 (mtt) cc_final: 0.1581 (ptp) REVERT: A 655 TYR cc_start: 0.2527 (p90) cc_final: 0.1066 (m-10) REVERT: A 673 MET cc_start: 0.2745 (mmp) cc_final: 0.2066 (mmm) REVERT: A 1314 MET cc_start: 0.0191 (tmm) cc_final: -0.0128 (tmm) REVERT: A 1330 TYR cc_start: 0.9613 (p90) cc_final: 0.8997 (p90) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1185 time to fit residues: 17.6196 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 : 0.434 Evaluate side-chains 236 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 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: symmetry clash revert: 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: 0.3448 (ptm) cc_final: 0.3213 (ptm) REVERT: D 132 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8470 (tm-30) REVERT: D 151 MET cc_start: 0.8571 (tpp) cc_final: 0.8297 (tpp) REVERT: D 221 VAL cc_start: 0.9431 (t) cc_final: 0.8745 (p) REVERT: D 312 LYS cc_start: 0.8428 (mppt) cc_final: 0.8219 (mmtm) REVERT: D 321 HIS cc_start: 0.9009 (p-80) cc_final: 0.8404 (p-80) REVERT: D 381 ASN cc_start: 0.9561 (m110) cc_final: 0.9203 (t0) REVERT: D 384 ILE cc_start: 0.9403 (pt) cc_final: 0.9124 (tp) REVERT: D 385 PHE cc_start: 0.9003 (m-80) cc_final: 0.8597 (m-80) REVERT: D 500 MET cc_start: 0.7888 (mtt) cc_final: 0.7392 (mtt) REVERT: D 557 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8726 (mptt) REVERT: D 672 ASP cc_start: 0.9216 (t0) cc_final: 0.8868 (t0) REVERT: D 933 LEU cc_start: 0.8994 (mp) cc_final: 0.8547 (mp) REVERT: D 983 ASN cc_start: 0.8827 (m110) cc_final: 0.8487 (m110) REVERT: D 1003 LYS cc_start: 0.7807 (tptp) cc_final: 0.7150 (tptp) REVERT: D 1007 TYR cc_start: 0.8889 (m-80) cc_final: 0.8310 (m-80) REVERT: D 1110 LEU cc_start: 0.9139 (tp) cc_final: 0.8739 (tp) REVERT: D 1126 PHE cc_start: 0.9144 (m-10) cc_final: 0.8775 (m-10) REVERT: D 1152 TYR cc_start: 0.8030 (t80) cc_final: 0.7490 (t80) REVERT: D 1208 MET cc_start: 0.8523 (ppp) cc_final: 0.8175 (ppp) REVERT: D 1209 THR cc_start: 0.8574 (m) cc_final: 0.8230 (m) REVERT: D 1248 PHE cc_start: 0.8101 (t80) cc_final: 0.7718 (t80) REVERT: D 1264 TYR cc_start: 0.7283 (t80) cc_final: 0.6979 (t80) REVERT: D 1314 MET cc_start: 0.9005 (mmp) cc_final: 0.8804 (mmm) REVERT: D 1315 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8642 (mmmm) REVERT: D 1331 ASN cc_start: 0.9086 (m-40) cc_final: 0.8884 (m-40) REVERT: D 1398 MET cc_start: 0.8125 (tmm) cc_final: 0.7885 (tpp) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.1092 time to fit residues: 36.3303 Evaluate side-chains 191 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.336 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 : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 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: 0.5980 chunk 179 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 359 optimal weight: 0.0030 chunk 475 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 418 optimal weight: 0.0010 chunk 367 optimal weight: 0.9980 chunk 413 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 983 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.154691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.136148 restraints weight = 96632.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.137212 restraints weight = 80419.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.138098 restraints weight = 67920.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.139028 restraints weight = 60250.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.139371 restraints weight = 54077.143| |-----------------------------------------------------------------------------| r_work (final): 0.4525 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.114979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087005 restraints weight = 46975.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.090071 restraints weight = 35518.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.092482 restraints weight = 28325.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.094398 restraints weight = 23490.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.095950 restraints weight = 20056.073| |-----------------------------------------------------------------------------| r_work (final): 0.3846 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.052652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.050620 restraints weight = 356.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051203 restraints weight = 119.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051639 restraints weight = 61.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.051802 restraints weight = 33.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.051802 restraints weight = 24.258| |-----------------------------------------------------------------------------| r_work (final): 0.2718 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070235 restraints weight = 469.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070235 restraints weight = 584.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070235 restraints weight = 560.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070235 restraints weight = 528.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070235 restraints weight = 572.604| |-----------------------------------------------------------------------------| r_work (final): 0.2960 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.040411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2199 r_free = 0.2199 target = 0.035527 restraints weight = 294.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2213 r_free = 0.2213 target = 0.036218 restraints weight = 196.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.036642 restraints weight = 158.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.036649 restraints weight = 137.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.036649 restraints weight = 136.726| |-----------------------------------------------------------------------------| r_work (final): 0.2177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45680 Z= 0.119 Angle : 0.726 14.541 62168 Z= 0.346 Chirality : 0.047 0.343 7198 Planarity : 0.005 0.073 7916 Dihedral : 7.138 59.455 6934 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 1.49 % Allowed : 13.91 % Favored : 84.59 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % 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: -4.58 (0.09), residues: 5620 helix: -2.66 (0.15), residues: 736 sheet: -2.54 (0.12), residues: 1578 loop : -3.54 (0.09), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 338 TYR 0.029 0.001 TYR B1216 PHE 0.021 0.001 PHE B1044 TRP 0.021 0.001 TRP C 436 HIS 0.008 0.001 HIS B1182 Details of bonding type rmsd covalent geometry : bond 0.00264 (45592) covalent geometry : angle 0.70821 (61950) SS BOND : bond 0.00336 ( 46) SS BOND : angle 0.98768 ( 92) hydrogen bonds : bond 0.05111 ( 384) hydrogen bonds : angle 6.23890 ( 1152) link_ALPHA1-6 : bond 0.00358 ( 2) link_ALPHA1-6 : angle 1.59123 ( 6) link_BETA1-4 : bond 0.00646 ( 10) link_BETA1-4 : angle 2.20681 ( 30) link_NAG-ASN : bond 0.00718 ( 30) link_NAG-ASN : angle 4.06191 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 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: A 151 MET cc_start: 0.6890 (tpp) cc_final: 0.6655 (tpp) REVERT: A 456 LYS cc_start: 0.9514 (pttm) cc_final: 0.8908 (tptt) REVERT: A 460 HIS cc_start: 0.8016 (t70) cc_final: 0.7405 (t70) REVERT: A 500 MET cc_start: 0.5594 (ptt) cc_final: 0.4225 (ttt) REVERT: A 607 MET cc_start: 0.4633 (mtt) cc_final: 0.3569 (ptp) REVERT: A 655 TYR cc_start: 0.2594 (p90) cc_final: 0.1158 (m-10) REVERT: A 673 MET cc_start: 0.3190 (mmp) cc_final: 0.2141 (mmm) REVERT: A 747 ASN cc_start: 0.8765 (m-40) cc_final: 0.8252 (p0) REVERT: A 817 TYR cc_start: 0.6076 (m-80) cc_final: 0.5391 (m-80) REVERT: A 1314 MET cc_start: 0.0350 (tmm) cc_final: -0.0186 (tmm) REVERT: A 1330 TYR cc_start: 0.9685 (p90) cc_final: 0.9336 (p90) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1125 time to fit residues: 16.1954 Evaluate side-chains 74 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.408 Evaluate side-chains 225 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.411 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: B 132 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8043 (tm-30) REVERT: B 151 MET cc_start: 0.8607 (tpp) cc_final: 0.8315 (tpp) REVERT: B 183 LEU cc_start: 0.9470 (mp) cc_final: 0.9211 (mp) REVERT: B 221 VAL cc_start: 0.9538 (t) cc_final: 0.9048 (p) REVERT: B 321 HIS cc_start: 0.9059 (p-80) cc_final: 0.8491 (p-80) REVERT: B 381 ASN cc_start: 0.9545 (m110) cc_final: 0.9189 (t0) REVERT: B 384 ILE cc_start: 0.9394 (pt) cc_final: 0.9092 (tp) REVERT: B 385 PHE cc_start: 0.8998 (m-80) cc_final: 0.8601 (m-80) REVERT: B 422 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7657 (tpt170) REVERT: B 500 MET cc_start: 0.7935 (mtt) cc_final: 0.7693 (mmt) REVERT: B 502 LYS cc_start: 0.8795 (ptpt) cc_final: 0.8409 (ptmt) REVERT: B 539 ARG cc_start: 0.7173 (mtt180) cc_final: 0.5691 (mtt180) REVERT: B 557 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8700 (mptt) REVERT: B 607 MET cc_start: 0.6045 (ttp) cc_final: 0.5789 (ttp) REVERT: B 672 ASP cc_start: 0.9229 (t0) cc_final: 0.8874 (t0) REVERT: B 933 LEU cc_start: 0.8969 (mp) cc_final: 0.8519 (mp) REVERT: B 1003 LYS cc_start: 0.7746 (tptp) cc_final: 0.6989 (tptp) REVERT: B 1007 TYR cc_start: 0.8937 (m-80) cc_final: 0.8362 (m-80) REVERT: B 1110 LEU cc_start: 0.9163 (tp) cc_final: 0.8775 (tp) REVERT: B 1126 PHE cc_start: 0.9107 (m-10) cc_final: 0.8738 (m-10) REVERT: B 1152 TYR cc_start: 0.8189 (t80) cc_final: 0.7632 (t80) REVERT: B 1208 MET cc_start: 0.8653 (ppp) cc_final: 0.8212 (ppp) REVERT: B 1209 THR cc_start: 0.8555 (m) cc_final: 0.8266 (m) REVERT: B 1248 PHE cc_start: 0.8156 (t80) cc_final: 0.7760 (t80) REVERT: B 1264 TYR cc_start: 0.7318 (t80) cc_final: 0.6997 (t80) REVERT: B 1314 MET cc_start: 0.9072 (mmp) cc_final: 0.8621 (mmm) REVERT: B 1315 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8841 (mmtm) REVERT: B 1331 ASN cc_start: 0.9099 (m-40) cc_final: 0.8893 (m-40) REVERT: B 1398 MET cc_start: 0.8060 (tmm) cc_final: 0.7857 (tpp) REVERT: B 1450 TYR cc_start: 0.8662 (p90) cc_final: 0.8427 (p90) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1110 time to fit residues: 34.8601 Evaluate side-chains 179 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.399 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: 0.0011 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 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 305 optimal weight: 0.0170 chunk 380 optimal weight: 3.9990 chunk 512 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 540 optimal weight: 30.0000 chunk 532 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 476 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 893 HIS B 967 GLN B1123 ASN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.154835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.136227 restraints weight = 97416.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.137498 restraints weight = 80134.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.138442 restraints weight = 67970.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.138972 restraints weight = 59986.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.139851 restraints weight = 54965.854| |-----------------------------------------------------------------------------| r_work (final): 0.4502 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.114779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.085310 restraints weight = 44507.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.088713 restraints weight = 32744.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.091407 restraints weight = 25542.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.093549 restraints weight = 20779.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.095262 restraints weight = 17475.788| |-----------------------------------------------------------------------------| r_work (final): 0.3855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.051576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.049924 restraints weight = 523.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050553 restraints weight = 150.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.050854 restraints weight = 66.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.051035 restraints weight = 34.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.051181 restraints weight = 23.259| |-----------------------------------------------------------------------------| r_work (final): 0.2701 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069457 restraints weight = 472.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069537 restraints weight = 34.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069546 restraints weight = 6.625 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069545 restraints weight = 4.176 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069545 restraints weight = 4.166 | |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.040012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.035637 restraints weight = 275.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2231 r_free = 0.2231 target = 0.036271 restraints weight = 188.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2238 r_free = 0.2238 target = 0.036667 restraints weight = 151.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.036932 restraints weight = 131.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.037238 restraints weight = 118.613| |-----------------------------------------------------------------------------| r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45680 Z= 0.116 Angle : 0.710 14.561 62168 Z= 0.337 Chirality : 0.047 0.339 7198 Planarity : 0.005 0.071 7916 Dihedral : 7.037 59.225 6934 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 1.39 % Allowed : 14.02 % Favored : 84.59 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.10), residues: 5620 helix: -2.57 (0.16), residues: 726 sheet: -2.53 (0.12), residues: 1568 loop : -3.49 (0.09), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 338 TYR 0.028 0.001 TYR B1216 PHE 0.025 0.001 PHE D1044 TRP 0.017 0.001 TRP D 858 HIS 0.008 0.001 HIS D1182 Details of bonding type rmsd covalent geometry : bond 0.00258 (45592) covalent geometry : angle 0.69141 (61950) SS BOND : bond 0.00426 ( 46) SS BOND : angle 1.00297 ( 92) hydrogen bonds : bond 0.04975 ( 384) hydrogen bonds : angle 5.98026 ( 1152) link_ALPHA1-6 : bond 0.00672 ( 2) link_ALPHA1-6 : angle 1.57572 ( 6) link_BETA1-4 : bond 0.00573 ( 10) link_BETA1-4 : angle 2.18753 ( 30) link_NAG-ASN : bond 0.00726 ( 30) link_NAG-ASN : angle 3.98403 ( 90) =============================================================================== Job complete usr+sys time: 5376.36 seconds wall clock time: 96 minutes 46.35 seconds (5806.35 seconds total)