Starting phenix.real_space_refine on Tue Jul 7 02:02:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o7o_12751/07_2026/7o7o_12751.cif" } resolution = 4.8 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= 0.002 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 182 5.16 5 C 27066 2.51 5 N 7070 2.21 5 O 8324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42642 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 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: 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: "C" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.31, per 1000 atoms: 0.24 Number of scatterers: 42642 At special positions: 0 Unit cell: (210.447, 162.285, 194.742, 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 182 16.00 O 8324 8.00 N 7070 7.00 C 27066 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=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.06 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.04 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=2.04 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=2.05 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=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.04 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.03 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.06 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.04 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=2.04 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=2.05 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 247 " " NAG A2003 " - " ASN A 410 " " NAG A2004 " - " ASN A 869 " " NAG A2005 " - " ASN A 991 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 869 " " NAG B2004 " - " ASN B 991 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 247 " " NAG C2003 " - " ASN C 410 " " NAG C2004 " - " ASN C 869 " " NAG C2005 " - " ASN C 991 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 869 " " NAG D2004 " - " ASN D 991 " " NAG E 1 " - " ASN A 70 " " NAG F 1 " - " ASN A 396 " " NAG G 1 " - " ASN B 247 " " NAG H 1 " - " ASN B 396 " " NAG I 1 " - " ASN B 410 " " NAG J 1 " - " ASN B1424 " " NAG K 1 " - " ASN C 70 " " NAG L 1 " - " ASN C 396 " " NAG M 1 " - " ASN D 247 " " NAG N 1 " - " ASN D 396 " " NAG O 1 " - " ASN D 410 " " NAG P 1 " - " ASN D1424 " Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10092 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 16.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 6.200A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 4.191A pdb=" N THR A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 removed outlier: 3.529A pdb=" N LEU B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 671 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 962 removed outlier: 6.449A 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: 4.556A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 4.475A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B 989 " --> pdb=" O TYR B 985 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 992 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 3.933A pdb=" N GLY B1006 " --> pdb=" O SER B1002 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN B1013 " --> pdb=" O ASN B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1052 removed outlier: 4.281A pdb=" N LYS B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B1048 " --> pdb=" O PHE B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 3.653A pdb=" N ALA B1066 " --> pdb=" O HIS B1062 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B1073 " --> pdb=" O TRP B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 4.121A pdb=" N THR B1106 " --> pdb=" O SER B1102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1108 " --> pdb=" O TYR B1104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B1111 " --> pdb=" O ILE B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1137 Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.664A pdb=" N ALA B1148 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B1151 " --> pdb=" O LYS B1147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B1156 " --> pdb=" O TYR B1152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 3.501A pdb=" N GLU B1165 " --> pdb=" O ASP B1161 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B1168 " --> pdb=" O LYS B1164 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B1170 " --> pdb=" O VAL B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1217 removed outlier: 3.591A pdb=" N TYR B1211 " --> pdb=" O GLU B1207 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B1217 " --> pdb=" O LEU B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 4.061A pdb=" N THR B1229 " --> pdb=" O SER B1225 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B1231 " --> pdb=" O ASP B1227 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B1233 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B1236 " --> pdb=" O THR B1232 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B1238 " --> pdb=" O ILE B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 5.084A pdb=" N VAL B1255 " --> pdb=" O THR B1251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B1256 " --> pdb=" O GLN B1252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B1260 " --> pdb=" O VAL B1256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B1261 " --> pdb=" O ALA B1257 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B1263 " --> pdb=" O HIS B1259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR B1264 " --> pdb=" O ALA B1260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY B1265 " --> pdb=" O LEU B1261 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA B1266 " --> pdb=" O SER B1262 " (cutoff:3.500A) removed outlier: 3.786A 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 Processing helix chain 'C' and resid 953 through 965 removed outlier: 6.200A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1205 through 1217 removed outlier: 4.191A pdb=" N THR C1209 " --> pdb=" O GLU C1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 removed outlier: 3.529A pdb=" N LEU D 670 " --> pdb=" O MET D 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 671 " --> pdb=" O TYR D 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET D 673 " --> pdb=" O PHE D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 962 removed outlier: 6.449A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 958 through 962' Processing helix chain 'D' and resid 973 through 993 removed outlier: 4.905A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL D 978 " --> pdb=" O GLU D 974 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 4.475A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D 989 " --> pdb=" O TYR D 985 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D 992 " --> pdb=" O ASP D 988 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 993 " --> pdb=" O TYR D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.933A pdb=" N GLY D1006 " --> pdb=" O SER D1002 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN D1013 " --> pdb=" O ASN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 4.281A pdb=" N LYS D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR D1048 " --> pdb=" O PHE D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.653A pdb=" N ALA D1066 " --> pdb=" O HIS D1062 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D1073 " --> pdb=" O TRP D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 removed outlier: 4.121A pdb=" N THR D1106 " --> pdb=" O SER D1102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D1108 " --> pdb=" O TYR D1104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1137 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.664A pdb=" N ALA D1148 " --> pdb=" O VAL D1144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D1151 " --> pdb=" O LYS D1147 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 3.501A pdb=" N GLU D1165 " --> pdb=" O ASP D1161 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D1168 " --> pdb=" O LYS D1164 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1217 removed outlier: 3.591A pdb=" N TYR D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.061A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D1231 " --> pdb=" O ASP D1227 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D1233 " --> pdb=" O THR D1229 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D1236 " --> pdb=" O THR D1232 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 5.084A pdb=" N VAL D1255 " --> pdb=" O THR D1251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D1256 " --> pdb=" O GLN D1252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D1261 " --> pdb=" O ALA D1257 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D1263 " --> pdb=" O HIS D1259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR D1264 " --> pdb=" O ALA D1260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D1265 " --> pdb=" O LEU D1261 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA D1266 " --> pdb=" O SER D1262 " (cutoff:3.500A) removed outlier: 3.786A 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 482 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.07: 4 1.07 - 1.28: 7076 1.28 - 1.48: 17733 1.48 - 1.69: 18491 1.69 - 1.90: 270 Bond restraints: 43574 Sorted by residual: bond pdb=" C LEU C 54 " pdb=" N ASN C 55 " ideal model delta sigma weight residual 1.330 0.861 0.469 1.32e-02 5.74e+03 1.26e+03 bond pdb=" C LEU A 54 " pdb=" N ASN A 55 " ideal model delta sigma weight residual 1.330 0.861 0.469 1.32e-02 5.74e+03 1.26e+03 bond pdb=" C VAL D 978 " pdb=" N LEU D 979 " ideal model delta sigma weight residual 1.334 1.606 -0.271 1.20e-02 6.94e+03 5.11e+02 bond pdb=" C VAL A 868 " pdb=" N ASN A 869 " ideal model delta sigma weight residual 1.330 1.049 0.281 1.37e-02 5.33e+03 4.21e+02 bond pdb=" C VAL C 868 " pdb=" N ASN C 869 " ideal model delta sigma weight residual 1.330 1.049 0.281 1.37e-02 5.33e+03 4.21e+02 ... (remaining 43569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.59: 58947 5.59 - 11.18: 220 11.18 - 16.77: 15 16.77 - 22.36: 19 22.36 - 27.95: 3 Bond angle restraints: 59204 Sorted by residual: angle pdb=" O LEU D 990 " pdb=" C LEU D 990 " pdb=" N ASN D 991 " ideal model delta sigma weight residual 122.07 143.56 -21.49 1.03e+00 9.43e-01 4.35e+02 angle pdb=" O LEU B 990 " pdb=" C LEU B 990 " pdb=" N ASN B 991 " ideal model delta sigma weight residual 122.07 143.56 -21.49 1.03e+00 9.43e-01 4.35e+02 angle pdb=" CA LEU D 990 " pdb=" C LEU D 990 " pdb=" N ASN D 991 " ideal model delta sigma weight residual 117.07 95.96 21.11 1.14e+00 7.69e-01 3.43e+02 angle pdb=" CA LEU B 990 " pdb=" C LEU B 990 " pdb=" N ASN B 991 " ideal model delta sigma weight residual 117.07 95.96 21.11 1.14e+00 7.69e-01 3.43e+02 angle pdb=" C LEU D 990 " pdb=" N ASN D 991 " pdb=" CA ASN D 991 " ideal model delta sigma weight residual 122.09 94.14 27.95 1.79e+00 3.12e-01 2.44e+02 ... (remaining 59199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22829 17.95 - 35.90: 2510 35.90 - 53.85: 485 53.85 - 71.80: 116 71.80 - 89.75: 28 Dihedral angle restraints: 25968 sinusoidal: 10300 harmonic: 15668 Sorted by residual: dihedral pdb=" CB CYS C 847 " pdb=" SG CYS C 847 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 847 " pdb=" SG CYS A 847 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" C GLU A 908 " pdb=" N GLU A 908 " pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " ideal model delta harmonic sigma weight residual -122.60 -144.21 21.61 0 2.50e+00 1.60e-01 7.47e+01 ... (remaining 25965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 6791 0.168 - 0.336: 93 0.336 - 0.504: 12 0.504 - 0.672: 2 0.672 - 0.840: 2 Chirality restraints: 6900 Sorted by residual: 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 -2.02 -0.38 2.00e-02 2.50e+03 3.55e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.55e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.57e+02 ... (remaining 6897 not shown) Planarity restraints: 7584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG K 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG E 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG L 1 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.137 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.137 2.00e-02 2.50e+03 ... (remaining 7581 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 117 2.23 - 2.90: 18831 2.90 - 3.57: 69238 3.57 - 4.23: 105783 4.23 - 4.90: 160190 Nonbonded interactions: 354159 Sorted by model distance: nonbonded pdb=" SG CYS B 972 " pdb=" CD GLN B 975 " model vdw 1.564 3.630 nonbonded pdb=" SG CYS D 972 " pdb=" CD GLN D 975 " model vdw 1.659 3.630 nonbonded pdb=" OD1 ASN D 976 " pdb=" NH1 ARG D1014 " model vdw 1.960 3.120 nonbonded pdb=" OG1 THR B 915 " pdb=" O THR B1326 " model vdw 1.992 3.040 nonbonded pdb=" OG1 THR D 915 " pdb=" O THR D1326 " model vdw 1.992 3.040 ... (remaining 354154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2002 through 2005)) selection = (chain 'B' and (resid 26 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2004)) selection = (chain 'C' and (resid 26 through 974 or (resid 975 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1)) or resid 976 throug \ h 1337 or resid 2002 through 2005)) selection = (chain 'D' and (resid 26 through 695 or resid 730 through 1337 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 37.480 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 : 0.011 0.469 43672 Z= 0.605 Angle : 1.255 27.950 59452 Z= 0.719 Chirality : 0.063 0.840 6900 Planarity : 0.018 0.305 7554 Dihedral : 15.669 89.746 15738 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.47 % Allowed : 17.39 % Favored : 82.15 % Rotamer: Outliers : 0.43 % Allowed : 5.89 % Favored : 93.68 % Cbeta Deviations : 0.10 % 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: -5.42 (0.09), residues: 5360 helix: -2.94 (0.12), residues: 810 sheet: -3.33 (0.11), residues: 1496 loop : -4.08 (0.09), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 387 TYR 0.035 0.003 TYR D1418 PHE 0.033 0.003 PHE D1389 TRP 0.023 0.003 TRP B 741 HIS 0.012 0.002 HIS D 460 Details of bonding type rmsd/Z covalent geometry : bond 0.01063 / 0.61 (43574) covalent geometry : angle 1.23853 / 0.72 (59204) SS BOND : bond 0.00798 / 0.46 ( 46) SS BOND : angle 2.20495 / 1.33 ( 92) hydrogen bonds : bond 0.22005 / 14.64 ( 482) hydrogen bonds : angle 8.71462 / 5.85 ( 1446) link_ALPHA1-6 : bond 0.00119 / 0.06 ( 4) link_ALPHA1-6 : angle 1.47460 / 0.81 ( 12) link_BETA1-4 : bond 0.00991 / 0.63 ( 18) link_BETA1-4 : angle 3.32640 / 2.22 ( 54) link_NAG-ASN : bond 0.01036 / 0.52 ( 30) link_NAG-ASN : angle 4.45198 / 2.98 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 717 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9489 (mp) cc_final: 0.9289 (mp) REVERT: A 55 ASN cc_start: 0.6602 (p0) cc_final: 0.5206 (t0) REVERT: A 93 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7815 (mmtp) REVERT: A 151 MET cc_start: 0.9018 (ttm) cc_final: 0.8258 (tpp) REVERT: A 166 TYR cc_start: 0.7988 (p90) cc_final: 0.7590 (p90) REVERT: A 192 PHE cc_start: 0.7763 (t80) cc_final: 0.7421 (t80) REVERT: A 215 THR cc_start: 0.8867 (t) cc_final: 0.8493 (m) REVERT: A 368 GLN cc_start: 0.9193 (tt0) cc_final: 0.8991 (tm-30) REVERT: A 977 MET cc_start: 0.8244 (mmp) cc_final: 0.7859 (mmm) REVERT: A 1015 GLN cc_start: 0.9287 (tp40) cc_final: 0.8528 (tp40) REVERT: A 1065 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8264 (tp-100) REVERT: A 1086 LEU cc_start: 0.7567 (tp) cc_final: 0.7212 (tp) REVERT: A 1122 ARG cc_start: 0.9059 (ttp-110) cc_final: 0.8797 (tmm-80) REVERT: B 169 ASP cc_start: 0.9112 (t0) cc_final: 0.8462 (t70) REVERT: B 194 LEU cc_start: 0.9239 (tp) cc_final: 0.9014 (tp) REVERT: B 237 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8892 (mmmt) REVERT: B 297 HIS cc_start: 0.8818 (t70) cc_final: 0.8597 (m90) REVERT: B 366 PHE cc_start: 0.9161 (m-10) cc_final: 0.8948 (m-10) REVERT: B 393 TYR cc_start: 0.8782 (t80) cc_final: 0.8340 (t80) REVERT: B 410 ASN cc_start: 0.5906 (OUTLIER) cc_final: 0.5440 (t0) REVERT: B 569 ASP cc_start: 0.8370 (t0) cc_final: 0.8107 (t0) REVERT: B 916 PHE cc_start: 0.8999 (m-80) cc_final: 0.8707 (m-80) REVERT: B 960 GLN cc_start: 0.8166 (mp10) cc_final: 0.7776 (mt0) REVERT: B 1003 LYS cc_start: 0.8527 (tptt) cc_final: 0.8275 (tptt) REVERT: B 1132 TRP cc_start: 0.7224 (t-100) cc_final: 0.7003 (t-100) REVERT: B 1213 LEU cc_start: 0.9513 (tp) cc_final: 0.9296 (tp) REVERT: B 1297 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8615 (tmm-80) REVERT: B 1298 LEU cc_start: 0.9499 (pt) cc_final: 0.9255 (pt) REVERT: B 1325 GLN cc_start: 0.8783 (pp30) cc_final: 0.8565 (tm-30) REVERT: B 1328 LEU cc_start: 0.9356 (tt) cc_final: 0.8867 (tt) REVERT: B 1330 TYR cc_start: 0.9120 (p90) cc_final: 0.8752 (p90) REVERT: B 1393 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8719 (tptt) REVERT: B 1397 LYS cc_start: 0.9621 (pptt) cc_final: 0.8469 (pttm) REVERT: B 1451 ASP cc_start: 0.3496 (OUTLIER) cc_final: 0.2555 (p0) REVERT: C 34 LEU cc_start: 0.9490 (mp) cc_final: 0.9290 (mp) REVERT: C 55 ASN cc_start: 0.6605 (p0) cc_final: 0.5208 (t0) REVERT: C 93 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7810 (mmtp) REVERT: C 151 MET cc_start: 0.9017 (ttm) cc_final: 0.8253 (tpp) REVERT: C 166 TYR cc_start: 0.7996 (p90) cc_final: 0.7594 (p90) REVERT: C 192 PHE cc_start: 0.7763 (t80) cc_final: 0.7423 (t80) REVERT: C 215 THR cc_start: 0.8863 (t) cc_final: 0.8490 (m) REVERT: C 368 GLN cc_start: 0.9189 (tt0) cc_final: 0.8987 (tm-30) REVERT: C 977 MET cc_start: 0.8244 (mmp) cc_final: 0.7866 (mmm) REVERT: C 1015 GLN cc_start: 0.9287 (tp40) cc_final: 0.8522 (tp40) REVERT: C 1065 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8265 (tp-100) REVERT: C 1086 LEU cc_start: 0.7570 (tp) cc_final: 0.7210 (tp) REVERT: C 1122 ARG cc_start: 0.9061 (ttp-110) cc_final: 0.8797 (tmm-80) REVERT: D 169 ASP cc_start: 0.9111 (t0) cc_final: 0.8461 (t70) REVERT: D 194 LEU cc_start: 0.9237 (tp) cc_final: 0.9011 (tp) REVERT: D 237 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8891 (mmmt) REVERT: D 297 HIS cc_start: 0.8818 (t70) cc_final: 0.8596 (m90) REVERT: D 366 PHE cc_start: 0.9162 (m-10) cc_final: 0.8949 (m-10) REVERT: D 370 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8778 (ptm160) REVERT: D 393 TYR cc_start: 0.8783 (t80) cc_final: 0.8340 (t80) REVERT: D 410 ASN cc_start: 0.5902 (OUTLIER) cc_final: 0.5436 (t0) REVERT: D 569 ASP cc_start: 0.8379 (t0) cc_final: 0.8115 (t0) REVERT: D 916 PHE cc_start: 0.9002 (m-80) cc_final: 0.8708 (m-80) REVERT: D 960 GLN cc_start: 0.8170 (mp10) cc_final: 0.7780 (mt0) REVERT: D 1003 LYS cc_start: 0.8530 (tptt) cc_final: 0.8278 (tptt) REVERT: D 1132 TRP cc_start: 0.7225 (t-100) cc_final: 0.7003 (t-100) REVERT: D 1213 LEU cc_start: 0.9513 (tp) cc_final: 0.9295 (tp) REVERT: D 1297 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8614 (tmm-80) REVERT: D 1298 LEU cc_start: 0.9498 (pt) cc_final: 0.9253 (pt) REVERT: D 1325 GLN cc_start: 0.8788 (pp30) cc_final: 0.8570 (tm-30) REVERT: D 1328 LEU cc_start: 0.9355 (tt) cc_final: 0.8867 (tt) REVERT: D 1330 TYR cc_start: 0.9122 (p90) cc_final: 0.8753 (p90) REVERT: D 1393 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8723 (tptt) REVERT: D 1397 LYS cc_start: 0.9622 (pptt) cc_final: 0.8472 (pttm) REVERT: D 1451 ASP cc_start: 0.3501 (OUTLIER) cc_final: 0.2471 (p0) outliers start: 20 outliers final: 6 residues processed: 734 average time/residue: 0.2823 time to fit residues: 334.7002 Evaluate side-chains 519 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 507 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 0.0970 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 917 ASN A 938 ASN A1062 HIS A1118 HIS B 182 GLN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN B 917 ASN ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1302 GLN C 917 ASN C 938 ASN C1062 HIS C1118 HIS D 182 GLN ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN D 917 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1302 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070858 restraints weight = 275445.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.072993 restraints weight = 208169.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074610 restraints weight = 167820.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.075899 restraints weight = 141717.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.076890 restraints weight = 123562.441| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43672 Z= 0.192 Angle : 0.955 14.700 59452 Z= 0.465 Chirality : 0.054 0.342 6900 Planarity : 0.006 0.097 7554 Dihedral : 7.786 33.888 5740 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.15 % Favored : 86.66 % Rotamer: Outliers : 0.38 % Allowed : 7.68 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.09), residues: 5360 helix: -1.94 (0.15), residues: 802 sheet: -2.83 (0.11), residues: 1508 loop : -3.70 (0.09), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 270 TYR 0.031 0.002 TYR B1418 PHE 0.035 0.002 PHE D1049 TRP 0.029 0.003 TRP D1183 HIS 0.012 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (43574) covalent geometry : angle 0.92193 / 0.46 (59204) SS BOND : bond 0.00621 / 0.36 ( 46) SS BOND : angle 1.51999 / 0.95 ( 92) hydrogen bonds : bond 0.06713 / 4.48 ( 482) hydrogen bonds : angle 6.58510 / 4.46 ( 1446) link_ALPHA1-6 : bond 0.00780 / 0.38 ( 4) link_ALPHA1-6 : angle 1.40019 / 0.83 ( 12) link_BETA1-4 : bond 0.01170 / 0.63 ( 18) link_BETA1-4 : angle 3.63030 / 2.39 ( 54) link_NAG-ASN : bond 0.01103 / 0.66 ( 30) link_NAG-ASN : angle 5.76134 / 3.68 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 664 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8066 (tmtt) REVERT: A 34 LEU cc_start: 0.9492 (mp) cc_final: 0.9247 (mp) REVERT: A 55 ASN cc_start: 0.6745 (p0) cc_final: 0.5012 (t0) REVERT: A 151 MET cc_start: 0.8914 (ttm) cc_final: 0.8232 (tpp) REVERT: A 166 TYR cc_start: 0.8007 (p90) cc_final: 0.7508 (p90) REVERT: A 192 PHE cc_start: 0.7960 (t80) cc_final: 0.7727 (t80) REVERT: A 356 ASP cc_start: 0.8903 (t0) cc_final: 0.8690 (t0) REVERT: A 368 GLN cc_start: 0.9324 (tt0) cc_final: 0.9079 (tm-30) REVERT: A 464 MET cc_start: 0.7894 (mtt) cc_final: 0.7322 (mtt) REVERT: A 520 MET cc_start: 0.9003 (ptp) cc_final: 0.8797 (tmm) REVERT: A 732 ARG cc_start: 0.8723 (ptm160) cc_final: 0.8469 (ptm160) REVERT: A 917 ASN cc_start: 0.5442 (OUTLIER) cc_final: 0.4712 (p0) REVERT: A 931 LEU cc_start: 0.9233 (tt) cc_final: 0.8646 (mp) REVERT: A 968 MET cc_start: 0.2606 (mmt) cc_final: 0.2245 (mmt) REVERT: A 1003 LYS cc_start: 0.8598 (tptp) cc_final: 0.8176 (tptp) REVERT: A 1044 PHE cc_start: 0.9591 (m-80) cc_final: 0.9377 (m-80) REVERT: A 1122 ARG cc_start: 0.9077 (ttp-110) cc_final: 0.8775 (tmm-80) REVERT: A 1254 THR cc_start: 0.9325 (m) cc_final: 0.8979 (m) REVERT: B 151 MET cc_start: 0.8739 (mtp) cc_final: 0.8092 (mpp) REVERT: B 169 ASP cc_start: 0.8971 (t0) cc_final: 0.8653 (t0) REVERT: B 229 PHE cc_start: 0.9233 (p90) cc_final: 0.8994 (p90) REVERT: B 300 PHE cc_start: 0.8745 (t80) cc_final: 0.8502 (t80) REVERT: B 370 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8811 (ptm160) REVERT: B 393 TYR cc_start: 0.8684 (t80) cc_final: 0.8095 (t80) REVERT: B 546 LEU cc_start: 0.8789 (tp) cc_final: 0.8586 (tp) REVERT: B 552 ILE cc_start: 0.8341 (mm) cc_final: 0.7949 (mm) REVERT: B 569 ASP cc_start: 0.8508 (t0) cc_final: 0.8296 (t0) REVERT: B 571 SER cc_start: 0.9121 (t) cc_final: 0.8695 (p) REVERT: B 607 MET cc_start: 0.8704 (tmm) cc_final: 0.8454 (ptp) REVERT: B 817 TYR cc_start: 0.8415 (m-10) cc_final: 0.8105 (m-80) REVERT: B 977 MET cc_start: 0.6617 (mmp) cc_final: 0.6414 (mmp) REVERT: B 1020 HIS cc_start: 0.7973 (m170) cc_final: 0.7620 (m170) REVERT: B 1109 LEU cc_start: 0.9492 (mt) cc_final: 0.9206 (mt) REVERT: B 1132 TRP cc_start: 0.7225 (t-100) cc_final: 0.6838 (t-100) REVERT: B 1293 ASP cc_start: 0.9612 (m-30) cc_final: 0.8923 (m-30) REVERT: B 1299 LEU cc_start: 0.9518 (mm) cc_final: 0.9257 (mt) REVERT: B 1328 LEU cc_start: 0.9150 (tt) cc_final: 0.8670 (tt) REVERT: B 1330 TYR cc_start: 0.9268 (p90) cc_final: 0.8822 (p90) REVERT: B 1401 ARG cc_start: 0.9139 (tpp-160) cc_final: 0.8917 (mmm160) REVERT: B 1431 PHE cc_start: 0.8745 (p90) cc_final: 0.8461 (p90) REVERT: C 28 LYS cc_start: 0.8407 (tmtt) cc_final: 0.8064 (tmtt) REVERT: C 34 LEU cc_start: 0.9495 (mp) cc_final: 0.9252 (mp) REVERT: C 55 ASN cc_start: 0.6717 (p0) cc_final: 0.4989 (t0) REVERT: C 151 MET cc_start: 0.8917 (ttm) cc_final: 0.8232 (tpp) REVERT: C 166 TYR cc_start: 0.8006 (p90) cc_final: 0.7505 (p90) REVERT: C 192 PHE cc_start: 0.7967 (t80) cc_final: 0.7733 (t80) REVERT: C 356 ASP cc_start: 0.8901 (t0) cc_final: 0.8690 (t0) REVERT: C 368 GLN cc_start: 0.9323 (tt0) cc_final: 0.9078 (tm-30) REVERT: C 464 MET cc_start: 0.7899 (mtt) cc_final: 0.7333 (mtt) REVERT: C 732 ARG cc_start: 0.8724 (ptm160) cc_final: 0.8469 (ptm160) REVERT: C 917 ASN cc_start: 0.5477 (OUTLIER) cc_final: 0.4746 (p0) REVERT: C 931 LEU cc_start: 0.9238 (tt) cc_final: 0.8648 (mp) REVERT: C 968 MET cc_start: 0.2524 (mmt) cc_final: 0.2237 (mmt) REVERT: C 1003 LYS cc_start: 0.8595 (tptp) cc_final: 0.8179 (tptp) REVERT: C 1044 PHE cc_start: 0.9590 (m-80) cc_final: 0.9376 (m-80) REVERT: C 1122 ARG cc_start: 0.9075 (ttp-110) cc_final: 0.8775 (tmm-80) REVERT: C 1254 THR cc_start: 0.9313 (m) cc_final: 0.8959 (m) REVERT: D 151 MET cc_start: 0.8752 (mtp) cc_final: 0.8107 (mpp) REVERT: D 169 ASP cc_start: 0.8972 (t0) cc_final: 0.8651 (t0) REVERT: D 229 PHE cc_start: 0.9227 (p90) cc_final: 0.8986 (p90) REVERT: D 300 PHE cc_start: 0.8744 (t80) cc_final: 0.8500 (t80) REVERT: D 370 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8815 (ptm160) REVERT: D 393 TYR cc_start: 0.8682 (t80) cc_final: 0.8095 (t80) REVERT: D 546 LEU cc_start: 0.8789 (tp) cc_final: 0.8587 (tp) REVERT: D 552 ILE cc_start: 0.8332 (mm) cc_final: 0.7939 (mm) REVERT: D 569 ASP cc_start: 0.8534 (t0) cc_final: 0.8322 (t0) REVERT: D 571 SER cc_start: 0.9133 (t) cc_final: 0.8706 (p) REVERT: D 607 MET cc_start: 0.8700 (tmm) cc_final: 0.8454 (ptp) REVERT: D 817 TYR cc_start: 0.8410 (m-10) cc_final: 0.8105 (m-80) REVERT: D 1020 HIS cc_start: 0.7933 (m170) cc_final: 0.7582 (m170) REVERT: D 1109 LEU cc_start: 0.9485 (mt) cc_final: 0.9200 (mt) REVERT: D 1132 TRP cc_start: 0.7218 (t-100) cc_final: 0.6830 (t-100) REVERT: D 1293 ASP cc_start: 0.9613 (m-30) cc_final: 0.8926 (m-30) REVERT: D 1299 LEU cc_start: 0.9512 (mm) cc_final: 0.9251 (mt) REVERT: D 1328 LEU cc_start: 0.9153 (tt) cc_final: 0.8667 (tt) REVERT: D 1330 TYR cc_start: 0.9269 (p90) cc_final: 0.8819 (p90) REVERT: D 1401 ARG cc_start: 0.9113 (tpp-160) cc_final: 0.8887 (mmm160) REVERT: D 1431 PHE cc_start: 0.8718 (p90) cc_final: 0.8438 (p90) outliers start: 18 outliers final: 5 residues processed: 680 average time/residue: 0.2684 time to fit residues: 300.7850 Evaluate side-chains 503 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 496 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 57 optimal weight: 20.0000 chunk 492 optimal weight: 7.9990 chunk 491 optimal weight: 9.9990 chunk 479 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 846 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 GLN ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 846 HIS C 917 ASN C 938 ASN C1062 HIS ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.092350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068117 restraints weight = 288464.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.069964 restraints weight = 222287.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.071382 restraints weight = 181693.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072448 restraints weight = 154888.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.073334 restraints weight = 136389.545| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43672 Z= 0.231 Angle : 0.913 13.555 59452 Z= 0.459 Chirality : 0.052 0.381 6900 Planarity : 0.006 0.089 7554 Dihedral : 7.658 37.382 5740 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.38 % Favored : 85.43 % Rotamer: Outliers : 0.51 % Allowed : 7.23 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.10), residues: 5360 helix: -1.51 (0.16), residues: 812 sheet: -2.75 (0.12), residues: 1478 loop : -3.55 (0.09), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1053 TYR 0.039 0.003 TYR D1418 PHE 0.040 0.003 PHE D1049 TRP 0.033 0.003 TRP B1183 HIS 0.014 0.002 HIS D1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (43574) covalent geometry : angle 0.89077 / 0.45 (59204) SS BOND : bond 0.00880 / 0.51 ( 46) SS BOND : angle 2.02222 / 1.25 ( 92) hydrogen bonds : bond 0.06686 / 4.44 ( 482) hydrogen bonds : angle 6.39939 / 4.37 ( 1446) link_ALPHA1-6 : bond 0.00537 / 0.27 ( 4) link_ALPHA1-6 : angle 1.49506 / 0.90 ( 12) link_BETA1-4 : bond 0.00972 / 0.58 ( 18) link_BETA1-4 : angle 2.57367 / 1.74 ( 54) link_NAG-ASN : bond 0.00986 / 0.60 ( 30) link_NAG-ASN : angle 4.52364 / 2.89 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 603 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6619 (p0) cc_final: 0.4940 (t0) REVERT: A 121 MET cc_start: 0.9453 (pmm) cc_final: 0.9229 (pmm) REVERT: A 166 TYR cc_start: 0.8475 (p90) cc_final: 0.8254 (p90) REVERT: A 192 PHE cc_start: 0.7805 (t80) cc_final: 0.7391 (t80) REVERT: A 356 ASP cc_start: 0.8899 (t0) cc_final: 0.8673 (t0) REVERT: A 464 MET cc_start: 0.7967 (mtt) cc_final: 0.7412 (mtt) REVERT: A 520 MET cc_start: 0.8972 (ptp) cc_final: 0.8601 (tmm) REVERT: A 931 LEU cc_start: 0.9315 (tt) cc_final: 0.8760 (mp) REVERT: A 968 MET cc_start: 0.3210 (mmt) cc_final: 0.2889 (mmt) REVERT: A 1003 LYS cc_start: 0.8575 (tptp) cc_final: 0.8272 (tppt) REVERT: A 1015 GLN cc_start: 0.9252 (tp40) cc_final: 0.8923 (tp40) REVERT: A 1122 ARG cc_start: 0.9019 (ttp-110) cc_final: 0.8619 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6649 (tt) cc_final: 0.6252 (tt) REVERT: B 151 MET cc_start: 0.8998 (mtp) cc_final: 0.8371 (mpp) REVERT: B 169 ASP cc_start: 0.8944 (t0) cc_final: 0.8614 (t70) REVERT: B 194 LEU cc_start: 0.9599 (mt) cc_final: 0.9262 (tp) REVERT: B 214 ARG cc_start: 0.9369 (mtt180) cc_final: 0.9109 (mtm-85) REVERT: B 370 ARG cc_start: 0.9177 (ptm160) cc_final: 0.8851 (ptm160) REVERT: B 552 ILE cc_start: 0.8632 (mm) cc_final: 0.8160 (mm) REVERT: B 569 ASP cc_start: 0.8683 (t0) cc_final: 0.8475 (p0) REVERT: B 571 SER cc_start: 0.9126 (t) cc_final: 0.8716 (p) REVERT: B 804 ARG cc_start: 0.5564 (tpm170) cc_final: 0.5302 (tpm170) REVERT: B 817 TYR cc_start: 0.8250 (m-10) cc_final: 0.8030 (m-80) REVERT: B 1007 TYR cc_start: 0.9388 (m-10) cc_final: 0.9183 (m-80) REVERT: B 1020 HIS cc_start: 0.7636 (m170) cc_final: 0.7424 (m170) REVERT: B 1109 LEU cc_start: 0.9595 (mt) cc_final: 0.9351 (mt) REVERT: B 1132 TRP cc_start: 0.7203 (t-100) cc_final: 0.6676 (t-100) REVERT: B 1291 GLN cc_start: 0.8744 (pp30) cc_final: 0.8172 (pp30) REVERT: B 1293 ASP cc_start: 0.9512 (m-30) cc_final: 0.8869 (m-30) REVERT: B 1298 LEU cc_start: 0.9537 (pt) cc_final: 0.9322 (mt) REVERT: B 1299 LEU cc_start: 0.9519 (mm) cc_final: 0.9276 (mt) REVERT: C 55 ASN cc_start: 0.6624 (p0) cc_final: 0.4944 (t0) REVERT: C 121 MET cc_start: 0.9453 (pmm) cc_final: 0.9228 (pmm) REVERT: C 166 TYR cc_start: 0.8472 (p90) cc_final: 0.8251 (p90) REVERT: C 192 PHE cc_start: 0.7801 (t80) cc_final: 0.7387 (t80) REVERT: C 356 ASP cc_start: 0.8896 (t0) cc_final: 0.8672 (t0) REVERT: C 464 MET cc_start: 0.7975 (mtt) cc_final: 0.7422 (mtt) REVERT: C 917 ASN cc_start: 0.5833 (OUTLIER) cc_final: 0.4857 (p0) REVERT: C 931 LEU cc_start: 0.9319 (tt) cc_final: 0.8728 (mp) REVERT: C 968 MET cc_start: 0.3181 (mmt) cc_final: 0.2864 (mmt) REVERT: C 1003 LYS cc_start: 0.8572 (tptp) cc_final: 0.8270 (tppt) REVERT: C 1122 ARG cc_start: 0.9018 (ttp-110) cc_final: 0.8620 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6635 (tt) cc_final: 0.6233 (tt) REVERT: D 151 MET cc_start: 0.9007 (mtp) cc_final: 0.8383 (mpp) REVERT: D 169 ASP cc_start: 0.8945 (t0) cc_final: 0.8619 (t70) REVERT: D 194 LEU cc_start: 0.9598 (mt) cc_final: 0.9254 (tp) REVERT: D 214 ARG cc_start: 0.9371 (mtt180) cc_final: 0.9110 (mtm-85) REVERT: D 370 ARG cc_start: 0.9176 (ptm160) cc_final: 0.8848 (ptm160) REVERT: D 552 ILE cc_start: 0.8628 (mm) cc_final: 0.8152 (mm) REVERT: D 569 ASP cc_start: 0.8687 (t0) cc_final: 0.8480 (p0) REVERT: D 571 SER cc_start: 0.9127 (t) cc_final: 0.8716 (p) REVERT: D 804 ARG cc_start: 0.5550 (tpm170) cc_final: 0.5296 (tpm170) REVERT: D 817 TYR cc_start: 0.8246 (m-10) cc_final: 0.8029 (m-80) REVERT: D 1007 TYR cc_start: 0.9381 (m-10) cc_final: 0.9155 (m-80) REVERT: D 1109 LEU cc_start: 0.9589 (mt) cc_final: 0.9343 (mt) REVERT: D 1291 GLN cc_start: 0.8745 (pp30) cc_final: 0.8168 (pp30) REVERT: D 1293 ASP cc_start: 0.9510 (m-30) cc_final: 0.8868 (m-30) REVERT: D 1298 LEU cc_start: 0.9537 (pt) cc_final: 0.9321 (mt) REVERT: D 1299 LEU cc_start: 0.9521 (mm) cc_final: 0.9281 (mt) outliers start: 24 outliers final: 9 residues processed: 624 average time/residue: 0.2647 time to fit residues: 272.9540 Evaluate side-chains 483 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 473 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 72 optimal weight: 9.9990 chunk 242 optimal weight: 0.2980 chunk 306 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 119 optimal weight: 6.9990 chunk 193 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 203 optimal weight: 0.5980 chunk 467 optimal weight: 6.9990 chunk 449 optimal weight: 1.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN A 938 ASN A1062 HIS A1159 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 168 GLN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1414 HIS ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN C 938 ASN C1062 HIS C1159 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 168 GLN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1414 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.099492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074192 restraints weight = 282733.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.076358 restraints weight = 214129.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078030 restraints weight = 172864.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.079320 restraints weight = 145961.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080298 restraints weight = 127547.250| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43672 Z= 0.149 Angle : 0.848 16.328 59452 Z= 0.412 Chirality : 0.051 0.389 6900 Planarity : 0.006 0.074 7554 Dihedral : 7.004 37.901 5740 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.90 % Favored : 87.99 % Rotamer: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.10), residues: 5360 helix: -1.03 (0.17), residues: 810 sheet: -2.39 (0.12), residues: 1462 loop : -3.40 (0.09), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 598 TYR 0.030 0.002 TYR C1152 PHE 0.040 0.002 PHE B1049 TRP 0.024 0.002 TRP C1040 HIS 0.013 0.001 HIS D1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (43574) covalent geometry : angle 0.81965 / 0.41 (59204) SS BOND : bond 0.00553 / 0.32 ( 46) SS BOND : angle 1.71640 / 1.03 ( 92) hydrogen bonds : bond 0.05886 / 3.91 ( 482) hydrogen bonds : angle 5.92128 / 4.05 ( 1446) link_ALPHA1-6 : bond 0.00538 / 0.27 ( 4) link_ALPHA1-6 : angle 1.42537 / 0.84 ( 12) link_BETA1-4 : bond 0.00890 / 0.52 ( 18) link_BETA1-4 : angle 2.64491 / 1.77 ( 54) link_NAG-ASN : bond 0.00777 / 0.42 ( 30) link_NAG-ASN : angle 5.00467 / 3.13 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 655 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8072 (tmtt) REVERT: A 34 LEU cc_start: 0.9515 (mt) cc_final: 0.9304 (mp) REVERT: A 55 ASN cc_start: 0.6527 (p0) cc_final: 0.4783 (t0) REVERT: A 84 LEU cc_start: 0.7955 (tt) cc_final: 0.7681 (tp) REVERT: A 151 MET cc_start: 0.8936 (ttm) cc_final: 0.8515 (tpp) REVERT: A 191 SER cc_start: 0.7902 (t) cc_final: 0.7618 (t) REVERT: A 310 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8565 (tp-100) REVERT: A 356 ASP cc_start: 0.8938 (t0) cc_final: 0.8716 (t0) REVERT: A 373 ASP cc_start: 0.9354 (p0) cc_final: 0.8902 (m-30) REVERT: A 464 MET cc_start: 0.8038 (mtt) cc_final: 0.7374 (mtt) REVERT: A 562 ASN cc_start: 0.7648 (t0) cc_final: 0.7241 (t0) REVERT: A 673 MET cc_start: 0.9060 (mpp) cc_final: 0.8696 (mpp) REVERT: A 917 ASN cc_start: 0.5168 (OUTLIER) cc_final: 0.4274 (p0) REVERT: A 931 LEU cc_start: 0.9033 (tt) cc_final: 0.8488 (mp) REVERT: A 968 MET cc_start: 0.2723 (mmt) cc_final: 0.2441 (mmt) REVERT: A 1003 LYS cc_start: 0.8468 (tptp) cc_final: 0.8161 (tppt) REVERT: A 1122 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8717 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6279 (tt) cc_final: 0.5940 (pp) REVERT: B 145 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7496 (ttpt) REVERT: B 151 MET cc_start: 0.9023 (mtp) cc_final: 0.8772 (ttt) REVERT: B 169 ASP cc_start: 0.8345 (t0) cc_final: 0.7862 (t70) REVERT: B 300 PHE cc_start: 0.8690 (t80) cc_final: 0.8098 (t80) REVERT: B 370 ARG cc_start: 0.9218 (ptm160) cc_final: 0.8947 (ptm160) REVERT: B 495 PHE cc_start: 0.7234 (m-80) cc_final: 0.6724 (m-80) REVERT: B 500 MET cc_start: 0.2530 (mmm) cc_final: 0.2199 (mmm) REVERT: B 546 LEU cc_start: 0.9016 (tp) cc_final: 0.8802 (tp) REVERT: B 552 ILE cc_start: 0.8455 (mm) cc_final: 0.8147 (mm) REVERT: B 741 TRP cc_start: 0.7928 (t-100) cc_final: 0.7069 (t-100) REVERT: B 804 ARG cc_start: 0.4897 (tpm170) cc_final: 0.4636 (tpm170) REVERT: B 817 TYR cc_start: 0.8204 (m-10) cc_final: 0.7977 (m-80) REVERT: B 1080 PHE cc_start: 0.6913 (p90) cc_final: 0.6596 (p90) REVERT: B 1109 LEU cc_start: 0.9528 (mt) cc_final: 0.9252 (mt) REVERT: B 1132 TRP cc_start: 0.7253 (t-100) cc_final: 0.6720 (t-100) REVERT: B 1150 LEU cc_start: 0.8833 (mt) cc_final: 0.8592 (mt) REVERT: B 1168 LYS cc_start: 0.9505 (tptt) cc_final: 0.8637 (tptt) REVERT: B 1293 ASP cc_start: 0.9486 (m-30) cc_final: 0.9157 (m-30) REVERT: B 1299 LEU cc_start: 0.9495 (mm) cc_final: 0.9263 (mt) REVERT: B 1330 TYR cc_start: 0.9308 (p90) cc_final: 0.9035 (p90) REVERT: B 1353 ASP cc_start: 0.8125 (m-30) cc_final: 0.7680 (p0) REVERT: B 1389 PHE cc_start: 0.8997 (m-80) cc_final: 0.8391 (m-80) REVERT: B 1431 PHE cc_start: 0.8653 (p90) cc_final: 0.8381 (p90) REVERT: C 28 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8084 (tmtt) REVERT: C 34 LEU cc_start: 0.9521 (mt) cc_final: 0.9309 (mp) REVERT: C 55 ASN cc_start: 0.6533 (p0) cc_final: 0.4790 (t0) REVERT: C 84 LEU cc_start: 0.7961 (tt) cc_final: 0.7685 (tp) REVERT: C 151 MET cc_start: 0.8916 (ttm) cc_final: 0.8494 (tpp) REVERT: C 191 SER cc_start: 0.7897 (t) cc_final: 0.7611 (t) REVERT: C 310 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8558 (tp-100) REVERT: C 356 ASP cc_start: 0.8929 (t0) cc_final: 0.8711 (t0) REVERT: C 373 ASP cc_start: 0.9350 (p0) cc_final: 0.8895 (m-30) REVERT: C 464 MET cc_start: 0.8049 (mtt) cc_final: 0.7387 (mtt) REVERT: C 562 ASN cc_start: 0.7649 (t0) cc_final: 0.7240 (t0) REVERT: C 673 MET cc_start: 0.9058 (mpp) cc_final: 0.8698 (mpp) REVERT: C 917 ASN cc_start: 0.5325 (OUTLIER) cc_final: 0.4424 (p0) REVERT: C 931 LEU cc_start: 0.9059 (tt) cc_final: 0.8521 (mp) REVERT: C 968 MET cc_start: 0.2699 (mmt) cc_final: 0.2417 (mmt) REVERT: C 1003 LYS cc_start: 0.8460 (tptp) cc_final: 0.8156 (tppt) REVERT: C 1122 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8718 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6266 (tt) cc_final: 0.5930 (pp) REVERT: D 151 MET cc_start: 0.9032 (mtp) cc_final: 0.8765 (ttt) REVERT: D 169 ASP cc_start: 0.8342 (t0) cc_final: 0.7856 (t70) REVERT: D 300 PHE cc_start: 0.8691 (t80) cc_final: 0.8102 (t80) REVERT: D 370 ARG cc_start: 0.9216 (ptm160) cc_final: 0.8944 (ptm160) REVERT: D 495 PHE cc_start: 0.7247 (m-80) cc_final: 0.6740 (m-80) REVERT: D 500 MET cc_start: 0.2515 (mmm) cc_final: 0.2176 (mmm) REVERT: D 546 LEU cc_start: 0.9021 (tp) cc_final: 0.8807 (tp) REVERT: D 552 ILE cc_start: 0.8464 (mm) cc_final: 0.8158 (mm) REVERT: D 804 ARG cc_start: 0.4915 (tpm170) cc_final: 0.4652 (tpm170) REVERT: D 817 TYR cc_start: 0.8199 (m-10) cc_final: 0.7976 (m-80) REVERT: D 1019 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8414 (tttt) REVERT: D 1020 HIS cc_start: 0.7492 (m170) cc_final: 0.7199 (m170) REVERT: D 1098 GLU cc_start: 0.9473 (pp20) cc_final: 0.9083 (tm-30) REVERT: D 1109 LEU cc_start: 0.9524 (mt) cc_final: 0.9245 (mt) REVERT: D 1132 TRP cc_start: 0.7208 (t-100) cc_final: 0.6588 (t-100) REVERT: D 1150 LEU cc_start: 0.8968 (mt) cc_final: 0.8724 (mt) REVERT: D 1168 LYS cc_start: 0.9507 (tptt) cc_final: 0.8632 (tptt) REVERT: D 1293 ASP cc_start: 0.9495 (m-30) cc_final: 0.9172 (m-30) REVERT: D 1299 LEU cc_start: 0.9491 (mm) cc_final: 0.9255 (mt) REVERT: D 1330 TYR cc_start: 0.9310 (p90) cc_final: 0.9028 (p90) REVERT: D 1353 ASP cc_start: 0.8134 (m-30) cc_final: 0.7685 (p0) REVERT: D 1389 PHE cc_start: 0.8986 (m-80) cc_final: 0.8366 (m-80) REVERT: D 1431 PHE cc_start: 0.8641 (p90) cc_final: 0.8378 (p90) outliers start: 5 outliers final: 1 residues processed: 657 average time/residue: 0.2503 time to fit residues: 273.6310 Evaluate side-chains 507 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 248 optimal weight: 0.0670 chunk 419 optimal weight: 20.0000 chunk 185 optimal weight: 0.0770 chunk 199 optimal weight: 10.0000 chunk 534 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 461 optimal weight: 7.9990 chunk 455 optimal weight: 0.1980 chunk 232 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 917 ASN A 938 ASN A 975 GLN A1062 HIS A1077 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 917 ASN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN C 938 ASN C 975 GLN C1062 HIS C1077 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 303 GLN D 917 ASN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.130964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.117604 restraints weight = 271296.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.119628 restraints weight = 184548.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.121106 restraints weight = 136844.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.122158 restraints weight = 107010.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.122921 restraints weight = 87934.611| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43672 Z= 0.141 Angle : 0.801 13.576 59452 Z= 0.391 Chirality : 0.050 0.393 6900 Planarity : 0.006 0.115 7554 Dihedral : 6.604 38.426 5740 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.83 % Favored : 88.06 % Rotamer: Outliers : 0.19 % Allowed : 3.40 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.10), residues: 5360 helix: -0.94 (0.17), residues: 800 sheet: -2.23 (0.13), residues: 1470 loop : -3.31 (0.10), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 732 TYR 0.042 0.002 TYR D1418 PHE 0.021 0.001 PHE B 980 TRP 0.018 0.002 TRP A1040 HIS 0.016 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (43574) covalent geometry : angle 0.77776 / 0.39 (59204) SS BOND : bond 0.00530 / 0.33 ( 46) SS BOND : angle 1.73960 / 1.02 ( 92) hydrogen bonds : bond 0.05884 / 3.93 ( 482) hydrogen bonds : angle 5.83733 / 3.96 ( 1446) link_ALPHA1-6 : bond 0.00494 / 0.25 ( 4) link_ALPHA1-6 : angle 1.45585 / 0.87 ( 12) link_BETA1-4 : bond 0.00972 / 0.55 ( 18) link_BETA1-4 : angle 2.48710 / 1.67 ( 54) link_NAG-ASN : bond 0.00804 / 0.44 ( 30) link_NAG-ASN : angle 4.28877 / 2.67 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 642 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9455 (mt) cc_final: 0.9230 (mp) REVERT: A 39 LEU cc_start: 0.9328 (pp) cc_final: 0.9078 (pt) REVERT: A 55 ASN cc_start: 0.6773 (p0) cc_final: 0.4941 (t0) REVERT: A 151 MET cc_start: 0.8847 (ttm) cc_final: 0.8219 (tpp) REVERT: A 310 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8598 (tp-100) REVERT: A 356 ASP cc_start: 0.9039 (t0) cc_final: 0.8830 (t0) REVERT: A 373 ASP cc_start: 0.9332 (p0) cc_final: 0.8861 (m-30) REVERT: A 464 MET cc_start: 0.8226 (mtt) cc_final: 0.7511 (mtt) REVERT: A 562 ASN cc_start: 0.7548 (t0) cc_final: 0.7123 (t0) REVERT: A 576 GLN cc_start: 0.3863 (OUTLIER) cc_final: 0.3209 (pp30) REVERT: A 917 ASN cc_start: 0.3761 (OUTLIER) cc_final: 0.3095 (p0) REVERT: A 931 LEU cc_start: 0.9046 (tt) cc_final: 0.8568 (mp) REVERT: A 1122 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8596 (tmm-80) REVERT: A 1214 LEU cc_start: 0.7251 (tt) cc_final: 0.6924 (pp) REVERT: B 145 LYS cc_start: 0.7932 (ptmt) cc_final: 0.7617 (ttpt) REVERT: B 151 MET cc_start: 0.9010 (mtp) cc_final: 0.8768 (ttt) REVERT: B 303 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: B 415 MET cc_start: 0.6699 (ttp) cc_final: 0.6226 (tmm) REVERT: B 495 PHE cc_start: 0.7119 (m-80) cc_final: 0.6659 (m-80) REVERT: B 552 ILE cc_start: 0.8259 (mm) cc_final: 0.7829 (mm) REVERT: B 741 TRP cc_start: 0.7945 (t-100) cc_final: 0.6935 (t-100) REVERT: B 804 ARG cc_start: 0.4870 (tpm170) cc_final: 0.4596 (tpm170) REVERT: B 1109 LEU cc_start: 0.9413 (mt) cc_final: 0.9108 (mt) REVERT: B 1132 TRP cc_start: 0.6739 (t-100) cc_final: 0.6190 (t-100) REVERT: B 1145 TYR cc_start: 0.8281 (m-80) cc_final: 0.7170 (m-80) REVERT: B 1168 LYS cc_start: 0.9551 (tptt) cc_final: 0.8862 (tptt) REVERT: B 1208 MET cc_start: 0.9338 (ppp) cc_final: 0.9114 (ppp) REVERT: B 1328 LEU cc_start: 0.9228 (tt) cc_final: 0.9013 (tt) REVERT: B 1330 TYR cc_start: 0.9227 (p90) cc_final: 0.8979 (p90) REVERT: B 1353 ASP cc_start: 0.8272 (m-30) cc_final: 0.7741 (p0) REVERT: B 1389 PHE cc_start: 0.8991 (m-80) cc_final: 0.8411 (m-80) REVERT: B 1431 PHE cc_start: 0.8667 (p90) cc_final: 0.8379 (p90) REVERT: C 34 LEU cc_start: 0.9469 (mt) cc_final: 0.9253 (mp) REVERT: C 39 LEU cc_start: 0.9335 (pp) cc_final: 0.9082 (pt) REVERT: C 55 ASN cc_start: 0.6776 (p0) cc_final: 0.4942 (t0) REVERT: C 151 MET cc_start: 0.8842 (ttm) cc_final: 0.8221 (tpp) REVERT: C 310 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8598 (tp-100) REVERT: C 356 ASP cc_start: 0.9043 (t0) cc_final: 0.8831 (t0) REVERT: C 373 ASP cc_start: 0.9327 (p0) cc_final: 0.8857 (m-30) REVERT: C 464 MET cc_start: 0.8232 (mtt) cc_final: 0.7557 (mtt) REVERT: C 562 ASN cc_start: 0.7559 (t0) cc_final: 0.7154 (t0) REVERT: C 576 GLN cc_start: 0.3872 (OUTLIER) cc_final: 0.3216 (pp30) REVERT: C 917 ASN cc_start: 0.3806 (OUTLIER) cc_final: 0.3145 (p0) REVERT: C 931 LEU cc_start: 0.9040 (tt) cc_final: 0.8564 (mp) REVERT: C 1122 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8597 (tmm-80) REVERT: C 1214 LEU cc_start: 0.7250 (tt) cc_final: 0.6924 (pp) REVERT: D 151 MET cc_start: 0.8981 (mtp) cc_final: 0.8766 (ttt) REVERT: D 303 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: D 415 MET cc_start: 0.6694 (ttp) cc_final: 0.6223 (tmm) REVERT: D 495 PHE cc_start: 0.7123 (m-80) cc_final: 0.6654 (m-80) REVERT: D 552 ILE cc_start: 0.8257 (mm) cc_final: 0.7816 (mm) REVERT: D 804 ARG cc_start: 0.4874 (tpm170) cc_final: 0.4596 (tpm170) REVERT: D 1098 GLU cc_start: 0.9397 (pp20) cc_final: 0.8694 (tm-30) REVERT: D 1109 LEU cc_start: 0.9413 (mt) cc_final: 0.9112 (mt) REVERT: D 1132 TRP cc_start: 0.6777 (t-100) cc_final: 0.6177 (t-100) REVERT: D 1145 TYR cc_start: 0.8244 (m-80) cc_final: 0.7133 (m-80) REVERT: D 1168 LYS cc_start: 0.9539 (tptt) cc_final: 0.8784 (tptt) REVERT: D 1208 MET cc_start: 0.9348 (ppp) cc_final: 0.9081 (ppp) REVERT: D 1328 LEU cc_start: 0.9235 (tt) cc_final: 0.8633 (tt) REVERT: D 1330 TYR cc_start: 0.9257 (p90) cc_final: 0.8949 (p90) REVERT: D 1353 ASP cc_start: 0.8280 (m-30) cc_final: 0.7744 (p0) REVERT: D 1389 PHE cc_start: 0.8992 (m-80) cc_final: 0.8396 (m-80) REVERT: D 1431 PHE cc_start: 0.8645 (p90) cc_final: 0.8374 (p90) outliers start: 9 outliers final: 1 residues processed: 648 average time/residue: 0.2526 time to fit residues: 272.2554 Evaluate side-chains 517 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 510 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 324 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 535 optimal weight: 0.3980 chunk 472 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 319 optimal weight: 0.1980 chunk 492 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 438 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** B1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1435 GLN C 85 HIS ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS D 168 GLN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 HIS ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1435 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.095109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070343 restraints weight = 273061.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.072229 restraints weight = 210550.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073697 restraints weight = 172234.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.074836 restraints weight = 146815.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.075696 restraints weight = 129196.335| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43672 Z= 0.184 Angle : 0.836 12.524 59452 Z= 0.410 Chirality : 0.050 0.385 6900 Planarity : 0.006 0.073 7554 Dihedral : 6.644 37.676 5740 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.97 % Favored : 86.92 % Rotamer: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.10), residues: 5360 helix: -0.94 (0.17), residues: 824 sheet: -2.19 (0.13), residues: 1508 loop : -3.30 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1297 TYR 0.047 0.002 TYR B1145 PHE 0.039 0.002 PHE B1049 TRP 0.021 0.002 TRP B1183 HIS 0.022 0.002 HIS A1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (43574) covalent geometry : angle 0.80694 / 0.40 (59204) SS BOND : bond 0.00468 / 0.28 ( 46) SS BOND : angle 1.35210 / 0.81 ( 92) hydrogen bonds : bond 0.05925 / 3.89 ( 482) hydrogen bonds : angle 6.03071 / 4.11 ( 1446) link_ALPHA1-6 : bond 0.00474 / 0.24 ( 4) link_ALPHA1-6 : angle 1.46821 / 0.88 ( 12) link_BETA1-4 : bond 0.00937 / 0.54 ( 18) link_BETA1-4 : angle 2.54536 / 1.72 ( 54) link_NAG-ASN : bond 0.00920 / 0.56 ( 30) link_NAG-ASN : angle 5.22516 / 3.28 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 596 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6473 (p0) cc_final: 0.4937 (t0) REVERT: A 151 MET cc_start: 0.8875 (ttm) cc_final: 0.8192 (tpp) REVERT: A 356 ASP cc_start: 0.8977 (t0) cc_final: 0.8718 (t0) REVERT: A 373 ASP cc_start: 0.9457 (p0) cc_final: 0.8903 (m-30) REVERT: A 576 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4567 (pp30) REVERT: A 931 LEU cc_start: 0.9337 (tt) cc_final: 0.8804 (mp) REVERT: A 938 ASN cc_start: 0.7632 (t0) cc_final: 0.7328 (m-40) REVERT: A 1044 PHE cc_start: 0.9555 (m-80) cc_final: 0.9239 (m-80) REVERT: A 1086 LEU cc_start: 0.7459 (tp) cc_final: 0.6694 (tp) REVERT: A 1208 MET cc_start: 0.8934 (ppp) cc_final: 0.8636 (ppp) REVERT: A 1211 TYR cc_start: 0.8679 (m-80) cc_final: 0.8454 (m-80) REVERT: A 1214 LEU cc_start: 0.6519 (tt) cc_final: 0.6092 (pp) REVERT: B 101 MET cc_start: 0.8697 (ttt) cc_final: 0.7952 (ttt) REVERT: B 151 MET cc_start: 0.9078 (mtp) cc_final: 0.8711 (ttm) REVERT: B 318 MET cc_start: 0.6849 (ppp) cc_final: 0.6482 (ppp) REVERT: B 415 MET cc_start: 0.7117 (ttp) cc_final: 0.5917 (tmm) REVERT: B 495 PHE cc_start: 0.7257 (m-80) cc_final: 0.6897 (m-80) REVERT: B 500 MET cc_start: 0.4300 (mmm) cc_final: 0.3998 (mmm) REVERT: B 1044 PHE cc_start: 0.8460 (t80) cc_final: 0.8081 (t80) REVERT: B 1106 THR cc_start: 0.9540 (p) cc_final: 0.9255 (p) REVERT: B 1109 LEU cc_start: 0.9499 (mt) cc_final: 0.9261 (mt) REVERT: B 1145 TYR cc_start: 0.8531 (m-80) cc_final: 0.8118 (m-80) REVERT: B 1168 LYS cc_start: 0.9561 (tptt) cc_final: 0.9215 (tptt) REVERT: B 1328 LEU cc_start: 0.9348 (tt) cc_final: 0.8975 (tt) REVERT: B 1330 TYR cc_start: 0.9397 (p90) cc_final: 0.9119 (p90) REVERT: B 1353 ASP cc_start: 0.8092 (m-30) cc_final: 0.7624 (p0) REVERT: B 1389 PHE cc_start: 0.8889 (m-80) cc_final: 0.8350 (m-80) REVERT: C 55 ASN cc_start: 0.6497 (p0) cc_final: 0.4950 (t0) REVERT: C 151 MET cc_start: 0.8877 (ttm) cc_final: 0.8195 (tpp) REVERT: C 356 ASP cc_start: 0.8995 (t0) cc_final: 0.8735 (t0) REVERT: C 373 ASP cc_start: 0.9462 (p0) cc_final: 0.8893 (m-30) REVERT: C 576 GLN cc_start: 0.4940 (OUTLIER) cc_final: 0.4471 (pp30) REVERT: C 917 ASN cc_start: 0.5206 (OUTLIER) cc_final: 0.4073 (p0) REVERT: C 931 LEU cc_start: 0.9355 (tt) cc_final: 0.8794 (mp) REVERT: C 938 ASN cc_start: 0.7633 (t0) cc_final: 0.7328 (m-40) REVERT: C 1044 PHE cc_start: 0.9557 (m-80) cc_final: 0.9240 (m-80) REVERT: C 1086 LEU cc_start: 0.7507 (tp) cc_final: 0.6750 (tp) REVERT: C 1208 MET cc_start: 0.8924 (ppp) cc_final: 0.8629 (ppp) REVERT: C 1211 TYR cc_start: 0.8646 (m-80) cc_final: 0.8416 (m-80) REVERT: C 1214 LEU cc_start: 0.6514 (tt) cc_final: 0.6083 (pp) REVERT: D 101 MET cc_start: 0.8704 (ttt) cc_final: 0.7959 (ttt) REVERT: D 151 MET cc_start: 0.9076 (mtp) cc_final: 0.8752 (ttm) REVERT: D 318 MET cc_start: 0.6853 (ppp) cc_final: 0.6488 (ppp) REVERT: D 415 MET cc_start: 0.7085 (ttp) cc_final: 0.6384 (tmm) REVERT: D 495 PHE cc_start: 0.7271 (m-80) cc_final: 0.6907 (m-80) REVERT: D 500 MET cc_start: 0.4295 (mmm) cc_final: 0.3989 (mmm) REVERT: D 597 LEU cc_start: 0.8900 (mp) cc_final: 0.8657 (mp) REVERT: D 741 TRP cc_start: 0.7785 (t-100) cc_final: 0.7560 (t-100) REVERT: D 1044 PHE cc_start: 0.8527 (t80) cc_final: 0.8225 (t80) REVERT: D 1098 GLU cc_start: 0.9407 (pp20) cc_final: 0.8991 (tm-30) REVERT: D 1106 THR cc_start: 0.9514 (p) cc_final: 0.9224 (p) REVERT: D 1109 LEU cc_start: 0.9485 (mt) cc_final: 0.9237 (mt) REVERT: D 1145 TYR cc_start: 0.8553 (m-80) cc_final: 0.7991 (m-80) REVERT: D 1330 TYR cc_start: 0.9427 (p90) cc_final: 0.9208 (p90) REVERT: D 1353 ASP cc_start: 0.8099 (m-30) cc_final: 0.7629 (p0) REVERT: D 1389 PHE cc_start: 0.8904 (m-80) cc_final: 0.8359 (m-80) outliers start: 4 outliers final: 1 residues processed: 599 average time/residue: 0.2405 time to fit residues: 241.7854 Evaluate side-chains 467 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 463 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 382 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 350 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 646 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 646 HIS C 917 ASN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.095521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.070500 restraints weight = 271998.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.072519 restraints weight = 208141.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073978 restraints weight = 168991.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.075149 restraints weight = 143801.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076045 restraints weight = 126276.535| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43672 Z= 0.159 Angle : 0.801 12.965 59452 Z= 0.393 Chirality : 0.050 0.380 6900 Planarity : 0.005 0.065 7554 Dihedral : 6.619 37.109 5740 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.19 % Favored : 86.70 % Rotamer: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.10), residues: 5360 helix: -0.92 (0.17), residues: 834 sheet: -2.11 (0.13), residues: 1488 loop : -3.26 (0.10), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1297 TYR 0.042 0.002 TYR D1216 PHE 0.041 0.002 PHE D1049 TRP 0.051 0.003 TRP A 739 HIS 0.014 0.001 HIS D1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (43574) covalent geometry : angle 0.77758 / 0.39 (59204) SS BOND : bond 0.00657 / 0.39 ( 46) SS BOND : angle 1.55881 / 0.98 ( 92) hydrogen bonds : bond 0.05710 / 3.75 ( 482) hydrogen bonds : angle 5.95158 / 4.06 ( 1446) link_ALPHA1-6 : bond 0.00478 / 0.24 ( 4) link_ALPHA1-6 : angle 1.45841 / 0.87 ( 12) link_BETA1-4 : bond 0.01001 / 0.56 ( 18) link_BETA1-4 : angle 2.42963 / 1.64 ( 54) link_NAG-ASN : bond 0.00854 / 0.50 ( 30) link_NAG-ASN : angle 4.50239 / 2.83 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 589 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6512 (p0) cc_final: 0.4854 (t0) REVERT: A 151 MET cc_start: 0.8946 (ttm) cc_final: 0.8193 (tpp) REVERT: A 356 ASP cc_start: 0.8979 (t0) cc_final: 0.8723 (t0) REVERT: A 373 ASP cc_start: 0.9435 (p0) cc_final: 0.8945 (m-30) REVERT: A 464 MET cc_start: 0.8072 (mtt) cc_final: 0.7592 (mtt) REVERT: A 576 GLN cc_start: 0.5262 (OUTLIER) cc_final: 0.4867 (pp30) REVERT: A 931 LEU cc_start: 0.9255 (tt) cc_final: 0.8737 (mp) REVERT: A 938 ASN cc_start: 0.7734 (t0) cc_final: 0.7386 (m-40) REVERT: A 975 GLN cc_start: 0.7847 (mm110) cc_final: 0.7636 (mm-40) REVERT: A 1214 LEU cc_start: 0.6467 (tt) cc_final: 0.6066 (pp) REVERT: B 101 MET cc_start: 0.8500 (ttt) cc_final: 0.7790 (ttt) REVERT: B 151 MET cc_start: 0.9102 (mtp) cc_final: 0.8683 (ttm) REVERT: B 318 MET cc_start: 0.6768 (ppp) cc_final: 0.6472 (ppp) REVERT: B 415 MET cc_start: 0.7068 (ttp) cc_final: 0.6004 (tmm) REVERT: B 495 PHE cc_start: 0.7383 (m-80) cc_final: 0.7049 (m-80) REVERT: B 552 ILE cc_start: 0.8549 (mm) cc_final: 0.8136 (mm) REVERT: B 1044 PHE cc_start: 0.8499 (t80) cc_final: 0.8025 (t80) REVERT: B 1106 THR cc_start: 0.9549 (p) cc_final: 0.9287 (p) REVERT: B 1109 LEU cc_start: 0.9542 (mt) cc_final: 0.9303 (mt) REVERT: B 1132 TRP cc_start: 0.7315 (t-100) cc_final: 0.7110 (t60) REVERT: B 1145 TYR cc_start: 0.8274 (m-80) cc_final: 0.7951 (m-80) REVERT: B 1168 LYS cc_start: 0.9545 (tptt) cc_final: 0.9325 (tptp) REVERT: B 1328 LEU cc_start: 0.9335 (tt) cc_final: 0.9085 (tt) REVERT: B 1330 TYR cc_start: 0.9372 (p90) cc_final: 0.9103 (p90) REVERT: B 1353 ASP cc_start: 0.7940 (m-30) cc_final: 0.7550 (p0) REVERT: B 1389 PHE cc_start: 0.8840 (m-80) cc_final: 0.8279 (m-80) REVERT: C 55 ASN cc_start: 0.6543 (p0) cc_final: 0.4883 (t0) REVERT: C 151 MET cc_start: 0.8946 (ttm) cc_final: 0.8186 (tpp) REVERT: C 356 ASP cc_start: 0.8992 (t0) cc_final: 0.8736 (t0) REVERT: C 373 ASP cc_start: 0.9434 (p0) cc_final: 0.8944 (m-30) REVERT: C 464 MET cc_start: 0.8136 (mtt) cc_final: 0.7674 (mtt) REVERT: C 520 MET cc_start: 0.8515 (mmm) cc_final: 0.8121 (mmm) REVERT: C 576 GLN cc_start: 0.5202 (OUTLIER) cc_final: 0.4805 (pp30) REVERT: C 917 ASN cc_start: 0.5299 (OUTLIER) cc_final: 0.4226 (p0) REVERT: C 931 LEU cc_start: 0.9261 (tt) cc_final: 0.8697 (mp) REVERT: C 938 ASN cc_start: 0.7735 (t0) cc_final: 0.7392 (m-40) REVERT: C 975 GLN cc_start: 0.7846 (mm110) cc_final: 0.7635 (mm-40) REVERT: C 1214 LEU cc_start: 0.6453 (tt) cc_final: 0.6049 (pp) REVERT: D 101 MET cc_start: 0.8506 (ttt) cc_final: 0.7795 (ttt) REVERT: D 151 MET cc_start: 0.9069 (mtp) cc_final: 0.8686 (ttm) REVERT: D 318 MET cc_start: 0.6785 (ppp) cc_final: 0.6483 (ppp) REVERT: D 385 PHE cc_start: 0.8302 (m-80) cc_final: 0.8094 (m-80) REVERT: D 415 MET cc_start: 0.7030 (ttp) cc_final: 0.5979 (tmm) REVERT: D 495 PHE cc_start: 0.7391 (m-80) cc_final: 0.7052 (m-80) REVERT: D 552 ILE cc_start: 0.8585 (mm) cc_final: 0.8170 (mm) REVERT: D 1044 PHE cc_start: 0.8568 (t80) cc_final: 0.8137 (t80) REVERT: D 1098 GLU cc_start: 0.9400 (pp20) cc_final: 0.8937 (tm-30) REVERT: D 1106 THR cc_start: 0.9506 (p) cc_final: 0.9238 (p) REVERT: D 1109 LEU cc_start: 0.9526 (mt) cc_final: 0.9281 (mt) REVERT: D 1145 TYR cc_start: 0.8382 (m-80) cc_final: 0.7996 (m-80) REVERT: D 1150 LEU cc_start: 0.9277 (mt) cc_final: 0.9047 (mm) REVERT: D 1353 ASP cc_start: 0.7946 (m-30) cc_final: 0.7555 (p0) REVERT: D 1389 PHE cc_start: 0.8869 (m-80) cc_final: 0.8297 (m-80) outliers start: 4 outliers final: 1 residues processed: 592 average time/residue: 0.2441 time to fit residues: 243.0749 Evaluate side-chains 464 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 460 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 298 optimal weight: 8.9990 chunk 492 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 333 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1159 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN C1062 HIS C1159 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.095022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.070063 restraints weight = 273848.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.072013 restraints weight = 208950.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073511 restraints weight = 169827.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074680 restraints weight = 144262.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.075580 restraints weight = 126577.384| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 43672 Z= 0.160 Angle : 0.804 13.698 59452 Z= 0.395 Chirality : 0.050 0.381 6900 Planarity : 0.005 0.063 7554 Dihedral : 6.581 37.416 5740 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.38 % Favored : 86.51 % Rotamer: Outliers : 0.09 % Allowed : 1.60 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.10), residues: 5360 helix: -0.94 (0.17), residues: 822 sheet: -2.02 (0.13), residues: 1436 loop : -3.20 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1401 TYR 0.043 0.002 TYR B1216 PHE 0.033 0.002 PHE B1049 TRP 0.074 0.003 TRP A 739 HIS 0.017 0.001 HIS D1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (43574) covalent geometry : angle 0.78228 / 0.39 (59204) SS BOND : bond 0.00551 / 0.33 ( 46) SS BOND : angle 1.58008 / 1.03 ( 92) hydrogen bonds : bond 0.05626 / 3.75 ( 482) hydrogen bonds : angle 6.06039 / 4.13 ( 1446) link_ALPHA1-6 : bond 0.00458 / 0.23 ( 4) link_ALPHA1-6 : angle 1.45977 / 0.87 ( 12) link_BETA1-4 : bond 0.01105 / 0.63 ( 18) link_BETA1-4 : angle 2.41266 / 1.65 ( 54) link_NAG-ASN : bond 0.00858 / 0.51 ( 30) link_NAG-ASN : angle 4.27432 / 2.68 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 589 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6875 (p0) cc_final: 0.5271 (t0) REVERT: A 151 MET cc_start: 0.8936 (ttm) cc_final: 0.8163 (tpp) REVERT: A 215 THR cc_start: 0.8701 (t) cc_final: 0.8396 (m) REVERT: A 356 ASP cc_start: 0.8983 (t0) cc_final: 0.8732 (t0) REVERT: A 373 ASP cc_start: 0.9462 (p0) cc_final: 0.8946 (m-30) REVERT: A 464 MET cc_start: 0.8035 (mtt) cc_final: 0.7557 (mtt) REVERT: A 576 GLN cc_start: 0.5184 (OUTLIER) cc_final: 0.4645 (pp30) REVERT: A 931 LEU cc_start: 0.9237 (tt) cc_final: 0.8692 (mp) REVERT: A 975 GLN cc_start: 0.7947 (mm110) cc_final: 0.7738 (mm-40) REVERT: A 1044 PHE cc_start: 0.9579 (m-10) cc_final: 0.9267 (m-80) REVERT: A 1208 MET cc_start: 0.8992 (ppp) cc_final: 0.8633 (ppp) REVERT: A 1211 TYR cc_start: 0.8728 (m-80) cc_final: 0.8402 (m-80) REVERT: A 1214 LEU cc_start: 0.6572 (tt) cc_final: 0.6166 (pp) REVERT: B 101 MET cc_start: 0.8554 (ttt) cc_final: 0.7840 (ttt) REVERT: B 151 MET cc_start: 0.9142 (mtp) cc_final: 0.8691 (ttm) REVERT: B 318 MET cc_start: 0.6984 (ppp) cc_final: 0.6687 (ppp) REVERT: B 371 LEU cc_start: 0.9238 (tp) cc_final: 0.8988 (tp) REVERT: B 385 PHE cc_start: 0.8339 (m-80) cc_final: 0.8116 (m-80) REVERT: B 415 MET cc_start: 0.7010 (ttp) cc_final: 0.5991 (tmm) REVERT: B 495 PHE cc_start: 0.7394 (m-80) cc_final: 0.7096 (m-80) REVERT: B 552 ILE cc_start: 0.8591 (mm) cc_final: 0.8210 (mm) REVERT: B 1044 PHE cc_start: 0.8623 (t80) cc_final: 0.8144 (t80) REVERT: B 1109 LEU cc_start: 0.9559 (mt) cc_final: 0.9285 (mt) REVERT: B 1145 TYR cc_start: 0.8294 (m-80) cc_final: 0.7976 (m-80) REVERT: B 1248 PHE cc_start: 0.7890 (t80) cc_final: 0.7324 (t80) REVERT: B 1328 LEU cc_start: 0.9393 (tt) cc_final: 0.9040 (tt) REVERT: B 1330 TYR cc_start: 0.9440 (p90) cc_final: 0.8863 (p90) REVERT: B 1353 ASP cc_start: 0.8095 (m-30) cc_final: 0.7615 (p0) REVERT: B 1389 PHE cc_start: 0.8771 (m-80) cc_final: 0.8240 (m-80) REVERT: C 55 ASN cc_start: 0.6870 (p0) cc_final: 0.5268 (t0) REVERT: C 151 MET cc_start: 0.8944 (ttm) cc_final: 0.8168 (tpp) REVERT: C 215 THR cc_start: 0.8706 (t) cc_final: 0.8404 (m) REVERT: C 356 ASP cc_start: 0.8998 (t0) cc_final: 0.8737 (t0) REVERT: C 373 ASP cc_start: 0.9446 (p0) cc_final: 0.8932 (m-30) REVERT: C 464 MET cc_start: 0.8037 (mtt) cc_final: 0.7559 (mtt) REVERT: C 520 MET cc_start: 0.8496 (mmm) cc_final: 0.8075 (mmm) REVERT: C 576 GLN cc_start: 0.5178 (OUTLIER) cc_final: 0.4639 (pp30) REVERT: C 917 ASN cc_start: 0.5071 (OUTLIER) cc_final: 0.4052 (p0) REVERT: C 931 LEU cc_start: 0.9262 (tt) cc_final: 0.8724 (mp) REVERT: C 975 GLN cc_start: 0.7943 (mm110) cc_final: 0.7733 (mm-40) REVERT: C 1044 PHE cc_start: 0.9579 (m-10) cc_final: 0.9270 (m-80) REVERT: C 1208 MET cc_start: 0.8992 (ppp) cc_final: 0.8633 (ppp) REVERT: C 1211 TYR cc_start: 0.8726 (m-80) cc_final: 0.8399 (m-80) REVERT: C 1214 LEU cc_start: 0.6567 (tt) cc_final: 0.6159 (pp) REVERT: D 101 MET cc_start: 0.8556 (ttt) cc_final: 0.7839 (ttt) REVERT: D 151 MET cc_start: 0.9136 (mtp) cc_final: 0.8701 (ttm) REVERT: D 318 MET cc_start: 0.6985 (ppp) cc_final: 0.6687 (ppp) REVERT: D 385 PHE cc_start: 0.8337 (m-80) cc_final: 0.8136 (m-80) REVERT: D 415 MET cc_start: 0.6982 (ttp) cc_final: 0.5973 (tmm) REVERT: D 490 LEU cc_start: 0.6895 (mt) cc_final: 0.6658 (mp) REVERT: D 495 PHE cc_start: 0.7401 (m-80) cc_final: 0.7099 (m-80) REVERT: D 552 ILE cc_start: 0.8600 (mm) cc_final: 0.8228 (mm) REVERT: D 558 TYR cc_start: 0.8910 (m-80) cc_final: 0.8681 (m-80) REVERT: D 597 LEU cc_start: 0.9045 (mp) cc_final: 0.8840 (mp) REVERT: D 1044 PHE cc_start: 0.8612 (t80) cc_final: 0.8173 (t80) REVERT: D 1109 LEU cc_start: 0.9529 (mt) cc_final: 0.9296 (mt) REVERT: D 1145 TYR cc_start: 0.8173 (m-80) cc_final: 0.7717 (m-80) REVERT: D 1168 LYS cc_start: 0.9532 (tptt) cc_final: 0.9231 (tptt) REVERT: D 1248 PHE cc_start: 0.7870 (t80) cc_final: 0.7250 (t80) REVERT: D 1330 TYR cc_start: 0.9459 (p90) cc_final: 0.9059 (p90) REVERT: D 1353 ASP cc_start: 0.8099 (m-30) cc_final: 0.7621 (p0) REVERT: D 1389 PHE cc_start: 0.8794 (m-80) cc_final: 0.8262 (m-80) REVERT: D 1431 PHE cc_start: 0.8594 (p90) cc_final: 0.8390 (p90) outliers start: 4 outliers final: 1 residues processed: 592 average time/residue: 0.2474 time to fit residues: 246.6980 Evaluate side-chains 467 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 463 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 55 optimal weight: 30.0000 chunk 390 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 440 optimal weight: 6.9990 chunk 399 optimal weight: 0.5980 chunk 250 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 479 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN D 566 ASN ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.067914 restraints weight = 276204.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.069768 restraints weight = 210697.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071240 restraints weight = 171655.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072361 restraints weight = 146095.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.073225 restraints weight = 128557.882| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 43672 Z= 0.187 Angle : 0.842 13.440 59452 Z= 0.414 Chirality : 0.051 0.379 6900 Planarity : 0.006 0.086 7554 Dihedral : 6.740 39.734 5740 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.20 % Favored : 85.69 % Rotamer: Outliers : 0.02 % Allowed : 0.94 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.10), residues: 5360 helix: -1.12 (0.16), residues: 834 sheet: -2.09 (0.13), residues: 1404 loop : -3.21 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 370 TYR 0.044 0.002 TYR B1216 PHE 0.041 0.002 PHE D1049 TRP 0.043 0.003 TRP A 739 HIS 0.019 0.002 HIS D1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (43574) covalent geometry : angle 0.82058 / 0.41 (59204) SS BOND : bond 0.00590 / 0.35 ( 46) SS BOND : angle 1.69438 / 1.10 ( 92) hydrogen bonds : bond 0.05700 / 3.80 ( 482) hydrogen bonds : angle 6.11718 / 4.17 ( 1446) link_ALPHA1-6 : bond 0.00455 / 0.23 ( 4) link_ALPHA1-6 : angle 1.48455 / 0.89 ( 12) link_BETA1-4 : bond 0.01070 / 0.60 ( 18) link_BETA1-4 : angle 2.39822 / 1.66 ( 54) link_NAG-ASN : bond 0.00866 / 0.52 ( 30) link_NAG-ASN : angle 4.28076 / 2.66 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 569 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 39 LEU cc_start: 0.9508 (pt) cc_final: 0.9301 (pt) REVERT: A 55 ASN cc_start: 0.6860 (p0) cc_final: 0.5328 (t0) REVERT: A 191 SER cc_start: 0.7337 (t) cc_final: 0.7131 (t) REVERT: A 215 THR cc_start: 0.8835 (t) cc_final: 0.8606 (m) REVERT: A 356 ASP cc_start: 0.8960 (t0) cc_final: 0.8677 (t0) REVERT: A 373 ASP cc_start: 0.9496 (p0) cc_final: 0.8994 (m-30) REVERT: A 464 MET cc_start: 0.8018 (mtt) cc_final: 0.7517 (mtt) REVERT: A 666 MET cc_start: 0.8958 (tpp) cc_final: 0.8570 (tpt) REVERT: A 931 LEU cc_start: 0.9238 (tt) cc_final: 0.8692 (mp) REVERT: A 975 GLN cc_start: 0.7960 (mm110) cc_final: 0.7742 (mm-40) REVERT: A 1044 PHE cc_start: 0.9665 (m-10) cc_final: 0.9303 (m-80) REVERT: A 1208 MET cc_start: 0.9003 (ppp) cc_final: 0.8645 (ppp) REVERT: A 1211 TYR cc_start: 0.8723 (m-80) cc_final: 0.8393 (m-80) REVERT: A 1214 LEU cc_start: 0.6606 (tt) cc_final: 0.6190 (pp) REVERT: B 101 MET cc_start: 0.8626 (ttt) cc_final: 0.7943 (ttt) REVERT: B 145 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7363 (mptt) REVERT: B 151 MET cc_start: 0.9184 (mtp) cc_final: 0.8700 (ttm) REVERT: B 223 GLU cc_start: 0.7822 (tp30) cc_final: 0.7527 (tp30) REVERT: B 318 MET cc_start: 0.7092 (ppp) cc_final: 0.6812 (ppp) REVERT: B 415 MET cc_start: 0.7162 (ttp) cc_final: 0.6514 (tmm) REVERT: B 495 PHE cc_start: 0.7473 (m-80) cc_final: 0.7203 (m-80) REVERT: B 500 MET cc_start: 0.4544 (mmm) cc_final: 0.3427 (mmt) REVERT: B 552 ILE cc_start: 0.8666 (mm) cc_final: 0.8279 (mm) REVERT: B 586 ARG cc_start: 0.8719 (ttt180) cc_final: 0.8094 (tpt170) REVERT: B 597 LEU cc_start: 0.8960 (mp) cc_final: 0.8694 (mp) REVERT: B 1044 PHE cc_start: 0.8571 (t80) cc_final: 0.8062 (t80) REVERT: B 1092 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9159 (mmmt) REVERT: B 1109 LEU cc_start: 0.9592 (mt) cc_final: 0.9314 (mt) REVERT: B 1248 PHE cc_start: 0.8033 (t80) cc_final: 0.7457 (t80) REVERT: B 1253 ASP cc_start: 0.8185 (m-30) cc_final: 0.7717 (m-30) REVERT: B 1330 TYR cc_start: 0.9459 (p90) cc_final: 0.9054 (p90) REVERT: B 1353 ASP cc_start: 0.8036 (m-30) cc_final: 0.7578 (p0) REVERT: B 1389 PHE cc_start: 0.8727 (m-80) cc_final: 0.8220 (m-80) REVERT: B 1395 THR cc_start: 0.8956 (p) cc_final: 0.8704 (p) REVERT: B 1431 PHE cc_start: 0.8585 (p90) cc_final: 0.8381 (p90) REVERT: C 39 LEU cc_start: 0.9505 (pt) cc_final: 0.9301 (pt) REVERT: C 55 ASN cc_start: 0.6882 (p0) cc_final: 0.5353 (t0) REVERT: C 191 SER cc_start: 0.7327 (t) cc_final: 0.7119 (t) REVERT: C 215 THR cc_start: 0.8825 (t) cc_final: 0.8594 (m) REVERT: C 356 ASP cc_start: 0.8954 (t0) cc_final: 0.8681 (t0) REVERT: C 373 ASP cc_start: 0.9483 (p0) cc_final: 0.8981 (m-30) REVERT: C 464 MET cc_start: 0.8012 (mtt) cc_final: 0.7512 (mtt) REVERT: C 520 MET cc_start: 0.8593 (mmm) cc_final: 0.8173 (mmm) REVERT: C 931 LEU cc_start: 0.9263 (tt) cc_final: 0.8738 (mp) REVERT: C 975 GLN cc_start: 0.7959 (mm110) cc_final: 0.7742 (mm-40) REVERT: C 1044 PHE cc_start: 0.9669 (m-10) cc_final: 0.9324 (m-80) REVERT: C 1208 MET cc_start: 0.9009 (ppp) cc_final: 0.8648 (ppp) REVERT: C 1211 TYR cc_start: 0.8721 (m-80) cc_final: 0.8384 (m-80) REVERT: C 1214 LEU cc_start: 0.6620 (tt) cc_final: 0.6208 (pp) REVERT: D 101 MET cc_start: 0.8625 (ttt) cc_final: 0.7939 (ttt) REVERT: D 151 MET cc_start: 0.9173 (mtp) cc_final: 0.8691 (ttm) REVERT: D 223 GLU cc_start: 0.7829 (tp30) cc_final: 0.7535 (tp30) REVERT: D 318 MET cc_start: 0.7092 (ppp) cc_final: 0.6812 (ppp) REVERT: D 370 ARG cc_start: 0.9190 (ptm160) cc_final: 0.8864 (ptm160) REVERT: D 415 MET cc_start: 0.7137 (ttp) cc_final: 0.6500 (tmm) REVERT: D 495 PHE cc_start: 0.7469 (m-80) cc_final: 0.7192 (m-80) REVERT: D 500 MET cc_start: 0.4493 (mmm) cc_final: 0.3372 (mmt) REVERT: D 552 ILE cc_start: 0.8631 (mm) cc_final: 0.8247 (mm) REVERT: D 558 TYR cc_start: 0.8931 (m-80) cc_final: 0.8684 (m-80) REVERT: D 586 ARG cc_start: 0.8718 (ttt180) cc_final: 0.8095 (tpt170) REVERT: D 597 LEU cc_start: 0.8969 (mp) cc_final: 0.8726 (mp) REVERT: D 1044 PHE cc_start: 0.8688 (t80) cc_final: 0.8203 (t80) REVERT: D 1106 THR cc_start: 0.9491 (p) cc_final: 0.9234 (p) REVERT: D 1109 LEU cc_start: 0.9566 (mt) cc_final: 0.9329 (mt) REVERT: D 1145 TYR cc_start: 0.8207 (m-80) cc_final: 0.7919 (m-80) REVERT: D 1248 PHE cc_start: 0.8017 (t80) cc_final: 0.7426 (t80) REVERT: D 1328 LEU cc_start: 0.9428 (tt) cc_final: 0.9077 (tt) REVERT: D 1330 TYR cc_start: 0.9483 (p90) cc_final: 0.8969 (p90) REVERT: D 1353 ASP cc_start: 0.8038 (m-30) cc_final: 0.7580 (p0) REVERT: D 1389 PHE cc_start: 0.8746 (m-80) cc_final: 0.8235 (m-80) REVERT: D 1395 THR cc_start: 0.8912 (p) cc_final: 0.8611 (p) REVERT: D 1431 PHE cc_start: 0.8610 (p90) cc_final: 0.8399 (p90) outliers start: 1 outliers final: 1 residues processed: 569 average time/residue: 0.2404 time to fit residues: 229.9974 Evaluate side-chains 464 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 95 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 436 optimal weight: 0.0370 chunk 396 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 chunk 378 optimal weight: 1.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1325 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.094352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.068995 restraints weight = 267088.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070989 restraints weight = 202590.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072524 restraints weight = 163915.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073657 restraints weight = 138798.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074583 restraints weight = 121978.137| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43672 Z= 0.153 Angle : 0.806 14.372 59452 Z= 0.393 Chirality : 0.050 0.374 6900 Planarity : 0.005 0.063 7554 Dihedral : 6.583 38.497 5740 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.21 % Favored : 86.68 % Rotamer: Outliers : 0.04 % Allowed : 0.47 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.10), residues: 5360 helix: -0.99 (0.17), residues: 822 sheet: -2.03 (0.13), residues: 1412 loop : -3.18 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 147 TYR 0.046 0.002 TYR D1216 PHE 0.049 0.002 PHE B1049 TRP 0.049 0.003 TRP A 739 HIS 0.014 0.001 HIS D1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (43574) covalent geometry : angle 0.78599 / 0.39 (59204) SS BOND : bond 0.00535 / 0.30 ( 46) SS BOND : angle 1.54130 / 0.99 ( 92) hydrogen bonds : bond 0.05415 / 3.63 ( 482) hydrogen bonds : angle 6.04193 / 4.12 ( 1446) link_ALPHA1-6 : bond 0.00473 / 0.24 ( 4) link_ALPHA1-6 : angle 1.47432 / 0.88 ( 12) link_BETA1-4 : bond 0.01046 / 0.59 ( 18) link_BETA1-4 : angle 2.33902 / 1.60 ( 54) link_NAG-ASN : bond 0.00829 / 0.49 ( 30) link_NAG-ASN : angle 4.10284 / 2.55 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 578 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9568 (pt) cc_final: 0.9355 (pt) REVERT: A 55 ASN cc_start: 0.6800 (p0) cc_final: 0.5296 (t0) REVERT: A 151 MET cc_start: 0.8947 (ttm) cc_final: 0.8474 (tpp) REVERT: A 356 ASP cc_start: 0.9007 (t0) cc_final: 0.8741 (t0) REVERT: A 373 ASP cc_start: 0.9473 (p0) cc_final: 0.8984 (m-30) REVERT: A 464 MET cc_start: 0.7924 (mtt) cc_final: 0.7461 (mtt) REVERT: A 666 MET cc_start: 0.8971 (tpp) cc_final: 0.8659 (tpt) REVERT: A 931 LEU cc_start: 0.9133 (tt) cc_final: 0.8665 (mp) REVERT: A 975 GLN cc_start: 0.7962 (mm110) cc_final: 0.7738 (mm-40) REVERT: A 1044 PHE cc_start: 0.9699 (m-10) cc_final: 0.9324 (m-80) REVERT: A 1122 ARG cc_start: 0.9017 (mtp180) cc_final: 0.8810 (mtp85) REVERT: A 1214 LEU cc_start: 0.6620 (tt) cc_final: 0.6224 (pp) REVERT: B 101 MET cc_start: 0.8623 (ttt) cc_final: 0.7947 (ttt) REVERT: B 151 MET cc_start: 0.9216 (mtp) cc_final: 0.8681 (ttm) REVERT: B 223 GLU cc_start: 0.7795 (tp30) cc_final: 0.7491 (tp30) REVERT: B 318 MET cc_start: 0.6990 (ppp) cc_final: 0.6728 (ppp) REVERT: B 385 PHE cc_start: 0.8379 (m-80) cc_final: 0.8140 (m-80) REVERT: B 415 MET cc_start: 0.7075 (ttp) cc_final: 0.6081 (tmm) REVERT: B 495 PHE cc_start: 0.7435 (m-80) cc_final: 0.7204 (m-80) REVERT: B 500 MET cc_start: 0.4590 (mmm) cc_final: 0.3749 (mmt) REVERT: B 552 ILE cc_start: 0.8740 (mm) cc_final: 0.8365 (mm) REVERT: B 586 ARG cc_start: 0.8696 (ttt180) cc_final: 0.7965 (tpt90) REVERT: B 597 LEU cc_start: 0.8959 (mp) cc_final: 0.8682 (mp) REVERT: B 786 LEU cc_start: 0.8785 (tt) cc_final: 0.8208 (mp) REVERT: B 1044 PHE cc_start: 0.8686 (t80) cc_final: 0.8163 (t80) REVERT: B 1092 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9168 (mmmt) REVERT: B 1106 THR cc_start: 0.9554 (p) cc_final: 0.9344 (p) REVERT: B 1109 LEU cc_start: 0.9571 (mt) cc_final: 0.9287 (mt) REVERT: B 1145 TYR cc_start: 0.8096 (m-80) cc_final: 0.7891 (m-10) REVERT: B 1168 LYS cc_start: 0.9453 (tptt) cc_final: 0.8517 (tptt) REVERT: B 1248 PHE cc_start: 0.7955 (t80) cc_final: 0.7468 (t80) REVERT: B 1253 ASP cc_start: 0.8058 (m-30) cc_final: 0.7660 (m-30) REVERT: B 1328 LEU cc_start: 0.9440 (tt) cc_final: 0.9152 (tt) REVERT: B 1330 TYR cc_start: 0.9384 (p90) cc_final: 0.8948 (p90) REVERT: B 1353 ASP cc_start: 0.8081 (m-30) cc_final: 0.7624 (p0) REVERT: B 1389 PHE cc_start: 0.8804 (m-80) cc_final: 0.8280 (m-80) REVERT: B 1415 VAL cc_start: 0.8785 (m) cc_final: 0.8545 (p) REVERT: B 1431 PHE cc_start: 0.8649 (p90) cc_final: 0.8419 (p90) REVERT: B 1432 THR cc_start: 0.8197 (t) cc_final: 0.7790 (m) REVERT: C 39 LEU cc_start: 0.9515 (pt) cc_final: 0.9296 (pt) REVERT: C 55 ASN cc_start: 0.6784 (p0) cc_final: 0.5301 (t0) REVERT: C 151 MET cc_start: 0.8911 (ttm) cc_final: 0.8423 (tpp) REVERT: C 356 ASP cc_start: 0.9002 (t0) cc_final: 0.8730 (t0) REVERT: C 373 ASP cc_start: 0.9446 (p0) cc_final: 0.8959 (m-30) REVERT: C 464 MET cc_start: 0.7983 (mtt) cc_final: 0.7541 (mtt) REVERT: C 520 MET cc_start: 0.8508 (mmm) cc_final: 0.8089 (mmm) REVERT: C 917 ASN cc_start: 0.5298 (OUTLIER) cc_final: 0.4483 (p0) REVERT: C 931 LEU cc_start: 0.9169 (tt) cc_final: 0.8664 (mp) REVERT: C 975 GLN cc_start: 0.7960 (mm110) cc_final: 0.7735 (mm-40) REVERT: C 1044 PHE cc_start: 0.9701 (m-10) cc_final: 0.9325 (m-80) REVERT: C 1122 ARG cc_start: 0.9030 (mtp180) cc_final: 0.8808 (mtp85) REVERT: C 1214 LEU cc_start: 0.6633 (tt) cc_final: 0.6241 (pp) REVERT: D 101 MET cc_start: 0.8631 (ttt) cc_final: 0.7952 (ttt) REVERT: D 151 MET cc_start: 0.9198 (mtp) cc_final: 0.8674 (ttm) REVERT: D 223 GLU cc_start: 0.7792 (tp30) cc_final: 0.7502 (tp30) REVERT: D 318 MET cc_start: 0.6992 (ppp) cc_final: 0.6731 (ppp) REVERT: D 370 ARG cc_start: 0.9221 (ptm160) cc_final: 0.8905 (ptm160) REVERT: D 385 PHE cc_start: 0.8392 (m-80) cc_final: 0.8148 (m-80) REVERT: D 415 MET cc_start: 0.7072 (ttp) cc_final: 0.6084 (tmm) REVERT: D 495 PHE cc_start: 0.7435 (m-80) cc_final: 0.7198 (m-80) REVERT: D 500 MET cc_start: 0.4524 (mmm) cc_final: 0.3689 (mmt) REVERT: D 552 ILE cc_start: 0.8692 (mm) cc_final: 0.8307 (mm) REVERT: D 597 LEU cc_start: 0.8972 (mp) cc_final: 0.8710 (mp) REVERT: D 786 LEU cc_start: 0.7905 (tp) cc_final: 0.7607 (tp) REVERT: D 1044 PHE cc_start: 0.8684 (t80) cc_final: 0.8209 (t80) REVERT: D 1092 LYS cc_start: 0.9379 (mmpt) cc_final: 0.9095 (mmmt) REVERT: D 1106 THR cc_start: 0.9466 (p) cc_final: 0.9241 (p) REVERT: D 1109 LEU cc_start: 0.9551 (mt) cc_final: 0.9322 (mp) REVERT: D 1208 MET cc_start: 0.9264 (ppp) cc_final: 0.9010 (ppp) REVERT: D 1248 PHE cc_start: 0.8053 (t80) cc_final: 0.7503 (t80) REVERT: D 1328 LEU cc_start: 0.9423 (tt) cc_final: 0.9121 (tt) REVERT: D 1330 TYR cc_start: 0.9425 (p90) cc_final: 0.8946 (p90) REVERT: D 1353 ASP cc_start: 0.8089 (m-30) cc_final: 0.7627 (p0) REVERT: D 1389 PHE cc_start: 0.8810 (m-80) cc_final: 0.8290 (m-80) REVERT: D 1431 PHE cc_start: 0.8621 (p90) cc_final: 0.8378 (p90) REVERT: D 1432 THR cc_start: 0.8190 (t) cc_final: 0.7777 (m) outliers start: 2 outliers final: 1 residues processed: 579 average time/residue: 0.2431 time to fit residues: 237.5157 Evaluate side-chains 464 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 126 optimal weight: 20.0000 chunk 398 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 404 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 384 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN A1009 ASN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 460 HIS ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1325 GLN ** B1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 GLN C1009 ASN ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1077 ASN D1123 ASN ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.087192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.063354 restraints weight = 294881.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064993 restraints weight = 229006.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066239 restraints weight = 189016.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067199 restraints weight = 162719.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067943 restraints weight = 144514.850| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 43672 Z= 0.289 Angle : 0.995 17.210 59452 Z= 0.502 Chirality : 0.056 0.421 6900 Planarity : 0.007 0.065 7554 Dihedral : 7.434 39.937 5740 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 36.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.36 % Favored : 83.53 % Rotamer: Outliers : 0.02 % Allowed : 0.79 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.10), residues: 5360 helix: -1.43 (0.16), residues: 804 sheet: -2.39 (0.13), residues: 1430 loop : -3.32 (0.09), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 147 TYR 0.060 0.003 TYR D1145 PHE 0.036 0.003 PHE B1049 TRP 0.055 0.005 TRP B 741 HIS 0.021 0.002 HIS B1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.29 (43574) covalent geometry : angle 0.97413 / 0.50 (59204) SS BOND : bond 0.00751 / 0.42 ( 46) SS BOND : angle 2.07076 / 1.38 ( 92) hydrogen bonds : bond 0.06401 / 4.29 ( 482) hydrogen bonds : angle 6.52660 / 4.45 ( 1446) link_ALPHA1-6 : bond 0.00457 / 0.23 ( 4) link_ALPHA1-6 : angle 1.53431 / 0.93 ( 12) link_BETA1-4 : bond 0.01142 / 0.64 ( 18) link_BETA1-4 : angle 2.55355 / 1.77 ( 54) link_NAG-ASN : bond 0.00993 / 0.63 ( 30) link_NAG-ASN : angle 4.64289 / 2.82 ( 90) =============================================================================== Job complete usr+sys time: 10019.34 seconds wall clock time: 174 minutes 17.11 seconds (10457.11 seconds total)