Starting phenix.real_space_refine on Sun Feb 8 06:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7o_12751/02_2026/7o7o_12751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7o_12751/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7o7o_12751/02_2026/7o7o_12751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7o_12751/02_2026/7o7o_12751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7o_12751/02_2026/7o7o_12751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7o_12751/02_2026/7o7o_12751.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.88, per 1000 atoms: 0.23 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: 4.47 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: 0.82 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: 5.50 Time building geometry restraints manager: 5.60 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 - 21.16: 24510 21.16 - 42.32: 2113 42.32 - 63.48: 297 63.48 - 84.64: 90 84.64 - 105.80: 30 Dihedral angle restraints: 27040 sinusoidal: 11372 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 27037 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: 0.09 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: 2.400 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.070 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 16.355 105.802 16810 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 covalent geometry : bond 0.01063 (43574) covalent geometry : angle 1.23853 (59204) SS BOND : bond 0.00798 ( 46) SS BOND : angle 2.20495 ( 92) hydrogen bonds : bond 0.22005 ( 482) hydrogen bonds : angle 8.71462 ( 1446) link_ALPHA1-6 : bond 0.00119 ( 4) link_ALPHA1-6 : angle 1.47460 ( 12) link_BETA1-4 : bond 0.00991 ( 18) link_BETA1-4 : angle 3.32640 ( 54) link_NAG-ASN : bond 0.01036 ( 30) link_NAG-ASN : angle 4.45198 ( 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 : 1.718 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: 0.2719 time to fit residues: 321.4228 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 : 1.714 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.096672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070865 restraints weight = 275356.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.072981 restraints weight = 208404.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074630 restraints weight = 168059.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.075898 restraints weight = 141535.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.076892 restraints weight = 123519.230| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43672 Z= 0.194 Angle : 0.967 13.962 59452 Z= 0.469 Chirality : 0.053 0.415 6900 Planarity : 0.006 0.088 7554 Dihedral : 10.830 67.198 6812 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.99 % Favored : 86.83 % Rotamer: Outliers : 0.43 % Allowed : 7.53 % Favored : 92.05 % 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: -4.65 (0.09), residues: 5360 helix: -1.92 (0.15), residues: 802 sheet: -2.82 (0.11), residues: 1484 loop : -3.70 (0.09), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 270 TYR 0.030 0.002 TYR B1418 PHE 0.035 0.002 PHE D1049 TRP 0.029 0.002 TRP D1183 HIS 0.012 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00421 (43574) covalent geometry : angle 0.92819 (59204) SS BOND : bond 0.00586 ( 46) SS BOND : angle 1.56100 ( 92) hydrogen bonds : bond 0.06766 ( 482) hydrogen bonds : angle 6.57261 ( 1446) link_ALPHA1-6 : bond 0.00522 ( 4) link_ALPHA1-6 : angle 1.56532 ( 12) link_BETA1-4 : bond 0.01080 ( 18) link_BETA1-4 : angle 4.45235 ( 54) link_NAG-ASN : bond 0.01023 ( 30) link_NAG-ASN : angle 6.05010 ( 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 684 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 664 time to evaluate : 1.756 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: A 28 LYS cc_start: 0.8408 (tmtt) cc_final: 0.8064 (tmtt) REVERT: A 34 LEU cc_start: 0.9491 (mp) cc_final: 0.9248 (mp) REVERT: A 55 ASN cc_start: 0.6757 (p0) cc_final: 0.4888 (t0) REVERT: A 151 MET cc_start: 0.8917 (ttm) cc_final: 0.8230 (tpp) REVERT: A 166 TYR cc_start: 0.7997 (p90) cc_final: 0.7499 (p90) REVERT: A 192 PHE cc_start: 0.7957 (t80) cc_final: 0.7722 (t80) REVERT: A 356 ASP cc_start: 0.8908 (t0) cc_final: 0.8555 (p0) REVERT: A 368 GLN cc_start: 0.9329 (tt0) cc_final: 0.9087 (tm-30) REVERT: A 464 MET cc_start: 0.7922 (mtt) cc_final: 0.7390 (mtt) REVERT: A 520 MET cc_start: 0.9001 (ptp) cc_final: 0.8797 (tmm) REVERT: A 666 MET cc_start: 0.8873 (tpp) cc_final: 0.8672 (tpp) REVERT: A 732 ARG cc_start: 0.8711 (ptm160) cc_final: 0.8453 (ptm160) REVERT: A 917 ASN cc_start: 0.5277 (OUTLIER) cc_final: 0.4530 (p0) REVERT: A 931 LEU cc_start: 0.9230 (tt) cc_final: 0.8644 (mp) REVERT: A 968 MET cc_start: 0.2577 (mmt) cc_final: 0.2187 (mmt) REVERT: A 1003 LYS cc_start: 0.8606 (tptp) cc_final: 0.8190 (tptp) REVERT: A 1044 PHE cc_start: 0.9593 (m-80) cc_final: 0.9390 (m-80) REVERT: A 1122 ARG cc_start: 0.9076 (ttp-110) cc_final: 0.8773 (tmm-80) REVERT: B 151 MET cc_start: 0.8735 (mtp) cc_final: 0.7969 (mmm) REVERT: B 169 ASP cc_start: 0.8969 (t0) cc_final: 0.8647 (t0) REVERT: B 229 PHE cc_start: 0.9231 (p90) cc_final: 0.8989 (p90) REVERT: B 300 PHE cc_start: 0.8745 (t80) cc_final: 0.8500 (t80) REVERT: B 370 ARG cc_start: 0.9152 (ptm160) cc_final: 0.8871 (ptm160) REVERT: B 546 LEU cc_start: 0.8795 (tp) cc_final: 0.8593 (tp) REVERT: B 552 ILE cc_start: 0.8353 (mm) cc_final: 0.7954 (mm) REVERT: B 569 ASP cc_start: 0.8503 (t0) cc_final: 0.8299 (t0) REVERT: B 571 SER cc_start: 0.9123 (t) cc_final: 0.8701 (p) REVERT: B 607 MET cc_start: 0.8713 (tmm) cc_final: 0.8457 (ptp) REVERT: B 817 TYR cc_start: 0.8451 (m-10) cc_final: 0.8137 (m-80) REVERT: B 977 MET cc_start: 0.6565 (mmp) cc_final: 0.6364 (mmp) REVERT: B 1020 HIS cc_start: 0.7978 (m170) cc_final: 0.7637 (m170) REVERT: B 1109 LEU cc_start: 0.9488 (mt) cc_final: 0.9202 (mt) REVERT: B 1132 TRP cc_start: 0.7221 (t-100) cc_final: 0.6821 (t-100) REVERT: B 1293 ASP cc_start: 0.9610 (m-30) cc_final: 0.8904 (m-30) REVERT: B 1298 LEU cc_start: 0.9511 (pt) cc_final: 0.9306 (mt) REVERT: B 1299 LEU cc_start: 0.9527 (mm) cc_final: 0.9257 (mt) REVERT: B 1328 LEU cc_start: 0.9151 (tt) cc_final: 0.8673 (tt) REVERT: B 1330 TYR cc_start: 0.9266 (p90) cc_final: 0.8824 (p90) REVERT: B 1401 ARG cc_start: 0.9142 (tpp-160) cc_final: 0.8916 (mmm160) REVERT: B 1415 VAL cc_start: 0.8245 (t) cc_final: 0.8044 (m) REVERT: B 1431 PHE cc_start: 0.8741 (p90) cc_final: 0.8463 (p90) REVERT: C 28 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8062 (tmtt) REVERT: C 34 LEU cc_start: 0.9494 (mp) cc_final: 0.9253 (mp) REVERT: C 55 ASN cc_start: 0.6732 (p0) cc_final: 0.4866 (t0) REVERT: C 151 MET cc_start: 0.8919 (ttm) cc_final: 0.8234 (tpp) REVERT: C 166 TYR cc_start: 0.7993 (p90) cc_final: 0.7493 (p90) REVERT: C 192 PHE cc_start: 0.7967 (t80) cc_final: 0.7729 (t80) REVERT: C 356 ASP cc_start: 0.8906 (t0) cc_final: 0.8555 (p0) REVERT: C 368 GLN cc_start: 0.9328 (tt0) cc_final: 0.9087 (tm-30) REVERT: C 464 MET cc_start: 0.7932 (mtt) cc_final: 0.7404 (mtt) REVERT: C 732 ARG cc_start: 0.8712 (ptm160) cc_final: 0.8454 (ptm160) REVERT: C 917 ASN cc_start: 0.5307 (OUTLIER) cc_final: 0.4558 (p0) REVERT: C 931 LEU cc_start: 0.9235 (tt) cc_final: 0.8646 (mp) REVERT: C 968 MET cc_start: 0.2492 (mmt) cc_final: 0.2181 (mmt) REVERT: C 1003 LYS cc_start: 0.8602 (tptp) cc_final: 0.8192 (tptp) REVERT: C 1044 PHE cc_start: 0.9590 (m-80) cc_final: 0.9389 (m-80) REVERT: C 1122 ARG cc_start: 0.9075 (ttp-110) cc_final: 0.8765 (tmm-80) REVERT: D 151 MET cc_start: 0.8746 (mtp) cc_final: 0.7978 (mmm) REVERT: D 169 ASP cc_start: 0.8971 (t0) cc_final: 0.8644 (t0) REVERT: D 229 PHE cc_start: 0.9228 (p90) cc_final: 0.8985 (p90) REVERT: D 300 PHE cc_start: 0.8743 (t80) cc_final: 0.8498 (t80) REVERT: D 370 ARG cc_start: 0.9156 (ptm160) cc_final: 0.8874 (ptm160) REVERT: D 546 LEU cc_start: 0.8795 (tp) cc_final: 0.8593 (tp) REVERT: D 552 ILE cc_start: 0.8343 (mm) cc_final: 0.7941 (mm) REVERT: D 569 ASP cc_start: 0.8533 (t0) cc_final: 0.8328 (t0) REVERT: D 571 SER cc_start: 0.9136 (t) cc_final: 0.8715 (p) REVERT: D 607 MET cc_start: 0.8707 (tmm) cc_final: 0.8455 (ptp) REVERT: D 817 TYR cc_start: 0.8448 (m-10) cc_final: 0.8138 (m-80) REVERT: D 1020 HIS cc_start: 0.7927 (m170) cc_final: 0.7581 (m170) REVERT: D 1109 LEU cc_start: 0.9481 (mt) cc_final: 0.9193 (mt) REVERT: D 1132 TRP cc_start: 0.7215 (t-100) cc_final: 0.6813 (t-100) REVERT: D 1293 ASP cc_start: 0.9612 (m-30) cc_final: 0.8909 (m-30) REVERT: D 1298 LEU cc_start: 0.9510 (pt) cc_final: 0.9305 (mt) REVERT: D 1299 LEU cc_start: 0.9521 (mm) cc_final: 0.9252 (mt) REVERT: D 1328 LEU cc_start: 0.9153 (tt) cc_final: 0.8669 (tt) REVERT: D 1330 TYR cc_start: 0.9267 (p90) cc_final: 0.8821 (p90) REVERT: D 1427 LEU cc_start: 0.9202 (pp) cc_final: 0.8963 (tt) REVERT: D 1431 PHE cc_start: 0.8734 (p90) cc_final: 0.8455 (p90) outliers start: 20 outliers final: 6 residues processed: 680 average time/residue: 0.2603 time to fit residues: 291.1434 Evaluate side-chains 506 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 498 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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: 0.0010 chunk 491 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 405 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 HIS A 917 ASN A 938 ASN A1062 HIS ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 GLN C 846 HIS C 917 ASN C 938 ASN C1062 HIS ** D1291 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.097124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.071587 restraints weight = 279906.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073676 restraints weight = 213314.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.075293 restraints weight = 172609.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.076547 restraints weight = 145973.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.077497 restraints weight = 127664.109| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43672 Z= 0.167 Angle : 0.861 12.981 59452 Z= 0.423 Chirality : 0.051 0.438 6900 Planarity : 0.006 0.075 7554 Dihedral : 9.255 59.902 6812 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.04 % Favored : 86.77 % Rotamer: Outliers : 0.30 % Allowed : 6.15 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -4.21 (0.10), residues: 5360 helix: -1.36 (0.16), residues: 802 sheet: -2.54 (0.12), residues: 1462 loop : -3.47 (0.09), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 270 TYR 0.031 0.002 TYR D1418 PHE 0.034 0.002 PHE C1057 TRP 0.028 0.003 TRP B1183 HIS 0.030 0.001 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00365 (43574) covalent geometry : angle 0.83296 (59204) SS BOND : bond 0.00559 ( 46) SS BOND : angle 1.66850 ( 92) hydrogen bonds : bond 0.06289 ( 482) hydrogen bonds : angle 6.17265 ( 1446) link_ALPHA1-6 : bond 0.00540 ( 4) link_ALPHA1-6 : angle 1.54721 ( 12) link_BETA1-4 : bond 0.01045 ( 18) link_BETA1-4 : angle 3.38894 ( 54) link_NAG-ASN : bond 0.00854 ( 30) link_NAG-ASN : angle 4.86208 ( 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 649 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 635 time to evaluate : 1.548 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: A 28 LYS cc_start: 0.8464 (tmtt) cc_final: 0.8124 (tmtt) REVERT: A 55 ASN cc_start: 0.6689 (p0) cc_final: 0.4902 (t0) REVERT: A 121 MET cc_start: 0.9433 (pmm) cc_final: 0.9195 (pmm) REVERT: A 151 MET cc_start: 0.8864 (ttm) cc_final: 0.8645 (ttm) REVERT: A 356 ASP cc_start: 0.8916 (t0) cc_final: 0.8689 (t0) REVERT: A 368 GLN cc_start: 0.9269 (tt0) cc_final: 0.9038 (tm-30) REVERT: A 464 MET cc_start: 0.7990 (mtt) cc_final: 0.7294 (mtt) REVERT: A 562 ASN cc_start: 0.7867 (t0) cc_final: 0.7447 (t0) REVERT: A 917 ASN cc_start: 0.5511 (OUTLIER) cc_final: 0.4489 (p0) REVERT: A 931 LEU cc_start: 0.9234 (tt) cc_final: 0.8642 (mp) REVERT: A 968 MET cc_start: 0.2921 (mmt) cc_final: 0.2659 (mmt) REVERT: A 1003 LYS cc_start: 0.8556 (tptp) cc_final: 0.8260 (tppt) REVERT: A 1122 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8717 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6521 (tt) cc_final: 0.6101 (tt) REVERT: B 151 MET cc_start: 0.8970 (mtp) cc_final: 0.8286 (mpp) REVERT: B 164 LEU cc_start: 0.8976 (pt) cc_final: 0.8654 (pp) REVERT: B 169 ASP cc_start: 0.8977 (t0) cc_final: 0.8642 (t0) REVERT: B 194 LEU cc_start: 0.9598 (mt) cc_final: 0.9254 (tp) REVERT: B 370 ARG cc_start: 0.9147 (ptm160) cc_final: 0.8811 (ptm160) REVERT: B 393 TYR cc_start: 0.8507 (m-10) cc_final: 0.8267 (m-10) REVERT: B 520 MET cc_start: 0.6421 (tpp) cc_final: 0.6162 (tpp) REVERT: B 552 ILE cc_start: 0.8570 (mm) cc_final: 0.8093 (mm) REVERT: B 597 LEU cc_start: 0.8962 (mp) cc_final: 0.8672 (mp) REVERT: B 607 MET cc_start: 0.8692 (tmm) cc_final: 0.8373 (ptp) REVERT: B 804 ARG cc_start: 0.5222 (tpm170) cc_final: 0.4941 (tpm170) REVERT: B 817 TYR cc_start: 0.8298 (m-10) cc_final: 0.8021 (m-80) REVERT: B 1020 HIS cc_start: 0.7417 (m170) cc_final: 0.7173 (m170) REVERT: B 1109 LEU cc_start: 0.9528 (mt) cc_final: 0.9271 (mt) REVERT: B 1132 TRP cc_start: 0.7187 (t-100) cc_final: 0.6671 (t-100) REVERT: B 1293 ASP cc_start: 0.9578 (m-30) cc_final: 0.9306 (m-30) REVERT: B 1299 LEU cc_start: 0.9504 (mm) cc_final: 0.9269 (mt) REVERT: B 1353 ASP cc_start: 0.8101 (m-30) cc_final: 0.7658 (p0) REVERT: B 1431 PHE cc_start: 0.8782 (p90) cc_final: 0.8561 (p90) REVERT: C 28 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8127 (tmtt) REVERT: C 55 ASN cc_start: 0.6637 (p0) cc_final: 0.4858 (t0) REVERT: C 121 MET cc_start: 0.9433 (pmm) cc_final: 0.9194 (pmm) REVERT: C 151 MET cc_start: 0.8885 (ttm) cc_final: 0.8666 (ttm) REVERT: C 356 ASP cc_start: 0.8910 (t0) cc_final: 0.8683 (t0) REVERT: C 368 GLN cc_start: 0.9274 (tt0) cc_final: 0.9044 (tm-30) REVERT: C 464 MET cc_start: 0.7982 (mtt) cc_final: 0.7290 (mtt) REVERT: C 562 ASN cc_start: 0.7866 (t0) cc_final: 0.7450 (t0) REVERT: C 917 ASN cc_start: 0.5548 (OUTLIER) cc_final: 0.4530 (p0) REVERT: C 931 LEU cc_start: 0.9238 (tt) cc_final: 0.8644 (mp) REVERT: C 968 MET cc_start: 0.2915 (mmt) cc_final: 0.2655 (mmt) REVERT: C 1003 LYS cc_start: 0.8557 (tptp) cc_final: 0.8261 (tppt) REVERT: C 1122 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8718 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6526 (tt) cc_final: 0.6108 (tt) REVERT: D 151 MET cc_start: 0.8981 (mtp) cc_final: 0.8285 (mpp) REVERT: D 164 LEU cc_start: 0.8983 (pt) cc_final: 0.8659 (pp) REVERT: D 169 ASP cc_start: 0.8978 (t0) cc_final: 0.8640 (t0) REVERT: D 194 LEU cc_start: 0.9600 (mt) cc_final: 0.9258 (tp) REVERT: D 370 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8810 (ptm160) REVERT: D 393 TYR cc_start: 0.8505 (m-10) cc_final: 0.8267 (m-10) REVERT: D 520 MET cc_start: 0.6409 (tpp) cc_final: 0.6141 (tpp) REVERT: D 552 ILE cc_start: 0.8563 (mm) cc_final: 0.8086 (mm) REVERT: D 597 LEU cc_start: 0.8961 (mp) cc_final: 0.8672 (mp) REVERT: D 607 MET cc_start: 0.8699 (tmm) cc_final: 0.8375 (ptp) REVERT: D 804 ARG cc_start: 0.5213 (tpm170) cc_final: 0.4937 (tpm170) REVERT: D 817 TYR cc_start: 0.8301 (m-10) cc_final: 0.8028 (m-80) REVERT: D 1109 LEU cc_start: 0.9522 (mt) cc_final: 0.9260 (mt) REVERT: D 1132 TRP cc_start: 0.7183 (t-100) cc_final: 0.6664 (t-100) REVERT: D 1293 ASP cc_start: 0.9574 (m-30) cc_final: 0.9300 (m-30) REVERT: D 1299 LEU cc_start: 0.9509 (mm) cc_final: 0.9274 (mt) REVERT: D 1353 ASP cc_start: 0.8090 (m-30) cc_final: 0.7653 (p0) REVERT: D 1431 PHE cc_start: 0.8801 (p90) cc_final: 0.8570 (p90) outliers start: 14 outliers final: 4 residues processed: 646 average time/residue: 0.2641 time to fit residues: 282.2476 Evaluate side-chains 507 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 501 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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: 20.0000 chunk 242 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 30.0000 chunk 193 optimal weight: 0.0010 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 203 optimal weight: 9.9990 chunk 467 optimal weight: 0.1980 chunk 449 optimal weight: 7.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 917 ASN A 938 ASN A1062 HIS A1159 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 460 HIS ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS B1291 GLN C 177 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN C 938 ASN C1062 HIS C1159 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 460 HIS ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1346 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.099541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.073474 restraints weight = 263694.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.075637 restraints weight = 200911.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.077286 restraints weight = 162700.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078576 restraints weight = 137775.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.079552 restraints weight = 120636.540| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43672 Z= 0.143 Angle : 0.823 13.565 59452 Z= 0.400 Chirality : 0.050 0.422 6900 Planarity : 0.006 0.079 7554 Dihedral : 8.421 59.075 6812 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.16 % Favored : 87.72 % Rotamer: Outliers : 0.19 % Allowed : 4.87 % Favored : 94.94 % 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: -3.90 (0.10), residues: 5360 helix: -1.02 (0.17), residues: 808 sheet: -2.31 (0.13), residues: 1446 loop : -3.31 (0.10), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 338 TYR 0.027 0.002 TYR B1418 PHE 0.021 0.001 PHE D 980 TRP 0.024 0.002 TRP B1183 HIS 0.013 0.001 HIS D1020 Details of bonding type rmsd covalent geometry : bond 0.00315 (43574) covalent geometry : angle 0.79312 (59204) SS BOND : bond 0.00436 ( 46) SS BOND : angle 1.71379 ( 92) hydrogen bonds : bond 0.05830 ( 482) hydrogen bonds : angle 5.90953 ( 1446) link_ALPHA1-6 : bond 0.00541 ( 4) link_ALPHA1-6 : angle 1.50041 ( 12) link_BETA1-4 : bond 0.01129 ( 18) link_BETA1-4 : angle 3.04219 ( 54) link_NAG-ASN : bond 0.00773 ( 30) link_NAG-ASN : angle 4.96420 ( 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 670 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 661 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6571 (p0) cc_final: 0.4737 (t0) REVERT: A 121 MET cc_start: 0.9366 (pmm) cc_final: 0.9146 (pmm) REVERT: A 151 MET cc_start: 0.8688 (ttm) cc_final: 0.8461 (ttm) REVERT: A 356 ASP cc_start: 0.8926 (t0) cc_final: 0.8681 (t0) REVERT: A 368 GLN cc_start: 0.9252 (tt0) cc_final: 0.8967 (tm-30) REVERT: A 373 ASP cc_start: 0.9342 (p0) cc_final: 0.8982 (m-30) REVERT: A 464 MET cc_start: 0.8041 (mtt) cc_final: 0.7342 (mtt) REVERT: A 562 ASN cc_start: 0.7705 (t0) cc_final: 0.7332 (t0) REVERT: A 917 ASN cc_start: 0.5218 (OUTLIER) cc_final: 0.4259 (p0) REVERT: A 931 LEU cc_start: 0.9118 (tt) cc_final: 0.8549 (mp) REVERT: A 968 MET cc_start: 0.2730 (mmt) cc_final: 0.2514 (mmt) REVERT: A 1003 LYS cc_start: 0.8489 (tptp) cc_final: 0.8200 (tppt) REVERT: A 1122 ARG cc_start: 0.8998 (ttp-110) cc_final: 0.8711 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6484 (tt) cc_final: 0.6140 (pp) REVERT: B 151 MET cc_start: 0.8981 (mtp) cc_final: 0.8689 (ttm) REVERT: B 169 ASP cc_start: 0.8235 (t0) cc_final: 0.7775 (t70) REVERT: B 370 ARG cc_start: 0.9212 (ptm160) cc_final: 0.8945 (ptm160) REVERT: B 415 MET cc_start: 0.7358 (ttp) cc_final: 0.6556 (tmm) REVERT: B 495 PHE cc_start: 0.7060 (m-80) cc_final: 0.6515 (m-80) REVERT: B 546 LEU cc_start: 0.8983 (tp) cc_final: 0.8766 (tp) REVERT: B 552 ILE cc_start: 0.8647 (mm) cc_final: 0.8241 (mm) REVERT: B 570 LEU cc_start: 0.8192 (pp) cc_final: 0.7970 (pp) REVERT: B 597 LEU cc_start: 0.8803 (mp) cc_final: 0.8556 (mp) REVERT: B 741 TRP cc_start: 0.7853 (t60) cc_final: 0.7322 (t60) REVERT: B 804 ARG cc_start: 0.5043 (tpm170) cc_final: 0.4790 (tpm170) REVERT: B 817 TYR cc_start: 0.8216 (m-10) cc_final: 0.7969 (m-80) REVERT: B 968 MET cc_start: 0.1713 (mmp) cc_final: 0.1495 (mmp) REVERT: B 1109 LEU cc_start: 0.9497 (mt) cc_final: 0.9236 (mt) REVERT: B 1132 TRP cc_start: 0.7224 (t-100) cc_final: 0.6548 (t-100) REVERT: B 1299 LEU cc_start: 0.9462 (mm) cc_final: 0.9165 (mt) REVERT: B 1330 TYR cc_start: 0.9324 (p90) cc_final: 0.8982 (p90) REVERT: B 1353 ASP cc_start: 0.8141 (m-30) cc_final: 0.7675 (p0) REVERT: B 1389 PHE cc_start: 0.8994 (m-80) cc_final: 0.8400 (m-80) REVERT: C 55 ASN cc_start: 0.6600 (p0) cc_final: 0.4753 (t0) REVERT: C 121 MET cc_start: 0.9378 (pmm) cc_final: 0.9153 (pmm) REVERT: C 151 MET cc_start: 0.8691 (ttm) cc_final: 0.8465 (ttm) REVERT: C 250 VAL cc_start: 0.9027 (m) cc_final: 0.8826 (p) REVERT: C 356 ASP cc_start: 0.8934 (t0) cc_final: 0.8688 (t0) REVERT: C 368 GLN cc_start: 0.9252 (tt0) cc_final: 0.8968 (tm-30) REVERT: C 373 ASP cc_start: 0.9345 (p0) cc_final: 0.8986 (m-30) REVERT: C 464 MET cc_start: 0.8045 (mtt) cc_final: 0.7385 (mtt) REVERT: C 562 ASN cc_start: 0.7704 (t0) cc_final: 0.7332 (t0) REVERT: C 666 MET cc_start: 0.8842 (tpp) cc_final: 0.8606 (tpp) REVERT: C 917 ASN cc_start: 0.5243 (OUTLIER) cc_final: 0.4284 (p0) REVERT: C 931 LEU cc_start: 0.9117 (tt) cc_final: 0.8552 (mp) REVERT: C 968 MET cc_start: 0.2733 (mmt) cc_final: 0.2512 (mmt) REVERT: C 1003 LYS cc_start: 0.8492 (tptp) cc_final: 0.8203 (tppt) REVERT: C 1122 ARG cc_start: 0.8994 (ttp-110) cc_final: 0.8710 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6472 (tt) cc_final: 0.6128 (pp) REVERT: D 151 MET cc_start: 0.8991 (mtp) cc_final: 0.8688 (ttm) REVERT: D 370 ARG cc_start: 0.9206 (ptm160) cc_final: 0.8939 (ptm160) REVERT: D 415 MET cc_start: 0.7330 (ttp) cc_final: 0.6532 (tmm) REVERT: D 495 PHE cc_start: 0.7062 (m-80) cc_final: 0.6520 (m-80) REVERT: D 546 LEU cc_start: 0.8988 (tp) cc_final: 0.8770 (tp) REVERT: D 552 ILE cc_start: 0.8623 (mm) cc_final: 0.8212 (mm) REVERT: D 570 LEU cc_start: 0.8213 (pp) cc_final: 0.7984 (pp) REVERT: D 597 LEU cc_start: 0.8804 (mp) cc_final: 0.8557 (mp) REVERT: D 741 TRP cc_start: 0.7841 (t60) cc_final: 0.7312 (t60) REVERT: D 804 ARG cc_start: 0.5048 (tpm170) cc_final: 0.4796 (tpm170) REVERT: D 817 TYR cc_start: 0.8220 (m-10) cc_final: 0.7976 (m-80) REVERT: D 1109 LEU cc_start: 0.9492 (mt) cc_final: 0.9229 (mt) REVERT: D 1132 TRP cc_start: 0.7221 (t-100) cc_final: 0.6544 (t-100) REVERT: D 1168 LYS cc_start: 0.9490 (tptt) cc_final: 0.8641 (tptt) REVERT: D 1299 LEU cc_start: 0.9467 (mm) cc_final: 0.9169 (mt) REVERT: D 1330 TYR cc_start: 0.9318 (p90) cc_final: 0.8975 (p90) REVERT: D 1353 ASP cc_start: 0.8140 (m-30) cc_final: 0.7675 (p0) REVERT: D 1389 PHE cc_start: 0.9010 (m-80) cc_final: 0.8415 (m-80) REVERT: D 1431 PHE cc_start: 0.8678 (p90) cc_final: 0.8455 (p90) outliers start: 9 outliers final: 1 residues processed: 667 average time/residue: 0.2567 time to fit residues: 284.2161 Evaluate side-chains 525 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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: 0.1980 chunk 419 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 534 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 461 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A 975 GLN A1062 HIS A1077 ASN A1159 ASN B 477 GLN B 566 ASN ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 177 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN C 938 ASN C 975 GLN C1062 HIS C1077 ASN C1159 ASN D 477 GLN D 566 ASN ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.094661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.070098 restraints weight = 279397.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.071917 restraints weight = 216818.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.073295 restraints weight = 178513.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074376 restraints weight = 153197.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075200 restraints weight = 135833.262| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43672 Z= 0.190 Angle : 0.848 12.042 59452 Z= 0.420 Chirality : 0.050 0.437 6900 Planarity : 0.006 0.066 7554 Dihedral : 8.202 59.970 6812 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.08 % Favored : 86.77 % Rotamer: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % 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: -3.89 (0.10), residues: 5360 helix: -0.95 (0.17), residues: 806 sheet: -2.33 (0.12), residues: 1486 loop : -3.30 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 732 TYR 0.043 0.002 TYR D1145 PHE 0.043 0.002 PHE B1049 TRP 0.026 0.002 TRP B1183 HIS 0.013 0.002 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00404 (43574) covalent geometry : angle 0.81910 (59204) SS BOND : bond 0.00563 ( 46) SS BOND : angle 1.82193 ( 92) hydrogen bonds : bond 0.06114 ( 482) hydrogen bonds : angle 5.95883 ( 1446) link_ALPHA1-6 : bond 0.00494 ( 4) link_ALPHA1-6 : angle 1.45021 ( 12) link_BETA1-4 : bond 0.01091 ( 18) link_BETA1-4 : angle 2.95015 ( 54) link_NAG-ASN : bond 0.00821 ( 30) link_NAG-ASN : angle 4.99740 ( 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 618 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 612 time to evaluate : 1.691 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 55 ASN cc_start: 0.6446 (p0) cc_final: 0.4764 (t0) REVERT: A 121 MET cc_start: 0.9473 (pmm) cc_final: 0.9242 (pmm) REVERT: A 356 ASP cc_start: 0.8930 (t0) cc_final: 0.8647 (t0) REVERT: A 673 MET cc_start: 0.9011 (mmp) cc_final: 0.8740 (mmt) REVERT: A 931 LEU cc_start: 0.9257 (tt) cc_final: 0.8730 (mp) REVERT: A 1003 LYS cc_start: 0.8698 (tptp) cc_final: 0.8427 (tppt) REVERT: A 1044 PHE cc_start: 0.9489 (m-80) cc_final: 0.9264 (m-80) REVERT: A 1122 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8727 (tmm-80) REVERT: A 1211 TYR cc_start: 0.8482 (m-80) cc_final: 0.8242 (m-80) REVERT: A 1214 LEU cc_start: 0.6661 (tt) cc_final: 0.6333 (tt) REVERT: B 101 MET cc_start: 0.8672 (ttt) cc_final: 0.7923 (ttt) REVERT: B 151 MET cc_start: 0.9074 (mtp) cc_final: 0.8698 (ttm) REVERT: B 169 ASP cc_start: 0.8332 (t0) cc_final: 0.7848 (t70) REVERT: B 189 GLN cc_start: 0.9609 (pm20) cc_final: 0.9403 (pm20) REVERT: B 194 LEU cc_start: 0.9619 (mt) cc_final: 0.9219 (tp) REVERT: B 370 ARG cc_start: 0.9230 (ptm160) cc_final: 0.8900 (ptm160) REVERT: B 415 MET cc_start: 0.7470 (ttp) cc_final: 0.7140 (ttp) REVERT: B 428 ARG cc_start: 0.9036 (ptp90) cc_final: 0.8834 (tmt-80) REVERT: B 495 PHE cc_start: 0.7194 (m-80) cc_final: 0.6680 (m-80) REVERT: B 552 ILE cc_start: 0.8657 (mm) cc_final: 0.8273 (mm) REVERT: B 597 LEU cc_start: 0.8907 (mp) cc_final: 0.8701 (mp) REVERT: B 817 TYR cc_start: 0.8105 (m-10) cc_final: 0.7879 (m-80) REVERT: B 1044 PHE cc_start: 0.8555 (t80) cc_final: 0.8174 (t80) REVERT: B 1109 LEU cc_start: 0.9524 (mt) cc_final: 0.9217 (mt) REVERT: B 1132 TRP cc_start: 0.7272 (t-100) cc_final: 0.7050 (t-100) REVERT: B 1145 TYR cc_start: 0.8486 (m-80) cc_final: 0.7512 (m-80) REVERT: B 1330 TYR cc_start: 0.9443 (p90) cc_final: 0.9141 (p90) REVERT: B 1353 ASP cc_start: 0.8154 (m-30) cc_final: 0.7696 (p0) REVERT: B 1389 PHE cc_start: 0.8952 (m-80) cc_final: 0.8412 (m-80) REVERT: C 55 ASN cc_start: 0.6470 (p0) cc_final: 0.4792 (t0) REVERT: C 121 MET cc_start: 0.9491 (pmm) cc_final: 0.9254 (pmm) REVERT: C 250 VAL cc_start: 0.9160 (m) cc_final: 0.8922 (p) REVERT: C 356 ASP cc_start: 0.8939 (t0) cc_final: 0.8656 (t0) REVERT: C 666 MET cc_start: 0.8877 (tpp) cc_final: 0.8639 (tpp) REVERT: C 673 MET cc_start: 0.8981 (mmp) cc_final: 0.8727 (mmt) REVERT: C 917 ASN cc_start: 0.5492 (OUTLIER) cc_final: 0.4501 (p0) REVERT: C 931 LEU cc_start: 0.9261 (tt) cc_final: 0.8692 (mp) REVERT: C 1003 LYS cc_start: 0.8707 (tptp) cc_final: 0.8434 (tppt) REVERT: C 1044 PHE cc_start: 0.9490 (m-80) cc_final: 0.9261 (m-80) REVERT: C 1122 ARG cc_start: 0.9049 (ttp-110) cc_final: 0.8727 (tmm-80) REVERT: C 1211 TYR cc_start: 0.8478 (m-80) cc_final: 0.8238 (m-80) REVERT: C 1214 LEU cc_start: 0.6655 (tt) cc_final: 0.6328 (tt) REVERT: D 101 MET cc_start: 0.8671 (ttt) cc_final: 0.7920 (ttt) REVERT: D 151 MET cc_start: 0.9088 (mtp) cc_final: 0.8713 (ttm) REVERT: D 189 GLN cc_start: 0.9614 (pm20) cc_final: 0.9336 (pm20) REVERT: D 194 LEU cc_start: 0.9627 (mt) cc_final: 0.9227 (tp) REVERT: D 370 ARG cc_start: 0.9218 (ptm160) cc_final: 0.8882 (ptm160) REVERT: D 415 MET cc_start: 0.7458 (ttp) cc_final: 0.7126 (ttp) REVERT: D 428 ARG cc_start: 0.9041 (ptp90) cc_final: 0.8836 (tmt-80) REVERT: D 495 PHE cc_start: 0.7202 (m-80) cc_final: 0.6689 (m-80) REVERT: D 552 ILE cc_start: 0.8654 (mm) cc_final: 0.8267 (mm) REVERT: D 597 LEU cc_start: 0.8910 (mp) cc_final: 0.8704 (mp) REVERT: D 817 TYR cc_start: 0.8111 (m-10) cc_final: 0.7885 (m-80) REVERT: D 1109 LEU cc_start: 0.9524 (mt) cc_final: 0.9214 (mt) REVERT: D 1132 TRP cc_start: 0.7268 (t-100) cc_final: 0.7050 (t-100) REVERT: D 1145 TYR cc_start: 0.8463 (m-80) cc_final: 0.7420 (m-80) REVERT: D 1328 LEU cc_start: 0.9322 (tt) cc_final: 0.8928 (tt) REVERT: D 1330 TYR cc_start: 0.9440 (p90) cc_final: 0.9155 (p90) REVERT: D 1353 ASP cc_start: 0.8151 (m-30) cc_final: 0.7696 (p0) REVERT: D 1389 PHE cc_start: 0.8945 (m-80) cc_final: 0.8420 (m-80) outliers start: 6 outliers final: 1 residues processed: 615 average time/residue: 0.2582 time to fit residues: 265.4825 Evaluate side-chains 482 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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: 0.0270 chunk 535 optimal weight: 0.6980 chunk 472 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 492 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 3.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 917 ASN A 938 ASN A1062 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 179 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN C 938 ASN C1062 HIS ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN D1291 GLN ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3972 r_free = 0.3972 target = 0.094643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069887 restraints weight = 279489.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.071755 restraints weight = 215296.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073192 restraints weight = 176416.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.074304 restraints weight = 150773.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.075152 restraints weight = 133063.869| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43672 Z= 0.176 Angle : 0.833 11.863 59452 Z= 0.411 Chirality : 0.051 0.428 6900 Planarity : 0.006 0.065 7554 Dihedral : 8.153 59.652 6812 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.28 % Favored : 86.60 % Rotamer: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.58 % 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: -3.84 (0.10), residues: 5360 helix: -0.99 (0.17), residues: 818 sheet: -2.24 (0.13), residues: 1440 loop : -3.29 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 387 TYR 0.041 0.002 TYR B1145 PHE 0.041 0.002 PHE B1049 TRP 0.015 0.002 TRP D1183 HIS 0.018 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00378 (43574) covalent geometry : angle 0.80539 (59204) SS BOND : bond 0.00427 ( 46) SS BOND : angle 1.49539 ( 92) hydrogen bonds : bond 0.05906 ( 482) hydrogen bonds : angle 6.00222 ( 1446) link_ALPHA1-6 : bond 0.00534 ( 4) link_ALPHA1-6 : angle 1.44480 ( 12) link_BETA1-4 : bond 0.01086 ( 18) link_BETA1-4 : angle 2.89245 ( 54) link_NAG-ASN : bond 0.00886 ( 30) link_NAG-ASN : angle 4.94916 ( 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 620 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 615 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6681 (p0) cc_final: 0.5126 (t0) REVERT: A 121 MET cc_start: 0.9463 (pmm) cc_final: 0.9217 (pmm) REVERT: A 151 MET cc_start: 0.9032 (ttm) cc_final: 0.8338 (tpp) REVERT: A 356 ASP cc_start: 0.8939 (t0) cc_final: 0.8660 (t0) REVERT: A 373 ASP cc_start: 0.9402 (p0) cc_final: 0.9051 (t0) REVERT: A 464 MET cc_start: 0.8136 (mtt) cc_final: 0.7651 (mtt) REVERT: A 576 GLN cc_start: 0.4992 (OUTLIER) cc_final: 0.4536 (pp30) REVERT: A 673 MET cc_start: 0.8985 (mmp) cc_final: 0.8685 (mmt) REVERT: A 917 ASN cc_start: 0.5372 (OUTLIER) cc_final: 0.4249 (p0) REVERT: A 931 LEU cc_start: 0.9298 (tt) cc_final: 0.8702 (mp) REVERT: A 975 GLN cc_start: 0.7944 (mm110) cc_final: 0.7737 (mm-40) REVERT: A 1122 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.8577 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6411 (tt) cc_final: 0.5994 (pp) REVERT: B 101 MET cc_start: 0.8683 (ttt) cc_final: 0.7950 (ttt) REVERT: B 121 MET cc_start: 0.9281 (ptp) cc_final: 0.8980 (tmm) REVERT: B 145 LYS cc_start: 0.7240 (ptpt) cc_final: 0.6863 (ptmt) REVERT: B 151 MET cc_start: 0.9083 (mtp) cc_final: 0.8701 (ttm) REVERT: B 169 ASP cc_start: 0.8307 (t0) cc_final: 0.7764 (t70) REVERT: B 300 PHE cc_start: 0.8756 (t80) cc_final: 0.8291 (t80) REVERT: B 318 MET cc_start: 0.6842 (ppp) cc_final: 0.6546 (ppp) REVERT: B 415 MET cc_start: 0.7300 (ttp) cc_final: 0.6922 (ttp) REVERT: B 464 MET cc_start: 0.8368 (tmm) cc_final: 0.7521 (tmm) REVERT: B 495 PHE cc_start: 0.7344 (m-80) cc_final: 0.6910 (m-80) REVERT: B 552 ILE cc_start: 0.8702 (mm) cc_final: 0.8382 (mm) REVERT: B 558 TYR cc_start: 0.8874 (m-80) cc_final: 0.8559 (m-80) REVERT: B 597 LEU cc_start: 0.8928 (mp) cc_final: 0.8683 (mp) REVERT: B 1020 HIS cc_start: 0.7528 (m170) cc_final: 0.7174 (m90) REVERT: B 1044 PHE cc_start: 0.8465 (t80) cc_final: 0.8037 (t80) REVERT: B 1106 THR cc_start: 0.9580 (p) cc_final: 0.9344 (p) REVERT: B 1109 LEU cc_start: 0.9512 (mt) cc_final: 0.9309 (mt) REVERT: B 1145 TYR cc_start: 0.8136 (m-80) cc_final: 0.7727 (m-10) REVERT: B 1389 PHE cc_start: 0.8905 (m-80) cc_final: 0.8336 (m-80) REVERT: C 55 ASN cc_start: 0.6701 (p0) cc_final: 0.5144 (t0) REVERT: C 121 MET cc_start: 0.9462 (pmm) cc_final: 0.9216 (pmm) REVERT: C 151 MET cc_start: 0.9040 (ttm) cc_final: 0.8341 (tpp) REVERT: C 250 VAL cc_start: 0.9059 (m) cc_final: 0.8845 (p) REVERT: C 356 ASP cc_start: 0.8948 (t0) cc_final: 0.8667 (t0) REVERT: C 373 ASP cc_start: 0.9405 (p0) cc_final: 0.9057 (t0) REVERT: C 464 MET cc_start: 0.8141 (mtt) cc_final: 0.7658 (mtt) REVERT: C 576 GLN cc_start: 0.5004 (OUTLIER) cc_final: 0.4547 (pp30) REVERT: C 673 MET cc_start: 0.8972 (mmp) cc_final: 0.8643 (mmt) REVERT: C 917 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.4327 (p0) REVERT: C 931 LEU cc_start: 0.9299 (tt) cc_final: 0.8704 (mp) REVERT: C 1122 ARG cc_start: 0.9040 (ttp-110) cc_final: 0.8574 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6405 (tt) cc_final: 0.5988 (pp) REVERT: D 101 MET cc_start: 0.8680 (ttt) cc_final: 0.7950 (ttt) REVERT: D 121 MET cc_start: 0.9285 (ptp) cc_final: 0.9055 (ppp) REVERT: D 145 LYS cc_start: 0.7279 (ptpt) cc_final: 0.6882 (ptmt) REVERT: D 151 MET cc_start: 0.9098 (mtp) cc_final: 0.8706 (ttm) REVERT: D 300 PHE cc_start: 0.8750 (t80) cc_final: 0.8279 (t80) REVERT: D 318 MET cc_start: 0.6847 (ppp) cc_final: 0.6554 (ppp) REVERT: D 415 MET cc_start: 0.7299 (ttp) cc_final: 0.6920 (ttp) REVERT: D 464 MET cc_start: 0.8379 (tmm) cc_final: 0.7524 (tmm) REVERT: D 495 PHE cc_start: 0.7355 (m-80) cc_final: 0.6918 (m-80) REVERT: D 552 ILE cc_start: 0.8706 (mm) cc_final: 0.8388 (mm) REVERT: D 558 TYR cc_start: 0.8880 (m-80) cc_final: 0.8562 (m-80) REVERT: D 597 LEU cc_start: 0.8922 (mp) cc_final: 0.8676 (mp) REVERT: D 1044 PHE cc_start: 0.8538 (t80) cc_final: 0.8145 (t80) REVERT: D 1106 THR cc_start: 0.9566 (p) cc_final: 0.9322 (p) REVERT: D 1109 LEU cc_start: 0.9511 (mt) cc_final: 0.9307 (mt) REVERT: D 1145 TYR cc_start: 0.8199 (m-80) cc_final: 0.7778 (m-80) REVERT: D 1208 MET cc_start: 0.9377 (ppp) cc_final: 0.9140 (ppp) REVERT: D 1209 THR cc_start: 0.8537 (t) cc_final: 0.8239 (t) REVERT: D 1330 TYR cc_start: 0.9420 (p90) cc_final: 0.9078 (p90) REVERT: D 1389 PHE cc_start: 0.8896 (m-80) cc_final: 0.8356 (m-80) outliers start: 5 outliers final: 1 residues processed: 619 average time/residue: 0.2407 time to fit residues: 250.5939 Evaluate side-chains 469 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 464 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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: 40.0000 chunk 163 optimal weight: 1.9990 chunk 187 optimal weight: 0.0970 chunk 350 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 295 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 389 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 646 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1089 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN B1291 GLN ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 646 HIS C 917 ASN C 938 ASN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS C1089 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 ASN D1051 GLN D1291 GLN ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.094885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.070314 restraints weight = 278540.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.072184 restraints weight = 215690.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073605 restraints weight = 176994.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074693 restraints weight = 151400.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.075572 restraints weight = 133850.526| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43672 Z= 0.157 Angle : 0.809 12.796 59452 Z= 0.396 Chirality : 0.050 0.419 6900 Planarity : 0.005 0.063 7554 Dihedral : 8.072 59.962 6812 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.34 % Favored : 86.55 % Rotamer: Outliers : 0.17 % Allowed : 2.47 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.10), residues: 5360 helix: -0.87 (0.17), residues: 812 sheet: -2.20 (0.13), residues: 1486 loop : -3.24 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 422 TYR 0.027 0.002 TYR A1152 PHE 0.021 0.002 PHE C1044 TRP 0.057 0.003 TRP C 739 HIS 0.018 0.001 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00338 (43574) covalent geometry : angle 0.78217 (59204) SS BOND : bond 0.00576 ( 46) SS BOND : angle 1.64488 ( 92) hydrogen bonds : bond 0.05640 ( 482) hydrogen bonds : angle 5.89003 ( 1446) link_ALPHA1-6 : bond 0.00546 ( 4) link_ALPHA1-6 : angle 1.45397 ( 12) link_BETA1-4 : bond 0.01078 ( 18) link_BETA1-4 : angle 2.76745 ( 54) link_NAG-ASN : bond 0.01038 ( 30) link_NAG-ASN : angle 4.72749 ( 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 596 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 588 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6724 (p0) cc_final: 0.5197 (t0) REVERT: A 121 MET cc_start: 0.9437 (pmm) cc_final: 0.9192 (pmm) REVERT: A 151 MET cc_start: 0.9010 (ttm) cc_final: 0.8274 (tpp) REVERT: A 215 THR cc_start: 0.8733 (t) cc_final: 0.8460 (m) REVERT: A 356 ASP cc_start: 0.8999 (t0) cc_final: 0.8725 (t0) REVERT: A 373 ASP cc_start: 0.9370 (p0) cc_final: 0.8954 (t0) REVERT: A 464 MET cc_start: 0.8057 (mtt) cc_final: 0.7555 (mtt) REVERT: A 576 GLN cc_start: 0.5087 (OUTLIER) cc_final: 0.4484 (pp30) REVERT: A 673 MET cc_start: 0.8976 (mmp) cc_final: 0.8640 (mmt) REVERT: A 931 LEU cc_start: 0.9294 (tt) cc_final: 0.8766 (mp) REVERT: A 975 GLN cc_start: 0.7874 (mm110) cc_final: 0.7653 (mm-40) REVERT: A 1044 PHE cc_start: 0.9581 (m-80) cc_final: 0.9292 (m-80) REVERT: A 1214 LEU cc_start: 0.6451 (tt) cc_final: 0.6040 (pp) REVERT: B 101 MET cc_start: 0.8567 (ttt) cc_final: 0.7868 (ttt) REVERT: B 151 MET cc_start: 0.9124 (mtp) cc_final: 0.8720 (ttm) REVERT: B 303 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8525 (mp-120) REVERT: B 318 MET cc_start: 0.6988 (ppp) cc_final: 0.6695 (ppp) REVERT: B 404 LEU cc_start: 0.9581 (tp) cc_final: 0.9234 (tp) REVERT: B 415 MET cc_start: 0.7160 (ttp) cc_final: 0.6605 (tmm) REVERT: B 495 PHE cc_start: 0.7396 (m-80) cc_final: 0.7077 (m-80) REVERT: B 552 ILE cc_start: 0.8626 (mm) cc_final: 0.8293 (mm) REVERT: B 597 LEU cc_start: 0.8899 (mp) cc_final: 0.8662 (mp) REVERT: B 933 LEU cc_start: 0.9414 (mp) cc_final: 0.9179 (mp) REVERT: B 1007 TYR cc_start: 0.9402 (m-80) cc_final: 0.9197 (m-80) REVERT: B 1044 PHE cc_start: 0.8511 (t80) cc_final: 0.7987 (t80) REVERT: B 1106 THR cc_start: 0.9575 (p) cc_final: 0.9360 (p) REVERT: B 1109 LEU cc_start: 0.9547 (mt) cc_final: 0.9261 (mt) REVERT: B 1150 LEU cc_start: 0.9207 (mt) cc_final: 0.8950 (mm) REVERT: B 1208 MET cc_start: 0.9368 (ppp) cc_final: 0.9148 (ppp) REVERT: B 1353 ASP cc_start: 0.8146 (m-30) cc_final: 0.7635 (p0) REVERT: B 1389 PHE cc_start: 0.8866 (m-80) cc_final: 0.8296 (m-80) REVERT: C 55 ASN cc_start: 0.6759 (p0) cc_final: 0.5226 (t0) REVERT: C 121 MET cc_start: 0.9424 (pmm) cc_final: 0.9182 (pmm) REVERT: C 151 MET cc_start: 0.9029 (ttm) cc_final: 0.8289 (tpp) REVERT: C 215 THR cc_start: 0.8725 (t) cc_final: 0.8452 (m) REVERT: C 356 ASP cc_start: 0.9008 (t0) cc_final: 0.8734 (t0) REVERT: C 373 ASP cc_start: 0.9371 (p0) cc_final: 0.8958 (t0) REVERT: C 464 MET cc_start: 0.8063 (mtt) cc_final: 0.7572 (mtt) REVERT: C 576 GLN cc_start: 0.5062 (OUTLIER) cc_final: 0.4458 (pp30) REVERT: C 673 MET cc_start: 0.9032 (mmp) cc_final: 0.8669 (mmt) REVERT: C 917 ASN cc_start: 0.5380 (OUTLIER) cc_final: 0.4307 (p0) REVERT: C 931 LEU cc_start: 0.9296 (tt) cc_final: 0.8734 (mp) REVERT: C 975 GLN cc_start: 0.7870 (mm110) cc_final: 0.7649 (mm-40) REVERT: C 1044 PHE cc_start: 0.9582 (m-80) cc_final: 0.9286 (m-80) REVERT: C 1214 LEU cc_start: 0.6460 (tt) cc_final: 0.6051 (pp) REVERT: D 101 MET cc_start: 0.8562 (ttt) cc_final: 0.7858 (ttt) REVERT: D 151 MET cc_start: 0.9163 (mtp) cc_final: 0.8724 (ttm) REVERT: D 303 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8531 (mp-120) REVERT: D 318 MET cc_start: 0.6997 (ppp) cc_final: 0.6705 (ppp) REVERT: D 404 LEU cc_start: 0.9577 (tp) cc_final: 0.9224 (tp) REVERT: D 415 MET cc_start: 0.7154 (ttp) cc_final: 0.6603 (tmm) REVERT: D 495 PHE cc_start: 0.7409 (m-80) cc_final: 0.7098 (m-80) REVERT: D 552 ILE cc_start: 0.8641 (mm) cc_final: 0.8306 (mm) REVERT: D 597 LEU cc_start: 0.8897 (mp) cc_final: 0.8660 (mp) REVERT: D 933 LEU cc_start: 0.9419 (mp) cc_final: 0.9185 (mp) REVERT: D 1044 PHE cc_start: 0.8451 (t80) cc_final: 0.7937 (t80) REVERT: D 1106 THR cc_start: 0.9559 (p) cc_final: 0.9339 (p) REVERT: D 1109 LEU cc_start: 0.9544 (mt) cc_final: 0.9263 (mt) REVERT: D 1150 LEU cc_start: 0.9220 (mt) cc_final: 0.8985 (mm) REVERT: D 1208 MET cc_start: 0.9454 (ppp) cc_final: 0.9254 (ppp) REVERT: D 1353 ASP cc_start: 0.8140 (m-30) cc_final: 0.7612 (p0) REVERT: D 1389 PHE cc_start: 0.8864 (m-80) cc_final: 0.8307 (m-80) outliers start: 8 outliers final: 1 residues processed: 595 average time/residue: 0.2378 time to fit residues: 238.3457 Evaluate side-chains 474 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 468 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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: 0.0870 chunk 492 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 167 optimal weight: 0.0470 chunk 3 optimal weight: 0.0980 chunk 128 optimal weight: 20.0000 overall best weight: 1.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1089 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1291 GLN B1325 GLN B1414 HIS ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 917 ASN C 938 ASN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS C1089 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1291 GLN D1325 GLN D1414 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.097022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.071950 restraints weight = 268839.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073953 restraints weight = 206233.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075390 restraints weight = 167620.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.076596 restraints weight = 143052.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.077511 restraints weight = 125567.165| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43672 Z= 0.138 Angle : 0.805 14.020 59452 Z= 0.392 Chirality : 0.050 0.401 6900 Planarity : 0.005 0.064 7554 Dihedral : 7.817 59.682 6812 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.15 % Favored : 87.74 % Rotamer: Outliers : 0.13 % Allowed : 1.11 % Favored : 98.77 % 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: -3.64 (0.10), residues: 5360 helix: -0.82 (0.17), residues: 810 sheet: -2.11 (0.13), residues: 1448 loop : -3.15 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 370 TYR 0.026 0.002 TYR A1152 PHE 0.044 0.002 PHE B1049 TRP 0.083 0.003 TRP C 739 HIS 0.010 0.001 HIS A1020 Details of bonding type rmsd covalent geometry : bond 0.00302 (43574) covalent geometry : angle 0.77782 (59204) SS BOND : bond 0.00427 ( 46) SS BOND : angle 1.43346 ( 92) hydrogen bonds : bond 0.05540 ( 482) hydrogen bonds : angle 5.81707 ( 1446) link_ALPHA1-6 : bond 0.00494 ( 4) link_ALPHA1-6 : angle 1.40033 ( 12) link_BETA1-4 : bond 0.01000 ( 18) link_BETA1-4 : angle 2.71840 ( 54) link_NAG-ASN : bond 0.00914 ( 30) link_NAG-ASN : angle 4.83648 ( 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 613 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 607 time to evaluate : 2.012 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: A 55 ASN cc_start: 0.6749 (p0) cc_final: 0.5260 (t0) REVERT: A 101 MET cc_start: 0.9305 (mpp) cc_final: 0.9088 (mpp) REVERT: A 121 MET cc_start: 0.9410 (pmm) cc_final: 0.9166 (pmm) REVERT: A 151 MET cc_start: 0.8821 (ttm) cc_final: 0.8080 (tpp) REVERT: A 215 THR cc_start: 0.8764 (t) cc_final: 0.8463 (m) REVERT: A 310 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8718 (tp-100) REVERT: A 356 ASP cc_start: 0.9040 (t0) cc_final: 0.8768 (t0) REVERT: A 373 ASP cc_start: 0.9348 (p0) cc_final: 0.8789 (m-30) REVERT: A 464 MET cc_start: 0.8101 (mtt) cc_final: 0.7619 (mtt) REVERT: A 576 GLN cc_start: 0.5039 (OUTLIER) cc_final: 0.4525 (pp30) REVERT: A 673 MET cc_start: 0.9017 (mmp) cc_final: 0.8697 (mmt) REVERT: A 931 LEU cc_start: 0.9189 (tt) cc_final: 0.8675 (mp) REVERT: A 975 GLN cc_start: 0.7906 (mm110) cc_final: 0.7695 (mm-40) REVERT: A 1044 PHE cc_start: 0.9551 (m-80) cc_final: 0.9305 (m-80) REVERT: A 1214 LEU cc_start: 0.6349 (tt) cc_final: 0.6022 (pp) REVERT: B 101 MET cc_start: 0.8513 (ttt) cc_final: 0.7827 (ttt) REVERT: B 151 MET cc_start: 0.9133 (mtp) cc_final: 0.8765 (ttt) REVERT: B 318 MET cc_start: 0.6952 (ppp) cc_final: 0.6687 (ppp) REVERT: B 385 PHE cc_start: 0.8380 (m-80) cc_final: 0.8145 (m-80) REVERT: B 415 MET cc_start: 0.7142 (ttp) cc_final: 0.6238 (tmm) REVERT: B 428 ARG cc_start: 0.8488 (tmt170) cc_final: 0.8234 (tmt-80) REVERT: B 432 TYR cc_start: 0.9023 (t80) cc_final: 0.8719 (t80) REVERT: B 464 MET cc_start: 0.8284 (tmm) cc_final: 0.7272 (tmm) REVERT: B 495 PHE cc_start: 0.7363 (m-80) cc_final: 0.7052 (m-80) REVERT: B 552 ILE cc_start: 0.8269 (mm) cc_final: 0.8048 (mm) REVERT: B 558 TYR cc_start: 0.8860 (m-80) cc_final: 0.8559 (m-80) REVERT: B 597 LEU cc_start: 0.8856 (mp) cc_final: 0.8600 (mp) REVERT: B 916 PHE cc_start: 0.8696 (m-10) cc_final: 0.8486 (m-10) REVERT: B 933 LEU cc_start: 0.9350 (mp) cc_final: 0.9112 (mp) REVERT: B 984 ILE cc_start: 0.7817 (mm) cc_final: 0.7570 (mm) REVERT: B 1044 PHE cc_start: 0.8518 (t80) cc_final: 0.7885 (t80) REVERT: B 1109 LEU cc_start: 0.9528 (mt) cc_final: 0.9278 (mt) REVERT: B 1145 TYR cc_start: 0.7853 (m-10) cc_final: 0.7549 (m-10) REVERT: B 1150 LEU cc_start: 0.9242 (mt) cc_final: 0.8958 (mm) REVERT: B 1168 LYS cc_start: 0.9532 (tptt) cc_final: 0.8635 (tptt) REVERT: B 1208 MET cc_start: 0.9313 (ppp) cc_final: 0.9089 (ppp) REVERT: B 1328 LEU cc_start: 0.9191 (tt) cc_final: 0.8825 (tt) REVERT: B 1330 TYR cc_start: 0.9382 (p90) cc_final: 0.9102 (p90) REVERT: B 1353 ASP cc_start: 0.8075 (m-30) cc_final: 0.7568 (p0) REVERT: B 1389 PHE cc_start: 0.8892 (m-80) cc_final: 0.8376 (m-80) REVERT: B 1431 PHE cc_start: 0.8589 (p90) cc_final: 0.8351 (p90) REVERT: B 1432 THR cc_start: 0.8078 (t) cc_final: 0.7777 (m) REVERT: C 55 ASN cc_start: 0.6766 (p0) cc_final: 0.5274 (t0) REVERT: C 121 MET cc_start: 0.9405 (pmm) cc_final: 0.9164 (pmm) REVERT: C 151 MET cc_start: 0.8838 (ttm) cc_final: 0.8096 (tpp) REVERT: C 215 THR cc_start: 0.8758 (t) cc_final: 0.8450 (m) REVERT: C 310 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8714 (tp-100) REVERT: C 356 ASP cc_start: 0.9049 (t0) cc_final: 0.8778 (t0) REVERT: C 373 ASP cc_start: 0.9361 (p0) cc_final: 0.8820 (m-30) REVERT: C 464 MET cc_start: 0.8094 (mtt) cc_final: 0.7622 (mtt) REVERT: C 576 GLN cc_start: 0.5052 (OUTLIER) cc_final: 0.4539 (pp30) REVERT: C 673 MET cc_start: 0.8987 (mmp) cc_final: 0.8654 (mmt) REVERT: C 917 ASN cc_start: 0.4996 (OUTLIER) cc_final: 0.4038 (p0) REVERT: C 931 LEU cc_start: 0.9190 (tt) cc_final: 0.8634 (mp) REVERT: C 975 GLN cc_start: 0.7899 (mm110) cc_final: 0.7690 (mm-40) REVERT: C 1044 PHE cc_start: 0.9551 (m-80) cc_final: 0.9301 (m-80) REVERT: C 1214 LEU cc_start: 0.6375 (tt) cc_final: 0.6049 (pp) REVERT: D 101 MET cc_start: 0.8517 (ttt) cc_final: 0.7830 (ttt) REVERT: D 151 MET cc_start: 0.9134 (mtp) cc_final: 0.8763 (ttt) REVERT: D 318 MET cc_start: 0.6957 (ppp) cc_final: 0.6694 (ppp) REVERT: D 385 PHE cc_start: 0.8376 (m-80) cc_final: 0.8140 (m-80) REVERT: D 415 MET cc_start: 0.7132 (ttp) cc_final: 0.6229 (tmm) REVERT: D 428 ARG cc_start: 0.8481 (tmt170) cc_final: 0.8227 (tmt-80) REVERT: D 432 TYR cc_start: 0.9024 (t80) cc_final: 0.8724 (t80) REVERT: D 464 MET cc_start: 0.8302 (tmm) cc_final: 0.7277 (tmm) REVERT: D 490 LEU cc_start: 0.6860 (mt) cc_final: 0.6594 (mp) REVERT: D 495 PHE cc_start: 0.7378 (m-80) cc_final: 0.7063 (m-80) REVERT: D 552 ILE cc_start: 0.8277 (mm) cc_final: 0.8057 (mm) REVERT: D 558 TYR cc_start: 0.8860 (m-80) cc_final: 0.8572 (m-80) REVERT: D 597 LEU cc_start: 0.8821 (mp) cc_final: 0.8559 (mp) REVERT: D 916 PHE cc_start: 0.8688 (m-10) cc_final: 0.8477 (m-10) REVERT: D 933 LEU cc_start: 0.9362 (mp) cc_final: 0.9085 (mp) REVERT: D 984 ILE cc_start: 0.7757 (mm) cc_final: 0.7534 (mm) REVERT: D 1044 PHE cc_start: 0.8557 (t80) cc_final: 0.7929 (t80) REVERT: D 1109 LEU cc_start: 0.9530 (mt) cc_final: 0.9284 (mt) REVERT: D 1145 TYR cc_start: 0.7901 (m-10) cc_final: 0.7600 (m-10) REVERT: D 1150 LEU cc_start: 0.9240 (mt) cc_final: 0.8952 (mm) REVERT: D 1168 LYS cc_start: 0.9484 (tptt) cc_final: 0.8563 (tptt) REVERT: D 1330 TYR cc_start: 0.9371 (p90) cc_final: 0.9147 (p90) REVERT: D 1353 ASP cc_start: 0.8077 (m-30) cc_final: 0.7566 (p0) REVERT: D 1389 PHE cc_start: 0.8890 (m-80) cc_final: 0.8388 (m-80) REVERT: D 1431 PHE cc_start: 0.8568 (p90) cc_final: 0.8312 (p90) REVERT: D 1432 THR cc_start: 0.8085 (t) cc_final: 0.7784 (m) outliers start: 6 outliers final: 1 residues processed: 612 average time/residue: 0.2424 time to fit residues: 250.1111 Evaluate side-chains 496 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 492 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 5.9990 chunk 390 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 440 optimal weight: 10.0000 chunk 399 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 479 optimal weight: 10.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** 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** A 938 ASN A 967 GLN A 975 GLN A1051 GLN A1062 HIS B 182 GLN B 358 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 ASN ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** 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 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C 975 GLN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1062 HIS D 182 GLN D 474 GLN ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN D1051 GLN D1077 ASN ** D1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 HIS ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.091014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.066767 restraints weight = 285041.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068498 restraints weight = 221903.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.069784 restraints weight = 183039.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.070781 restraints weight = 157651.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071564 restraints weight = 140186.209| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 43672 Z= 0.214 Angle : 0.897 13.563 59452 Z= 0.442 Chirality : 0.052 0.423 6900 Planarity : 0.006 0.069 7554 Dihedral : 8.021 59.728 6812 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.01 % Favored : 85.88 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % 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: -3.78 (0.10), residues: 5360 helix: -1.16 (0.16), residues: 812 sheet: -2.20 (0.13), residues: 1480 loop : -3.17 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1053 TYR 0.031 0.003 TYR D1211 PHE 0.039 0.002 PHE D1049 TRP 0.052 0.004 TRP C 739 HIS 0.012 0.002 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00453 (43574) covalent geometry : angle 0.86636 (59204) SS BOND : bond 0.00791 ( 46) SS BOND : angle 1.74338 ( 92) hydrogen bonds : bond 0.05990 ( 482) hydrogen bonds : angle 6.02644 ( 1446) link_ALPHA1-6 : bond 0.00548 ( 4) link_ALPHA1-6 : angle 1.46705 ( 12) link_BETA1-4 : bond 0.00926 ( 18) link_BETA1-4 : angle 2.88215 ( 54) link_NAG-ASN : bond 0.00967 ( 30) link_NAG-ASN : angle 5.40332 ( 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 553 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 550 time to evaluate : 1.387 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: A 55 ASN cc_start: 0.6878 (p0) cc_final: 0.5433 (t0) REVERT: A 121 MET cc_start: 0.9431 (pmm) cc_final: 0.9210 (pmm) REVERT: A 151 MET cc_start: 0.9053 (ttm) cc_final: 0.8277 (tpp) REVERT: A 191 SER cc_start: 0.7157 (t) cc_final: 0.6936 (t) REVERT: A 356 ASP cc_start: 0.8987 (t0) cc_final: 0.8689 (t0) REVERT: A 373 ASP cc_start: 0.9485 (p0) cc_final: 0.8901 (m-30) REVERT: A 464 MET cc_start: 0.8099 (mtt) cc_final: 0.7486 (mtt) REVERT: A 673 MET cc_start: 0.9050 (mmp) cc_final: 0.8711 (mmt) REVERT: A 931 LEU cc_start: 0.9363 (tt) cc_final: 0.8864 (mp) REVERT: A 975 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7754 (mm-40) REVERT: A 1044 PHE cc_start: 0.9598 (m-80) cc_final: 0.9378 (m-80) REVERT: A 1122 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8812 (mtp85) REVERT: A 1214 LEU cc_start: 0.6740 (tt) cc_final: 0.6321 (pp) REVERT: B 101 MET cc_start: 0.8770 (ttt) cc_final: 0.8061 (ttt) REVERT: B 151 MET cc_start: 0.9247 (mtp) cc_final: 0.8684 (ttm) REVERT: B 223 GLU cc_start: 0.7802 (tp30) cc_final: 0.7520 (tp30) REVERT: B 318 MET cc_start: 0.7176 (ppp) cc_final: 0.6899 (ppp) REVERT: B 415 MET cc_start: 0.7360 (ttp) cc_final: 0.6746 (tmm) REVERT: B 428 ARG cc_start: 0.8541 (tmt170) cc_final: 0.8341 (tmt-80) REVERT: B 432 TYR cc_start: 0.9084 (t80) cc_final: 0.8840 (t80) REVERT: B 464 MET cc_start: 0.8269 (tmm) cc_final: 0.7297 (tmm) REVERT: B 495 PHE cc_start: 0.7511 (m-80) cc_final: 0.7287 (m-80) REVERT: B 558 TYR cc_start: 0.8896 (m-80) cc_final: 0.8480 (m-80) REVERT: B 586 ARG cc_start: 0.8716 (ttt180) cc_final: 0.8127 (tpt170) REVERT: B 597 LEU cc_start: 0.8978 (mp) cc_final: 0.8757 (mp) REVERT: B 916 PHE cc_start: 0.8889 (m-10) cc_final: 0.8633 (m-10) REVERT: B 933 LEU cc_start: 0.9408 (mp) cc_final: 0.9137 (mp) REVERT: B 1044 PHE cc_start: 0.8551 (t80) cc_final: 0.7992 (t80) REVERT: B 1092 LYS cc_start: 0.9322 (mmpt) cc_final: 0.9081 (mmmt) REVERT: B 1106 THR cc_start: 0.9555 (p) cc_final: 0.9348 (p) REVERT: B 1109 LEU cc_start: 0.9596 (mt) cc_final: 0.9325 (mt) REVERT: B 1145 TYR cc_start: 0.8048 (m-10) cc_final: 0.7744 (m-10) REVERT: B 1150 LEU cc_start: 0.9380 (mt) cc_final: 0.9164 (mm) REVERT: B 1208 MET cc_start: 0.9442 (ppp) cc_final: 0.9241 (ppp) REVERT: B 1389 PHE cc_start: 0.8702 (m-80) cc_final: 0.8231 (m-80) REVERT: B 1431 PHE cc_start: 0.8634 (p90) cc_final: 0.8384 (p90) REVERT: B 1432 THR cc_start: 0.8185 (t) cc_final: 0.7888 (m) REVERT: C 55 ASN cc_start: 0.6877 (p0) cc_final: 0.5420 (t0) REVERT: C 121 MET cc_start: 0.9429 (pmm) cc_final: 0.9198 (pmm) REVERT: C 151 MET cc_start: 0.9060 (ttm) cc_final: 0.8282 (tpp) REVERT: C 191 SER cc_start: 0.7158 (t) cc_final: 0.6937 (t) REVERT: C 356 ASP cc_start: 0.8995 (t0) cc_final: 0.8701 (t0) REVERT: C 373 ASP cc_start: 0.9485 (p0) cc_final: 0.8895 (m-30) REVERT: C 464 MET cc_start: 0.8097 (mtt) cc_final: 0.7485 (mtt) REVERT: C 666 MET cc_start: 0.9044 (tpp) cc_final: 0.8814 (tpt) REVERT: C 673 MET cc_start: 0.9030 (mmp) cc_final: 0.8695 (mmt) REVERT: C 931 LEU cc_start: 0.9368 (tt) cc_final: 0.8853 (mp) REVERT: C 975 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7759 (mm-40) REVERT: C 1044 PHE cc_start: 0.9599 (m-80) cc_final: 0.9378 (m-80) REVERT: C 1122 ARG cc_start: 0.9031 (mtp180) cc_final: 0.8815 (mtp85) REVERT: C 1214 LEU cc_start: 0.6742 (tt) cc_final: 0.6324 (pp) REVERT: D 101 MET cc_start: 0.8770 (ttt) cc_final: 0.8059 (ttt) REVERT: D 151 MET cc_start: 0.9250 (mtp) cc_final: 0.8677 (ttm) REVERT: D 223 GLU cc_start: 0.7822 (tp30) cc_final: 0.7540 (tp30) REVERT: D 318 MET cc_start: 0.7189 (ppp) cc_final: 0.6909 (ppp) REVERT: D 415 MET cc_start: 0.7339 (ttp) cc_final: 0.6731 (tmm) REVERT: D 428 ARG cc_start: 0.8543 (tmt170) cc_final: 0.8339 (tmt-80) REVERT: D 432 TYR cc_start: 0.9084 (t80) cc_final: 0.8840 (t80) REVERT: D 464 MET cc_start: 0.8265 (tmm) cc_final: 0.7306 (tmm) REVERT: D 495 PHE cc_start: 0.7514 (m-80) cc_final: 0.7286 (m-80) REVERT: D 558 TYR cc_start: 0.8907 (m-80) cc_final: 0.8500 (m-80) REVERT: D 586 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8130 (tpt170) REVERT: D 597 LEU cc_start: 0.8972 (mp) cc_final: 0.8750 (mp) REVERT: D 914 THR cc_start: 0.9407 (p) cc_final: 0.9110 (p) REVERT: D 916 PHE cc_start: 0.8920 (m-10) cc_final: 0.8653 (m-10) REVERT: D 933 LEU cc_start: 0.9410 (mp) cc_final: 0.9140 (mp) REVERT: D 1044 PHE cc_start: 0.8615 (t80) cc_final: 0.8070 (t80) REVERT: D 1092 LYS cc_start: 0.9332 (mmpt) cc_final: 0.9096 (mmmt) REVERT: D 1106 THR cc_start: 0.9554 (p) cc_final: 0.9347 (p) REVERT: D 1109 LEU cc_start: 0.9602 (mt) cc_final: 0.9321 (mt) REVERT: D 1208 MET cc_start: 0.9425 (ppp) cc_final: 0.9121 (ppp) REVERT: D 1248 PHE cc_start: 0.8127 (t80) cc_final: 0.7454 (t80) REVERT: D 1253 ASP cc_start: 0.8286 (m-30) cc_final: 0.7524 (m-30) REVERT: D 1353 ASP cc_start: 0.7980 (m-30) cc_final: 0.7492 (p0) REVERT: D 1389 PHE cc_start: 0.8673 (m-80) cc_final: 0.8214 (m-80) REVERT: D 1431 PHE cc_start: 0.8602 (p90) cc_final: 0.8329 (p90) REVERT: D 1432 THR cc_start: 0.8187 (t) cc_final: 0.7881 (m) outliers start: 3 outliers final: 1 residues processed: 553 average time/residue: 0.2495 time to fit residues: 231.6021 Evaluate side-chains 451 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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: 8.9990 chunk 161 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 525 optimal weight: 10.0000 chunk 378 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1062 HIS ** A1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 302 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 GLN ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1435 GLN ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C1062 HIS ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 302 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN D1015 GLN D1051 GLN ** D1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1143 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** D1435 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.090441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.065943 restraints weight = 287233.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067699 restraints weight = 223498.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.068954 restraints weight = 183959.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.069902 restraints weight = 158777.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.070676 restraints weight = 141373.072| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 43672 Z= 0.225 Angle : 0.902 13.255 59452 Z= 0.449 Chirality : 0.052 0.424 6900 Planarity : 0.006 0.076 7554 Dihedral : 8.165 59.960 6812 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.09 % Favored : 84.79 % Rotamer: Outliers : 0.02 % Allowed : 0.60 % Favored : 99.38 % 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: -3.92 (0.10), residues: 5360 helix: -1.33 (0.16), residues: 814 sheet: -2.26 (0.12), residues: 1472 loop : -3.26 (0.10), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1081 TYR 0.041 0.003 TYR D1145 PHE 0.026 0.002 PHE D1458 TRP 0.054 0.004 TRP C 739 HIS 0.012 0.002 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00477 (43574) covalent geometry : angle 0.87305 (59204) SS BOND : bond 0.00647 ( 46) SS BOND : angle 1.80068 ( 92) hydrogen bonds : bond 0.05807 ( 482) hydrogen bonds : angle 6.19793 ( 1446) link_ALPHA1-6 : bond 0.00511 ( 4) link_ALPHA1-6 : angle 1.45114 ( 12) link_BETA1-4 : bond 0.01115 ( 18) link_BETA1-4 : angle 2.79993 ( 54) link_NAG-ASN : bond 0.00995 ( 30) link_NAG-ASN : angle 5.25989 ( 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 558 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 1.862 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 55 ASN cc_start: 0.6884 (p0) cc_final: 0.5616 (t0) REVERT: A 121 MET cc_start: 0.9401 (pmm) cc_final: 0.9191 (pmm) REVERT: A 151 MET cc_start: 0.9052 (ttm) cc_final: 0.8216 (tpp) REVERT: A 250 VAL cc_start: 0.9068 (m) cc_final: 0.8850 (p) REVERT: A 356 ASP cc_start: 0.8973 (t0) cc_final: 0.8656 (t0) REVERT: A 373 ASP cc_start: 0.9338 (p0) cc_final: 0.9052 (m-30) REVERT: A 464 MET cc_start: 0.8130 (mtt) cc_final: 0.7543 (mtt) REVERT: A 638 ASP cc_start: 0.9191 (t70) cc_final: 0.8867 (t0) REVERT: A 673 MET cc_start: 0.9057 (mmp) cc_final: 0.8699 (mmt) REVERT: A 931 LEU cc_start: 0.9313 (tt) cc_final: 0.8738 (mp) REVERT: A 1044 PHE cc_start: 0.9613 (m-80) cc_final: 0.9377 (m-80) REVERT: A 1122 ARG cc_start: 0.9081 (mtp180) cc_final: 0.8860 (mtp85) REVERT: A 1208 MET cc_start: 0.8945 (ppp) cc_final: 0.8665 (ppp) REVERT: A 1211 TYR cc_start: 0.8672 (m-80) cc_final: 0.8143 (m-80) REVERT: A 1214 LEU cc_start: 0.6588 (tt) cc_final: 0.6146 (tt) REVERT: B 101 MET cc_start: 0.8830 (ttt) cc_final: 0.8153 (ttt) REVERT: B 151 MET cc_start: 0.9278 (mtp) cc_final: 0.8701 (ttm) REVERT: B 223 GLU cc_start: 0.7836 (tp30) cc_final: 0.7550 (tp30) REVERT: B 318 MET cc_start: 0.7364 (ppp) cc_final: 0.7098 (ppp) REVERT: B 415 MET cc_start: 0.7347 (ttp) cc_final: 0.6747 (tmm) REVERT: B 432 TYR cc_start: 0.9195 (t80) cc_final: 0.8924 (t80) REVERT: B 586 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8201 (tpt170) REVERT: B 597 LEU cc_start: 0.8921 (mp) cc_final: 0.8654 (mp) REVERT: B 786 LEU cc_start: 0.8789 (tt) cc_final: 0.8125 (mp) REVERT: B 916 PHE cc_start: 0.9036 (m-10) cc_final: 0.8817 (m-10) REVERT: B 933 LEU cc_start: 0.9398 (mp) cc_final: 0.9139 (mp) REVERT: B 1044 PHE cc_start: 0.8744 (t80) cc_final: 0.8175 (t80) REVERT: B 1092 LYS cc_start: 0.9405 (mmpt) cc_final: 0.9194 (mmmt) REVERT: B 1109 LEU cc_start: 0.9631 (mt) cc_final: 0.9358 (mt) REVERT: B 1145 TYR cc_start: 0.8069 (m-10) cc_final: 0.7832 (m-10) REVERT: B 1150 LEU cc_start: 0.9381 (mt) cc_final: 0.9033 (mm) REVERT: B 1208 MET cc_start: 0.9437 (ppp) cc_final: 0.9230 (ppp) REVERT: B 1366 SER cc_start: 0.9260 (p) cc_final: 0.8950 (t) REVERT: B 1389 PHE cc_start: 0.8614 (m-80) cc_final: 0.8177 (m-80) REVERT: B 1431 PHE cc_start: 0.8717 (p90) cc_final: 0.8446 (p90) REVERT: B 1432 THR cc_start: 0.8298 (t) cc_final: 0.7951 (m) REVERT: C 55 ASN cc_start: 0.6884 (p0) cc_final: 0.5604 (t0) REVERT: C 121 MET cc_start: 0.9402 (pmm) cc_final: 0.9191 (pmm) REVERT: C 151 MET cc_start: 0.9064 (ttm) cc_final: 0.8231 (tpp) REVERT: C 356 ASP cc_start: 0.8986 (t0) cc_final: 0.8671 (t0) REVERT: C 373 ASP cc_start: 0.9337 (p0) cc_final: 0.9044 (m-30) REVERT: C 464 MET cc_start: 0.8122 (mtt) cc_final: 0.7543 (mtt) REVERT: C 638 ASP cc_start: 0.9185 (t70) cc_final: 0.8859 (t0) REVERT: C 673 MET cc_start: 0.9002 (mmp) cc_final: 0.8675 (mmt) REVERT: C 931 LEU cc_start: 0.9313 (tt) cc_final: 0.8732 (mp) REVERT: C 1003 LYS cc_start: 0.8710 (tptp) cc_final: 0.8496 (tppt) REVERT: C 1044 PHE cc_start: 0.9613 (m-80) cc_final: 0.9374 (m-80) REVERT: C 1122 ARG cc_start: 0.9077 (mtp180) cc_final: 0.8865 (mtp85) REVERT: C 1208 MET cc_start: 0.8952 (ppp) cc_final: 0.8672 (ppp) REVERT: C 1211 TYR cc_start: 0.8679 (m-80) cc_final: 0.8146 (m-80) REVERT: C 1214 LEU cc_start: 0.6604 (tt) cc_final: 0.6163 (tt) REVERT: D 101 MET cc_start: 0.8828 (ttt) cc_final: 0.8151 (ttt) REVERT: D 151 MET cc_start: 0.9255 (mtp) cc_final: 0.8685 (ttm) REVERT: D 223 GLU cc_start: 0.7843 (tp30) cc_final: 0.7551 (tp30) REVERT: D 318 MET cc_start: 0.7371 (ppp) cc_final: 0.7107 (ppp) REVERT: D 415 MET cc_start: 0.7345 (ttp) cc_final: 0.6762 (tmm) REVERT: D 432 TYR cc_start: 0.9195 (t80) cc_final: 0.8926 (t80) REVERT: D 495 PHE cc_start: 0.7535 (m-80) cc_final: 0.7333 (m-80) REVERT: D 586 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8208 (tpt170) REVERT: D 597 LEU cc_start: 0.8921 (mp) cc_final: 0.8659 (mp) REVERT: D 914 THR cc_start: 0.9460 (p) cc_final: 0.9152 (p) REVERT: D 916 PHE cc_start: 0.8998 (m-10) cc_final: 0.8717 (m-10) REVERT: D 933 LEU cc_start: 0.9406 (mp) cc_final: 0.9147 (mp) REVERT: D 1044 PHE cc_start: 0.8615 (t80) cc_final: 0.8073 (t80) REVERT: D 1109 LEU cc_start: 0.9642 (mt) cc_final: 0.9365 (mt) REVERT: D 1208 MET cc_start: 0.9402 (ppp) cc_final: 0.9148 (ppp) REVERT: D 1366 SER cc_start: 0.9289 (p) cc_final: 0.8993 (t) REVERT: D 1389 PHE cc_start: 0.8549 (m-80) cc_final: 0.8138 (m-80) REVERT: D 1431 PHE cc_start: 0.8725 (p90) cc_final: 0.8443 (p90) REVERT: D 1432 THR cc_start: 0.8267 (t) cc_final: 0.7924 (m) outliers start: 1 outliers final: 1 residues processed: 558 average time/residue: 0.2547 time to fit residues: 239.5380 Evaluate side-chains 452 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 451 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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: 9.9990 chunk 398 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 384 optimal weight: 0.0270 chunk 325 optimal weight: 0.6980 overall best weight: 3.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1062 HIS A1252 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.091866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067291 restraints weight = 278968.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.069099 restraints weight = 214987.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070487 restraints weight = 175914.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.071548 restraints weight = 150289.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.072361 restraints weight = 132730.049| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43672 Z= 0.170 Angle : 0.846 13.402 59452 Z= 0.416 Chirality : 0.051 0.406 6900 Planarity : 0.006 0.066 7554 Dihedral : 8.017 59.908 6812 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.16 % Favored : 85.73 % Rotamer: Outliers : 0.02 % Allowed : 0.49 % 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: -3.83 (0.10), residues: 5360 helix: -1.20 (0.16), residues: 824 sheet: -2.18 (0.13), residues: 1452 loop : -3.24 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1297 TYR 0.043 0.002 TYR D1145 PHE 0.040 0.002 PHE B1049 TRP 0.053 0.003 TRP C 739 HIS 0.009 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00366 (43574) covalent geometry : angle 0.81905 (59204) SS BOND : bond 0.00522 ( 46) SS BOND : angle 1.51247 ( 92) hydrogen bonds : bond 0.05549 ( 482) hydrogen bonds : angle 5.96322 ( 1446) link_ALPHA1-6 : bond 0.00522 ( 4) link_ALPHA1-6 : angle 1.43143 ( 12) link_BETA1-4 : bond 0.01075 ( 18) link_BETA1-4 : angle 2.77564 ( 54) link_NAG-ASN : bond 0.00883 ( 30) link_NAG-ASN : angle 4.96222 ( 90) =============================================================================== Job complete usr+sys time: 10123.28 seconds wall clock time: 175 minutes 57.01 seconds (10557.01 seconds total)