Starting phenix.real_space_refine on Thu Dec 26 03:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7o_12751/12_2024/7o7o_12751.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 1.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 24.84, per 1000 atoms: 0.58 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: 13.55 Conformation dependent library (CDL) restraints added in 5.8 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: 2.91 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: 10.07 Time building geometry restraints manager: 15.35 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: 0.00 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.900 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 86.250 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.310 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.120 ------------------------------------------------------------------------------- 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 43574 Z= 0.708 Angle : 1.239 27.950 59204 Z= 0.716 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 : 17.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (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 TRP 0.023 0.003 TRP B 741 HIS 0.012 0.002 HIS D 460 PHE 0.033 0.003 PHE D1389 TYR 0.035 0.003 TYR D1418 ARG 0.013 0.001 ARG C 387 *********************** 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 : 4.857 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: 0.7987 (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: 0.9132 (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: 0.8254 (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: 0.8460 (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: 0.3502 (OUTLIER) cc_final: 0.2471 (p0) outliers start: 20 outliers final: 6 residues processed: 734 average time/residue: 0.5868 time to fit residues: 689.8626 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 : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 9.9990 chunk 406 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 420 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 486 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 917 ASN D1123 ASN ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1302 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43574 Z= 0.296 Angle : 0.938 14.090 59204 Z= 0.467 Chirality : 0.053 0.392 6900 Planarity : 0.007 0.083 7554 Dihedral : 10.887 67.789 6812 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.54 % Favored : 86.31 % Rotamer: Outliers : 0.36 % Allowed : 7.89 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.09), residues: 5360 helix: -1.95 (0.15), residues: 802 sheet: -2.86 (0.11), residues: 1508 loop : -3.73 (0.09), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D1183 HIS 0.012 0.001 HIS B1020 PHE 0.035 0.002 PHE D 808 TYR 0.033 0.002 TYR B1418 ARG 0.007 0.001 ARG D 270 *********************** 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 662 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 645 time to evaluate : 4.858 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: A 34 LEU cc_start: 0.9467 (mp) cc_final: 0.9211 (mp) REVERT: A 55 ASN cc_start: 0.6776 (p0) cc_final: 0.4888 (t0) REVERT: A 151 MET cc_start: 0.8945 (ttm) cc_final: 0.8209 (tpp) REVERT: A 192 PHE cc_start: 0.7980 (t80) cc_final: 0.7721 (t80) REVERT: A 356 ASP cc_start: 0.8939 (t0) cc_final: 0.8738 (t0) REVERT: A 368 GLN cc_start: 0.9245 (tt0) cc_final: 0.9015 (tm-30) REVERT: A 464 MET cc_start: 0.7993 (mtt) cc_final: 0.7468 (mtt) REVERT: A 666 MET cc_start: 0.8829 (tpp) cc_final: 0.8587 (tpp) REVERT: A 732 ARG cc_start: 0.8807 (ptm160) cc_final: 0.8496 (ptm160) REVERT: A 917 ASN cc_start: 0.4779 (OUTLIER) cc_final: 0.4052 (p0) REVERT: A 931 LEU cc_start: 0.9261 (tt) cc_final: 0.8708 (mp) REVERT: A 968 MET cc_start: 0.2611 (mmt) cc_final: 0.2264 (mmt) REVERT: A 1003 LYS cc_start: 0.8631 (tptp) cc_final: 0.8240 (tptp) REVERT: A 1101 LEU cc_start: 0.8347 (mp) cc_final: 0.8123 (mp) REVERT: A 1122 ARG cc_start: 0.9035 (ttp-110) cc_final: 0.8736 (tmm-80) REVERT: B 151 MET cc_start: 0.8709 (mtp) cc_final: 0.8481 (mtp) REVERT: B 169 ASP cc_start: 0.8930 (t0) cc_final: 0.8602 (t0) REVERT: B 229 PHE cc_start: 0.9188 (p90) cc_final: 0.8952 (p90) REVERT: B 300 PHE cc_start: 0.8667 (t80) cc_final: 0.8445 (t80) REVERT: B 370 ARG cc_start: 0.9169 (ptm160) cc_final: 0.8844 (ptm160) REVERT: B 393 TYR cc_start: 0.8745 (t80) cc_final: 0.8166 (t80) REVERT: B 546 LEU cc_start: 0.8846 (tp) cc_final: 0.8639 (tp) REVERT: B 552 ILE cc_start: 0.8440 (mm) cc_final: 0.8068 (mm) REVERT: B 569 ASP cc_start: 0.8459 (t0) cc_final: 0.8250 (t0) REVERT: B 571 SER cc_start: 0.9144 (t) cc_final: 0.8707 (p) REVERT: B 607 MET cc_start: 0.8653 (tmm) cc_final: 0.8421 (ptp) REVERT: B 817 TYR cc_start: 0.8399 (m-10) cc_final: 0.8090 (m-80) REVERT: B 1020 HIS cc_start: 0.8153 (m170) cc_final: 0.7837 (m170) REVERT: B 1109 LEU cc_start: 0.9523 (mt) cc_final: 0.9246 (mt) REVERT: B 1132 TRP cc_start: 0.7080 (t-100) cc_final: 0.6648 (t-100) REVERT: B 1293 ASP cc_start: 0.9598 (m-30) cc_final: 0.8910 (m-30) REVERT: B 1299 LEU cc_start: 0.9516 (mm) cc_final: 0.9270 (mt) REVERT: B 1328 LEU cc_start: 0.9234 (tt) cc_final: 0.8731 (tt) REVERT: B 1330 TYR cc_start: 0.9311 (p90) cc_final: 0.8873 (p90) REVERT: B 1431 PHE cc_start: 0.8788 (p90) cc_final: 0.8516 (p90) REVERT: C 34 LEU cc_start: 0.9469 (mp) cc_final: 0.9212 (mp) REVERT: C 55 ASN cc_start: 0.6771 (p0) cc_final: 0.4887 (t0) REVERT: C 151 MET cc_start: 0.8938 (ttm) cc_final: 0.8201 (tpp) REVERT: C 166 TYR cc_start: 0.8069 (p90) cc_final: 0.7866 (p90) REVERT: C 192 PHE cc_start: 0.7977 (t80) cc_final: 0.7720 (t80) REVERT: C 368 GLN cc_start: 0.9242 (tt0) cc_final: 0.9012 (tm-30) REVERT: C 464 MET cc_start: 0.7992 (mtt) cc_final: 0.7468 (mtt) REVERT: C 666 MET cc_start: 0.8829 (tpp) cc_final: 0.8589 (tpp) REVERT: C 732 ARG cc_start: 0.8808 (ptm160) cc_final: 0.8496 (ptm160) REVERT: C 917 ASN cc_start: 0.4800 (OUTLIER) cc_final: 0.4067 (p0) REVERT: C 931 LEU cc_start: 0.9264 (tt) cc_final: 0.8713 (mp) REVERT: C 968 MET cc_start: 0.2553 (mmt) cc_final: 0.2280 (mmt) REVERT: C 1003 LYS cc_start: 0.8633 (tptp) cc_final: 0.8243 (tptp) REVERT: C 1101 LEU cc_start: 0.8345 (mp) cc_final: 0.8124 (mp) REVERT: C 1122 ARG cc_start: 0.9035 (ttp-110) cc_final: 0.8724 (tmm-80) REVERT: D 151 MET cc_start: 0.8712 (mtp) cc_final: 0.8486 (mtp) REVERT: D 169 ASP cc_start: 0.8933 (t0) cc_final: 0.8600 (t0) REVERT: D 229 PHE cc_start: 0.9187 (p90) cc_final: 0.8950 (p90) REVERT: D 300 PHE cc_start: 0.8667 (t80) cc_final: 0.8446 (t80) REVERT: D 370 ARG cc_start: 0.9164 (ptm160) cc_final: 0.8842 (ptm160) REVERT: D 546 LEU cc_start: 0.8846 (tp) cc_final: 0.8639 (tp) REVERT: D 552 ILE cc_start: 0.8446 (mm) cc_final: 0.8071 (mm) REVERT: D 569 ASP cc_start: 0.8462 (t0) cc_final: 0.8257 (t0) REVERT: D 571 SER cc_start: 0.9145 (t) cc_final: 0.8710 (p) REVERT: D 607 MET cc_start: 0.8653 (tmm) cc_final: 0.8419 (ptp) REVERT: D 817 TYR cc_start: 0.8398 (m-10) cc_final: 0.8088 (m-80) REVERT: D 1020 HIS cc_start: 0.8148 (m170) cc_final: 0.7923 (m170) REVERT: D 1109 LEU cc_start: 0.9519 (mt) cc_final: 0.9241 (mt) REVERT: D 1132 TRP cc_start: 0.7082 (t-100) cc_final: 0.6648 (t-100) REVERT: D 1293 ASP cc_start: 0.9598 (m-30) cc_final: 0.8907 (m-30) REVERT: D 1299 LEU cc_start: 0.9516 (mm) cc_final: 0.9268 (mt) REVERT: D 1328 LEU cc_start: 0.9235 (tt) cc_final: 0.8732 (tt) REVERT: D 1330 TYR cc_start: 0.9314 (p90) cc_final: 0.8872 (p90) REVERT: D 1431 PHE cc_start: 0.8763 (p90) cc_final: 0.8494 (p90) outliers start: 17 outliers final: 5 residues processed: 660 average time/residue: 0.5575 time to fit residues: 604.3506 Evaluate side-chains 493 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 486 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 405 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 487 optimal weight: 5.9990 chunk 526 optimal weight: 9.9990 chunk 434 optimal weight: 4.9990 chunk 483 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 391 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 846 HIS ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN B 566 ASN B 693 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 GLN C 179 GLN C 846 HIS C 917 ASN C 938 ASN C1062 HIS ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43574 Z= 0.298 Angle : 0.878 13.526 59204 Z= 0.445 Chirality : 0.053 0.452 6900 Planarity : 0.006 0.065 7554 Dihedral : 9.406 59.595 6812 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.92 % Favored : 85.86 % Rotamer: Outliers : 0.40 % Allowed : 7.25 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.10), residues: 5360 helix: -1.48 (0.16), residues: 802 sheet: -2.75 (0.12), residues: 1478 loop : -3.53 (0.09), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1183 HIS 0.019 0.002 HIS A1020 PHE 0.044 0.002 PHE D1049 TYR 0.035 0.002 TYR D1418 ARG 0.015 0.001 ARG A 214 *********************** 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 621 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 602 time to evaluate : 4.823 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: A 55 ASN cc_start: 0.6628 (p0) cc_final: 0.4864 (t0) REVERT: A 121 MET cc_start: 0.9434 (pmm) cc_final: 0.9194 (pmm) REVERT: A 166 TYR cc_start: 0.7977 (p90) cc_final: 0.7615 (p90) REVERT: A 192 PHE cc_start: 0.7814 (t80) cc_final: 0.7473 (t80) REVERT: A 356 ASP cc_start: 0.8946 (t0) cc_final: 0.8736 (t0) REVERT: A 464 MET cc_start: 0.8019 (mtt) cc_final: 0.7509 (mtt) REVERT: A 666 MET cc_start: 0.8752 (tpp) cc_final: 0.8491 (tpp) REVERT: A 931 LEU cc_start: 0.9280 (tt) cc_final: 0.8740 (mp) REVERT: A 968 MET cc_start: 0.3045 (mmt) cc_final: 0.2735 (mmt) REVERT: A 1003 LYS cc_start: 0.8652 (tptp) cc_final: 0.8367 (tppt) REVERT: A 1015 GLN cc_start: 0.9211 (tp40) cc_final: 0.8874 (tp40) REVERT: A 1122 ARG cc_start: 0.8947 (ttp-110) cc_final: 0.8555 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6632 (tt) cc_final: 0.6258 (tt) REVERT: B 151 MET cc_start: 0.8895 (mtp) cc_final: 0.8147 (mmm) REVERT: B 169 ASP cc_start: 0.8897 (t0) cc_final: 0.8523 (t0) REVERT: B 194 LEU cc_start: 0.9583 (mt) cc_final: 0.9244 (tp) REVERT: B 214 ARG cc_start: 0.9285 (mtt180) cc_final: 0.9074 (mtm-85) REVERT: B 370 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8831 (ptm160) REVERT: B 500 MET cc_start: 0.3371 (mmm) cc_final: 0.3170 (mmm) REVERT: B 520 MET cc_start: 0.6343 (tpp) cc_final: 0.6138 (tpp) REVERT: B 571 SER cc_start: 0.9110 (t) cc_final: 0.8831 (p) REVERT: B 597 LEU cc_start: 0.8945 (mp) cc_final: 0.8735 (mp) REVERT: B 817 TYR cc_start: 0.8250 (m-10) cc_final: 0.8024 (m-80) REVERT: B 1109 LEU cc_start: 0.9592 (mt) cc_final: 0.9343 (mt) REVERT: B 1132 TRP cc_start: 0.7016 (t-100) cc_final: 0.6475 (t-100) REVERT: B 1291 GLN cc_start: 0.8758 (pp30) cc_final: 0.8138 (pp30) REVERT: B 1293 ASP cc_start: 0.9478 (m-30) cc_final: 0.8815 (m-30) REVERT: B 1298 LEU cc_start: 0.9508 (pt) cc_final: 0.9266 (mt) REVERT: B 1299 LEU cc_start: 0.9540 (mm) cc_final: 0.9304 (mt) REVERT: C 55 ASN cc_start: 0.6626 (p0) cc_final: 0.4866 (t0) REVERT: C 121 MET cc_start: 0.9433 (pmm) cc_final: 0.9193 (pmm) REVERT: C 166 TYR cc_start: 0.8204 (p90) cc_final: 0.7915 (p90) REVERT: C 192 PHE cc_start: 0.7803 (t80) cc_final: 0.7435 (t80) REVERT: C 464 MET cc_start: 0.8018 (mtt) cc_final: 0.7508 (mtt) REVERT: C 666 MET cc_start: 0.8751 (tpp) cc_final: 0.8493 (tpp) REVERT: C 917 ASN cc_start: 0.5154 (OUTLIER) cc_final: 0.4206 (p0) REVERT: C 931 LEU cc_start: 0.9286 (tt) cc_final: 0.8711 (mp) REVERT: C 968 MET cc_start: 0.3035 (mmt) cc_final: 0.2724 (mmt) REVERT: C 1003 LYS cc_start: 0.8630 (tptp) cc_final: 0.8339 (tppt) REVERT: C 1015 GLN cc_start: 0.9202 (tp40) cc_final: 0.8858 (tp40) REVERT: C 1122 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8563 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6637 (tt) cc_final: 0.6263 (tt) REVERT: D 151 MET cc_start: 0.8872 (mtp) cc_final: 0.8145 (mpp) REVERT: D 169 ASP cc_start: 0.8901 (t0) cc_final: 0.8530 (t0) REVERT: D 194 LEU cc_start: 0.9584 (mt) cc_final: 0.9241 (tp) REVERT: D 370 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8830 (ptm160) REVERT: D 393 TYR cc_start: 0.8575 (m-10) cc_final: 0.8364 (m-80) REVERT: D 500 MET cc_start: 0.3372 (mmm) cc_final: 0.3168 (mmm) REVERT: D 571 SER cc_start: 0.9112 (t) cc_final: 0.8837 (p) REVERT: D 597 LEU cc_start: 0.8958 (mp) cc_final: 0.8748 (mp) REVERT: D 817 TYR cc_start: 0.8248 (m-10) cc_final: 0.8021 (m-80) REVERT: D 1020 HIS cc_start: 0.7760 (m170) cc_final: 0.7555 (m170) REVERT: D 1109 LEU cc_start: 0.9586 (mt) cc_final: 0.9336 (mt) REVERT: D 1132 TRP cc_start: 0.7017 (t-100) cc_final: 0.6476 (t-100) REVERT: D 1291 GLN cc_start: 0.8757 (pp30) cc_final: 0.8140 (pp30) REVERT: D 1293 ASP cc_start: 0.9480 (m-30) cc_final: 0.8815 (m-30) REVERT: D 1298 LEU cc_start: 0.9507 (pt) cc_final: 0.9266 (mt) REVERT: D 1299 LEU cc_start: 0.9541 (mm) cc_final: 0.9302 (mt) outliers start: 19 outliers final: 7 residues processed: 618 average time/residue: 0.5594 time to fit residues: 570.5457 Evaluate side-chains 470 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 462 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 8.9990 chunk 366 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 232 optimal weight: 0.0870 chunk 327 optimal weight: 0.0980 chunk 489 optimal weight: 3.9990 chunk 518 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 463 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS A1159 ASN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN C 938 ASN C1062 HIS C1159 ASN ** D 960 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43574 Z= 0.222 Angle : 0.815 11.773 59204 Z= 0.407 Chirality : 0.050 0.437 6900 Planarity : 0.006 0.101 7554 Dihedral : 8.695 59.329 6812 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.04 % Favored : 86.81 % Rotamer: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.10), residues: 5360 helix: -1.10 (0.17), residues: 804 sheet: -2.45 (0.12), residues: 1462 loop : -3.42 (0.09), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1040 HIS 0.012 0.001 HIS B1020 PHE 0.040 0.002 PHE B1049 TYR 0.031 0.002 TYR D1418 ARG 0.007 0.001 ARG B 338 *********************** 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 622 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 618 time to evaluate : 4.927 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: A 32 MET cc_start: 0.9289 (tmm) cc_final: 0.8930 (tmm) REVERT: A 34 LEU cc_start: 0.9476 (mt) cc_final: 0.9203 (mp) REVERT: A 55 ASN cc_start: 0.6766 (p0) cc_final: 0.4980 (t0) REVERT: A 121 MET cc_start: 0.9384 (pmm) cc_final: 0.9165 (pmm) REVERT: A 151 MET cc_start: 0.8965 (ttm) cc_final: 0.8318 (tpp) REVERT: A 215 THR cc_start: 0.8836 (t) cc_final: 0.8611 (m) REVERT: A 356 ASP cc_start: 0.8979 (t0) cc_final: 0.8776 (t0) REVERT: A 373 ASP cc_start: 0.9451 (p0) cc_final: 0.9143 (t0) REVERT: A 562 ASN cc_start: 0.7741 (t0) cc_final: 0.7314 (t0) REVERT: A 931 LEU cc_start: 0.9131 (tt) cc_final: 0.8605 (mp) REVERT: A 1003 LYS cc_start: 0.8740 (tptp) cc_final: 0.8449 (tppt) REVERT: A 1122 ARG cc_start: 0.8998 (ttp-110) cc_final: 0.8699 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6497 (tt) cc_final: 0.6179 (tt) REVERT: A 1254 THR cc_start: 0.9293 (m) cc_final: 0.8954 (m) REVERT: B 169 ASP cc_start: 0.8362 (t0) cc_final: 0.7913 (t70) REVERT: B 194 LEU cc_start: 0.9596 (mt) cc_final: 0.9191 (tp) REVERT: B 370 ARG cc_start: 0.9186 (ptm160) cc_final: 0.8872 (ptm160) REVERT: B 393 TYR cc_start: 0.8125 (m-80) cc_final: 0.7858 (m-80) REVERT: B 495 PHE cc_start: 0.7367 (m-80) cc_final: 0.6739 (m-80) REVERT: B 546 LEU cc_start: 0.9093 (tp) cc_final: 0.8873 (tp) REVERT: B 571 SER cc_start: 0.9117 (t) cc_final: 0.8902 (p) REVERT: B 597 LEU cc_start: 0.8834 (mp) cc_final: 0.8605 (mp) REVERT: B 817 TYR cc_start: 0.8211 (m-10) cc_final: 0.7987 (m-80) REVERT: B 1020 HIS cc_start: 0.7639 (m170) cc_final: 0.7338 (m170) REVERT: B 1109 LEU cc_start: 0.9558 (mt) cc_final: 0.9284 (mt) REVERT: B 1132 TRP cc_start: 0.7110 (t-100) cc_final: 0.6602 (t-100) REVERT: B 1150 LEU cc_start: 0.9043 (mt) cc_final: 0.8789 (mt) REVERT: B 1293 ASP cc_start: 0.9425 (m-30) cc_final: 0.9092 (m-30) REVERT: B 1298 LEU cc_start: 0.9532 (pt) cc_final: 0.9316 (mt) REVERT: B 1299 LEU cc_start: 0.9536 (mm) cc_final: 0.9320 (mt) REVERT: B 1330 TYR cc_start: 0.9343 (p90) cc_final: 0.8965 (p90) REVERT: B 1353 ASP cc_start: 0.8167 (m-30) cc_final: 0.7719 (p0) REVERT: B 1389 PHE cc_start: 0.9007 (m-80) cc_final: 0.8457 (m-80) REVERT: C 32 MET cc_start: 0.9289 (tmm) cc_final: 0.8926 (tmm) REVERT: C 34 LEU cc_start: 0.9475 (mt) cc_final: 0.9202 (mp) REVERT: C 55 ASN cc_start: 0.6767 (p0) cc_final: 0.4983 (t0) REVERT: C 121 MET cc_start: 0.9380 (pmm) cc_final: 0.9163 (pmm) REVERT: C 151 MET cc_start: 0.8959 (ttm) cc_final: 0.8303 (tpp) REVERT: C 166 TYR cc_start: 0.8123 (p90) cc_final: 0.7832 (p90) REVERT: C 373 ASP cc_start: 0.9452 (p0) cc_final: 0.9140 (t0) REVERT: C 562 ASN cc_start: 0.7750 (t0) cc_final: 0.7319 (t0) REVERT: C 917 ASN cc_start: 0.4765 (OUTLIER) cc_final: 0.3813 (p0) REVERT: C 931 LEU cc_start: 0.9135 (tt) cc_final: 0.8562 (mp) REVERT: C 1003 LYS cc_start: 0.8743 (tptp) cc_final: 0.8452 (tppt) REVERT: C 1122 ARG cc_start: 0.8994 (ttp-110) cc_final: 0.8686 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6501 (tt) cc_final: 0.6183 (tt) REVERT: C 1254 THR cc_start: 0.9293 (m) cc_final: 0.8955 (m) REVERT: D 169 ASP cc_start: 0.8339 (t0) cc_final: 0.7894 (t70) REVERT: D 194 LEU cc_start: 0.9597 (mt) cc_final: 0.9186 (tp) REVERT: D 370 ARG cc_start: 0.9174 (ptm160) cc_final: 0.8870 (ptm160) REVERT: D 415 MET cc_start: 0.7302 (ttp) cc_final: 0.6463 (tmm) REVERT: D 495 PHE cc_start: 0.7374 (m-80) cc_final: 0.6747 (m-80) REVERT: D 546 LEU cc_start: 0.9090 (tp) cc_final: 0.8867 (tp) REVERT: D 571 SER cc_start: 0.9122 (t) cc_final: 0.8907 (p) REVERT: D 597 LEU cc_start: 0.8847 (mp) cc_final: 0.8616 (mp) REVERT: D 817 TYR cc_start: 0.8207 (m-10) cc_final: 0.7983 (m-80) REVERT: D 1020 HIS cc_start: 0.7561 (m170) cc_final: 0.7338 (m170) REVERT: D 1109 LEU cc_start: 0.9559 (mt) cc_final: 0.9284 (mt) REVERT: D 1132 TRP cc_start: 0.7116 (t-100) cc_final: 0.6600 (t-100) REVERT: D 1150 LEU cc_start: 0.9040 (mt) cc_final: 0.8787 (mt) REVERT: D 1293 ASP cc_start: 0.9424 (m-30) cc_final: 0.9091 (m-30) REVERT: D 1298 LEU cc_start: 0.9531 (pt) cc_final: 0.9317 (mt) REVERT: D 1299 LEU cc_start: 0.9537 (mm) cc_final: 0.9320 (mt) REVERT: D 1330 TYR cc_start: 0.9342 (p90) cc_final: 0.8963 (p90) REVERT: D 1353 ASP cc_start: 0.8166 (m-30) cc_final: 0.7719 (p0) REVERT: D 1389 PHE cc_start: 0.9006 (m-80) cc_final: 0.8459 (m-80) outliers start: 4 outliers final: 1 residues processed: 619 average time/residue: 0.5560 time to fit residues: 568.7170 Evaluate side-chains 474 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 472 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 0.8980 chunk 294 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 385 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 442 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 465 optimal weight: 0.0570 chunk 130 optimal weight: 50.0000 overall best weight: 5.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 173 ASN ** 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 A1051 GLN A1062 HIS A1077 ASN ** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 693 GLN ** B1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 ASN B1123 ASN B1143 HIS ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1435 GLN ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 173 ASN ** C 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 HIS ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1051 GLN C1062 HIS C1077 ASN ** C1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS D 477 GLN ** D 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1077 ASN D1123 ASN D1143 HIS ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1435 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 43574 Z= 0.313 Angle : 0.877 13.222 59204 Z= 0.447 Chirality : 0.052 0.458 6900 Planarity : 0.006 0.087 7554 Dihedral : 8.584 59.200 6812 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.07 % Favored : 84.78 % Rotamer: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.10), residues: 5360 helix: -1.22 (0.16), residues: 808 sheet: -2.53 (0.13), residues: 1432 loop : -3.42 (0.09), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D1132 HIS 0.011 0.002 HIS D1195 PHE 0.026 0.002 PHE A 192 TYR 0.039 0.003 TYR D1418 ARG 0.008 0.001 ARG D1073 *********************** 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 580 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 576 time to evaluate : 5.131 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: A 34 LEU cc_start: 0.9416 (mt) cc_final: 0.9118 (mp) REVERT: A 55 ASN cc_start: 0.6789 (p0) cc_final: 0.5170 (t0) REVERT: A 121 MET cc_start: 0.9501 (pmm) cc_final: 0.9294 (pmm) REVERT: A 151 MET cc_start: 0.9135 (ttm) cc_final: 0.8353 (tpp) REVERT: A 356 ASP cc_start: 0.8947 (t0) cc_final: 0.8714 (t0) REVERT: A 464 MET cc_start: 0.8217 (mtt) cc_final: 0.7713 (mtt) REVERT: A 670 LEU cc_start: 0.9556 (mt) cc_final: 0.9334 (tt) REVERT: A 931 LEU cc_start: 0.9286 (tt) cc_final: 0.8768 (mp) REVERT: A 975 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7605 (mm-40) REVERT: A 1003 LYS cc_start: 0.8657 (tptp) cc_final: 0.8395 (tppt) REVERT: A 1044 PHE cc_start: 0.9515 (m-80) cc_final: 0.9259 (m-80) REVERT: A 1047 LYS cc_start: 0.8540 (pttt) cc_final: 0.8247 (pttp) REVERT: A 1122 ARG cc_start: 0.8999 (ttp-110) cc_final: 0.8546 (tmm-80) REVERT: A 1214 LEU cc_start: 0.6908 (tt) cc_final: 0.6612 (tt) REVERT: B 101 MET cc_start: 0.8636 (ttt) cc_final: 0.7869 (ttt) REVERT: B 370 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8839 (ptm160) REVERT: B 415 MET cc_start: 0.7410 (ttp) cc_final: 0.6771 (ttt) REVERT: B 464 MET cc_start: 0.9115 (ppp) cc_final: 0.8837 (ppp) REVERT: B 495 PHE cc_start: 0.7486 (m-80) cc_final: 0.7010 (m-80) REVERT: B 558 TYR cc_start: 0.8996 (m-80) cc_final: 0.8698 (m-80) REVERT: B 570 LEU cc_start: 0.8338 (pp) cc_final: 0.8100 (pp) REVERT: B 571 SER cc_start: 0.9176 (t) cc_final: 0.8886 (p) REVERT: B 597 LEU cc_start: 0.8928 (mp) cc_final: 0.8686 (mp) REVERT: B 1104 TYR cc_start: 0.9420 (m-10) cc_final: 0.9209 (m-10) REVERT: B 1109 LEU cc_start: 0.9617 (mt) cc_final: 0.9313 (mt) REVERT: B 1145 TYR cc_start: 0.8539 (m-10) cc_final: 0.7822 (m-10) REVERT: B 1248 PHE cc_start: 0.7970 (t80) cc_final: 0.7404 (t80) REVERT: B 1298 LEU cc_start: 0.9563 (pt) cc_final: 0.9338 (mt) REVERT: B 1299 LEU cc_start: 0.9462 (mm) cc_final: 0.9245 (mt) REVERT: B 1389 PHE cc_start: 0.8966 (m-80) cc_final: 0.8410 (m-80) REVERT: C 34 LEU cc_start: 0.9414 (mt) cc_final: 0.9115 (mp) REVERT: C 55 ASN cc_start: 0.6792 (p0) cc_final: 0.5173 (t0) REVERT: C 121 MET cc_start: 0.9500 (pmm) cc_final: 0.9292 (pmm) REVERT: C 151 MET cc_start: 0.9126 (ttm) cc_final: 0.8344 (tpp) REVERT: C 464 MET cc_start: 0.8214 (mtt) cc_final: 0.7714 (mtt) REVERT: C 670 LEU cc_start: 0.9557 (mt) cc_final: 0.9335 (tt) REVERT: C 931 LEU cc_start: 0.9304 (tt) cc_final: 0.8793 (mp) REVERT: C 1003 LYS cc_start: 0.8660 (tptp) cc_final: 0.8400 (tppt) REVERT: C 1044 PHE cc_start: 0.9515 (m-80) cc_final: 0.9260 (m-80) REVERT: C 1047 LYS cc_start: 0.8540 (pttt) cc_final: 0.8252 (pttp) REVERT: C 1122 ARG cc_start: 0.8999 (ttp-110) cc_final: 0.8539 (tmm-80) REVERT: C 1214 LEU cc_start: 0.6869 (tt) cc_final: 0.6567 (tt) REVERT: D 101 MET cc_start: 0.8641 (ttt) cc_final: 0.7874 (ttt) REVERT: D 370 ARG cc_start: 0.9159 (ptm160) cc_final: 0.8839 (ptm160) REVERT: D 415 MET cc_start: 0.7523 (ttp) cc_final: 0.7218 (ttp) REVERT: D 428 ARG cc_start: 0.9095 (ptp90) cc_final: 0.8562 (tpt90) REVERT: D 495 PHE cc_start: 0.7492 (m-80) cc_final: 0.7012 (m-80) REVERT: D 570 LEU cc_start: 0.8338 (pp) cc_final: 0.8093 (pp) REVERT: D 571 SER cc_start: 0.9181 (t) cc_final: 0.8892 (p) REVERT: D 597 LEU cc_start: 0.8941 (mp) cc_final: 0.8712 (mp) REVERT: D 817 TYR cc_start: 0.8149 (m-10) cc_final: 0.7946 (m-80) REVERT: D 1104 TYR cc_start: 0.9408 (m-10) cc_final: 0.9129 (m-10) REVERT: D 1109 LEU cc_start: 0.9619 (mt) cc_final: 0.9366 (mt) REVERT: D 1145 TYR cc_start: 0.8585 (m-10) cc_final: 0.7977 (m-10) REVERT: D 1248 PHE cc_start: 0.7944 (t80) cc_final: 0.7411 (t80) REVERT: D 1298 LEU cc_start: 0.9563 (pt) cc_final: 0.9338 (mt) REVERT: D 1299 LEU cc_start: 0.9464 (mm) cc_final: 0.9247 (mt) REVERT: D 1389 PHE cc_start: 0.8967 (m-80) cc_final: 0.8416 (m-80) outliers start: 4 outliers final: 1 residues processed: 577 average time/residue: 0.5570 time to fit residues: 533.1356 Evaluate side-chains 456 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 9.9990 chunk 466 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 518 optimal weight: 5.9990 chunk 430 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 693 GLN ** B 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN B1171 ASN ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN ** C1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS D 566 ASN D 693 GLN ** D 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN D1051 GLN D1195 HIS ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43574 Z= 0.265 Angle : 0.836 11.735 59204 Z= 0.422 Chirality : 0.051 0.441 6900 Planarity : 0.006 0.063 7554 Dihedral : 8.515 59.748 6812 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.25 % Favored : 85.63 % Rotamer: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.10), residues: 5360 helix: -1.28 (0.16), residues: 818 sheet: -2.46 (0.13), residues: 1440 loop : -3.35 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C1040 HIS 0.027 0.002 HIS A1020 PHE 0.034 0.002 PHE D1049 TYR 0.035 0.002 TYR D1418 ARG 0.011 0.001 ARG C 598 *********************** 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 586 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 583 time to evaluate : 5.006 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: A 55 ASN cc_start: 0.6908 (p0) cc_final: 0.5223 (t0) REVERT: A 121 MET cc_start: 0.9467 (pmm) cc_final: 0.9231 (pmm) REVERT: A 151 MET cc_start: 0.9121 (ttm) cc_final: 0.8363 (tpp) REVERT: A 356 ASP cc_start: 0.8936 (t0) cc_final: 0.8700 (t0) REVERT: A 464 MET cc_start: 0.8205 (mtt) cc_final: 0.7644 (mtt) REVERT: A 576 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4589 (pp30) REVERT: A 975 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7463 (mm-40) REVERT: A 1044 PHE cc_start: 0.9619 (m-80) cc_final: 0.9326 (m-80) REVERT: A 1214 LEU cc_start: 0.6799 (tt) cc_final: 0.6423 (pp) REVERT: B 101 MET cc_start: 0.8617 (ttt) cc_final: 0.7831 (ttt) REVERT: B 318 MET cc_start: 0.7074 (ppp) cc_final: 0.6786 (ppp) REVERT: B 370 ARG cc_start: 0.9132 (ptm160) cc_final: 0.8803 (ptm160) REVERT: B 415 MET cc_start: 0.7355 (ttp) cc_final: 0.7017 (ttp) REVERT: B 464 MET cc_start: 0.9079 (ppp) cc_final: 0.8736 (ppp) REVERT: B 495 PHE cc_start: 0.7510 (m-80) cc_final: 0.7114 (m-80) REVERT: B 520 MET cc_start: 0.5286 (tpt) cc_final: 0.5084 (tpt) REVERT: B 546 LEU cc_start: 0.9168 (tp) cc_final: 0.8960 (tp) REVERT: B 558 TYR cc_start: 0.9050 (m-80) cc_final: 0.8764 (m-80) REVERT: B 571 SER cc_start: 0.9197 (t) cc_final: 0.8883 (p) REVERT: B 597 LEU cc_start: 0.8814 (mp) cc_final: 0.8581 (mp) REVERT: B 1044 PHE cc_start: 0.8456 (t80) cc_final: 0.8072 (t80) REVERT: B 1073 ARG cc_start: 0.6412 (ptp90) cc_final: 0.6032 (ptp90) REVERT: B 1106 THR cc_start: 0.9632 (p) cc_final: 0.9373 (p) REVERT: B 1109 LEU cc_start: 0.9619 (mt) cc_final: 0.9301 (mt) REVERT: B 1143 HIS cc_start: 0.8838 (t70) cc_final: 0.8625 (t70) REVERT: B 1145 TYR cc_start: 0.8362 (m-10) cc_final: 0.8039 (m-10) REVERT: B 1150 LEU cc_start: 0.9294 (mt) cc_final: 0.8550 (mm) REVERT: B 1248 PHE cc_start: 0.7946 (t80) cc_final: 0.7360 (t80) REVERT: B 1299 LEU cc_start: 0.9427 (mm) cc_final: 0.9178 (mt) REVERT: B 1389 PHE cc_start: 0.8911 (m-80) cc_final: 0.8332 (m-80) REVERT: B 1415 VAL cc_start: 0.8738 (m) cc_final: 0.8494 (p) REVERT: C 55 ASN cc_start: 0.6915 (p0) cc_final: 0.5230 (t0) REVERT: C 121 MET cc_start: 0.9466 (pmm) cc_final: 0.9231 (pmm) REVERT: C 151 MET cc_start: 0.9116 (ttm) cc_final: 0.8357 (tpp) REVERT: C 464 MET cc_start: 0.8202 (mtt) cc_final: 0.7647 (mtt) REVERT: C 576 GLN cc_start: 0.5398 (OUTLIER) cc_final: 0.4586 (pp30) REVERT: C 1044 PHE cc_start: 0.9618 (m-80) cc_final: 0.9325 (m-80) REVERT: C 1214 LEU cc_start: 0.6804 (tt) cc_final: 0.6426 (pp) REVERT: D 101 MET cc_start: 0.8621 (ttt) cc_final: 0.7834 (ttt) REVERT: D 318 MET cc_start: 0.7070 (ppp) cc_final: 0.6784 (ppp) REVERT: D 370 ARG cc_start: 0.9132 (ptm160) cc_final: 0.8801 (ptm160) REVERT: D 415 MET cc_start: 0.7276 (ttp) cc_final: 0.6638 (tmm) REVERT: D 432 TYR cc_start: 0.9067 (t80) cc_final: 0.8676 (t80) REVERT: D 495 PHE cc_start: 0.7520 (m-80) cc_final: 0.7124 (m-80) REVERT: D 571 SER cc_start: 0.9204 (t) cc_final: 0.8892 (p) REVERT: D 597 LEU cc_start: 0.8772 (mp) cc_final: 0.8552 (mp) REVERT: D 1019 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8544 (tttt) REVERT: D 1044 PHE cc_start: 0.8457 (t80) cc_final: 0.8060 (t80) REVERT: D 1104 TYR cc_start: 0.9334 (m-10) cc_final: 0.9111 (m-10) REVERT: D 1106 THR cc_start: 0.9637 (p) cc_final: 0.9381 (p) REVERT: D 1109 LEU cc_start: 0.9617 (mt) cc_final: 0.9299 (mt) REVERT: D 1145 TYR cc_start: 0.8362 (m-10) cc_final: 0.7763 (m-10) REVERT: D 1150 LEU cc_start: 0.9277 (mt) cc_final: 0.8498 (mm) REVERT: D 1248 PHE cc_start: 0.7999 (t80) cc_final: 0.7435 (t80) REVERT: D 1299 LEU cc_start: 0.9421 (mm) cc_final: 0.9173 (mt) REVERT: D 1389 PHE cc_start: 0.8904 (m-80) cc_final: 0.8334 (m-80) outliers start: 3 outliers final: 1 residues processed: 585 average time/residue: 0.5605 time to fit residues: 548.0598 Evaluate side-chains 453 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 450 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 516 optimal weight: 1.9990 chunk 323 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A1062 HIS A1159 ASN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 GLN B1051 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 ASN C1062 HIS C1089 ASN C1159 ASN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN D 995 GLN D1051 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1425 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43574 Z= 0.237 Angle : 0.812 11.546 59204 Z= 0.408 Chirality : 0.050 0.426 6900 Planarity : 0.006 0.061 7554 Dihedral : 8.274 59.988 6812 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.55 % Favored : 85.34 % Rotamer: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.10), residues: 5360 helix: -1.13 (0.16), residues: 814 sheet: -2.37 (0.13), residues: 1426 loop : -3.32 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1132 HIS 0.016 0.001 HIS A1259 PHE 0.031 0.002 PHE D1049 TYR 0.056 0.002 TYR D1216 ARG 0.005 0.001 ARG B1271 *********************** 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 589 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 582 time to evaluate : 5.315 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: A 55 ASN cc_start: 0.7154 (p0) cc_final: 0.5359 (t0) REVERT: A 121 MET cc_start: 0.9415 (pmm) cc_final: 0.9203 (pmm) REVERT: A 151 MET cc_start: 0.9086 (ttm) cc_final: 0.8287 (tpp) REVERT: A 250 VAL cc_start: 0.9065 (m) cc_final: 0.8826 (p) REVERT: A 356 ASP cc_start: 0.8976 (t0) cc_final: 0.8742 (t0) REVERT: A 464 MET cc_start: 0.8124 (mtt) cc_final: 0.7559 (mtt) REVERT: A 520 MET cc_start: 0.8514 (mmm) cc_final: 0.8089 (mmm) REVERT: A 576 GLN cc_start: 0.4735 (OUTLIER) cc_final: 0.4334 (pp30) REVERT: A 975 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7555 (mm-40) REVERT: A 1044 PHE cc_start: 0.9589 (m-80) cc_final: 0.9321 (m-80) REVERT: A 1053 ARG cc_start: 0.9144 (mmp-170) cc_final: 0.8514 (mtt-85) REVERT: A 1122 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8767 (mtp85) REVERT: A 1214 LEU cc_start: 0.6459 (tt) cc_final: 0.6118 (pp) REVERT: B 101 MET cc_start: 0.8502 (ttt) cc_final: 0.7797 (ttt) REVERT: B 318 MET cc_start: 0.7359 (ppp) cc_final: 0.7053 (ppp) REVERT: B 370 ARG cc_start: 0.9135 (ptm160) cc_final: 0.8785 (ptm160) REVERT: B 404 LEU cc_start: 0.9487 (mt) cc_final: 0.9174 (mt) REVERT: B 415 MET cc_start: 0.7180 (ttp) cc_final: 0.6567 (tmm) REVERT: B 464 MET cc_start: 0.9083 (ppp) cc_final: 0.8669 (ppp) REVERT: B 495 PHE cc_start: 0.7551 (m-80) cc_final: 0.7290 (m-80) REVERT: B 500 MET cc_start: 0.4430 (mmm) cc_final: 0.3656 (mmt) REVERT: B 520 MET cc_start: 0.5291 (tpt) cc_final: 0.5046 (tpt) REVERT: B 558 TYR cc_start: 0.8996 (m-80) cc_final: 0.8701 (m-80) REVERT: B 571 SER cc_start: 0.9155 (t) cc_final: 0.8863 (p) REVERT: B 916 PHE cc_start: 0.8940 (m-10) cc_final: 0.8612 (m-10) REVERT: B 933 LEU cc_start: 0.9369 (mp) cc_final: 0.9130 (mp) REVERT: B 1044 PHE cc_start: 0.8449 (t80) cc_final: 0.7894 (t80) REVERT: B 1106 THR cc_start: 0.9564 (p) cc_final: 0.9281 (p) REVERT: B 1109 LEU cc_start: 0.9584 (mt) cc_final: 0.9262 (mt) REVERT: B 1145 TYR cc_start: 0.8272 (m-10) cc_final: 0.8043 (m-10) REVERT: B 1150 LEU cc_start: 0.9391 (mt) cc_final: 0.8680 (mm) REVERT: B 1248 PHE cc_start: 0.7937 (t80) cc_final: 0.7356 (t80) REVERT: B 1299 LEU cc_start: 0.9406 (mm) cc_final: 0.9164 (mt) REVERT: B 1353 ASP cc_start: 0.8024 (m-30) cc_final: 0.7503 (p0) REVERT: B 1389 PHE cc_start: 0.8895 (m-80) cc_final: 0.8319 (m-80) REVERT: C 55 ASN cc_start: 0.7154 (p0) cc_final: 0.5361 (t0) REVERT: C 121 MET cc_start: 0.9412 (pmm) cc_final: 0.9201 (pmm) REVERT: C 151 MET cc_start: 0.9079 (ttm) cc_final: 0.8276 (tpp) REVERT: C 250 VAL cc_start: 0.9060 (m) cc_final: 0.8824 (p) REVERT: C 464 MET cc_start: 0.8122 (mtt) cc_final: 0.7562 (mtt) REVERT: C 520 MET cc_start: 0.8525 (mmm) cc_final: 0.8101 (mmm) REVERT: C 576 GLN cc_start: 0.4742 (OUTLIER) cc_final: 0.4338 (pp30) REVERT: C 1044 PHE cc_start: 0.9588 (m-80) cc_final: 0.9323 (m-80) REVERT: C 1053 ARG cc_start: 0.9147 (mmp-170) cc_final: 0.8562 (mtt-85) REVERT: C 1122 ARG cc_start: 0.8992 (mtp180) cc_final: 0.8782 (mtp85) REVERT: C 1214 LEU cc_start: 0.6468 (tt) cc_final: 0.6123 (pp) REVERT: D 101 MET cc_start: 0.8503 (ttt) cc_final: 0.7800 (ttt) REVERT: D 318 MET cc_start: 0.7359 (ppp) cc_final: 0.7053 (ppp) REVERT: D 370 ARG cc_start: 0.9136 (ptm160) cc_final: 0.8814 (ptm160) REVERT: D 385 PHE cc_start: 0.8402 (m-80) cc_final: 0.8177 (m-80) REVERT: D 415 MET cc_start: 0.7237 (ttp) cc_final: 0.6638 (tmm) REVERT: D 432 TYR cc_start: 0.9121 (t80) cc_final: 0.8754 (t80) REVERT: D 495 PHE cc_start: 0.7549 (m-80) cc_final: 0.7285 (m-80) REVERT: D 500 MET cc_start: 0.4413 (mmm) cc_final: 0.3634 (mmt) REVERT: D 558 TYR cc_start: 0.8995 (m-80) cc_final: 0.8759 (m-80) REVERT: D 571 SER cc_start: 0.9158 (t) cc_final: 0.8870 (p) REVERT: D 597 LEU cc_start: 0.8840 (mp) cc_final: 0.8632 (mp) REVERT: D 916 PHE cc_start: 0.8950 (m-10) cc_final: 0.8620 (m-10) REVERT: D 933 LEU cc_start: 0.9369 (mp) cc_final: 0.9109 (mp) REVERT: D 1044 PHE cc_start: 0.8496 (t80) cc_final: 0.8045 (t80) REVERT: D 1092 LYS cc_start: 0.9247 (mmpt) cc_final: 0.8921 (tmtt) REVERT: D 1106 THR cc_start: 0.9582 (p) cc_final: 0.9323 (p) REVERT: D 1109 LEU cc_start: 0.9592 (mt) cc_final: 0.9270 (mt) REVERT: D 1150 LEU cc_start: 0.9344 (mt) cc_final: 0.8608 (mm) REVERT: D 1208 MET cc_start: 0.9416 (ppp) cc_final: 0.9179 (ppp) REVERT: D 1248 PHE cc_start: 0.7976 (t80) cc_final: 0.7424 (t80) REVERT: D 1299 LEU cc_start: 0.9412 (mm) cc_final: 0.9171 (mt) REVERT: D 1353 ASP cc_start: 0.8023 (m-30) cc_final: 0.7502 (p0) REVERT: D 1389 PHE cc_start: 0.8887 (m-80) cc_final: 0.8323 (m-80) outliers start: 7 outliers final: 1 residues processed: 588 average time/residue: 0.5479 time to fit residues: 534.1507 Evaluate side-chains 457 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 454 time to evaluate : 4.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 8.9990 chunk 206 optimal weight: 0.6980 chunk 308 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 406 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 85 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 584 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 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 C1089 ASN C1252 GLN ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 584 HIS ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN D1051 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1425 GLN ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43574 Z= 0.211 Angle : 0.785 12.450 59204 Z= 0.392 Chirality : 0.049 0.409 6900 Planarity : 0.006 0.061 7554 Dihedral : 8.008 59.915 6812 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.62 % Favored : 86.27 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.10), residues: 5360 helix: -0.98 (0.17), residues: 808 sheet: -2.13 (0.13), residues: 1414 loop : -3.31 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 741 HIS 0.014 0.001 HIS D1020 PHE 0.040 0.002 PHE D1049 TYR 0.049 0.002 TYR D1216 ARG 0.010 0.001 ARG B 147 *********************** 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 599 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 597 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7082 (p0) cc_final: 0.5353 (t0) REVERT: A 121 MET cc_start: 0.9358 (pmm) cc_final: 0.9144 (pmm) REVERT: A 151 MET cc_start: 0.8998 (ttm) cc_final: 0.8190 (tpp) REVERT: A 250 VAL cc_start: 0.9114 (m) cc_final: 0.8893 (p) REVERT: A 356 ASP cc_start: 0.9031 (t0) cc_final: 0.8797 (t0) REVERT: A 464 MET cc_start: 0.8085 (mtt) cc_final: 0.7532 (mtt) REVERT: A 520 MET cc_start: 0.8424 (mmm) cc_final: 0.8081 (mmm) REVERT: A 975 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7658 (mm-40) REVERT: A 983 ASN cc_start: 0.8344 (m110) cc_final: 0.8144 (m-40) REVERT: A 1053 ARG cc_start: 0.9075 (mmp-170) cc_final: 0.8547 (mtt90) REVERT: A 1122 ARG cc_start: 0.8981 (mtp180) cc_final: 0.8781 (mtp85) REVERT: A 1214 LEU cc_start: 0.6499 (tt) cc_final: 0.6131 (pp) REVERT: B 101 MET cc_start: 0.8491 (ttt) cc_final: 0.7807 (ttt) REVERT: B 151 MET cc_start: 0.9103 (mpp) cc_final: 0.8669 (ttm) REVERT: B 189 GLN cc_start: 0.9421 (pm20) cc_final: 0.9121 (pm20) REVERT: B 223 GLU cc_start: 0.7468 (tp30) cc_final: 0.7143 (tp30) REVERT: B 318 MET cc_start: 0.7248 (ppp) cc_final: 0.6958 (ppp) REVERT: B 385 PHE cc_start: 0.8354 (m-80) cc_final: 0.8097 (m-80) REVERT: B 415 MET cc_start: 0.7163 (ttp) cc_final: 0.6182 (tmm) REVERT: B 464 MET cc_start: 0.9014 (ppp) cc_final: 0.8698 (ppp) REVERT: B 495 PHE cc_start: 0.7500 (m-80) cc_final: 0.7239 (m-80) REVERT: B 500 MET cc_start: 0.4306 (mmm) cc_final: 0.3625 (mmt) REVERT: B 520 MET cc_start: 0.5246 (tpt) cc_final: 0.5036 (tpt) REVERT: B 558 TYR cc_start: 0.8994 (m-80) cc_final: 0.8730 (m-80) REVERT: B 571 SER cc_start: 0.9003 (t) cc_final: 0.8799 (p) REVERT: B 786 LEU cc_start: 0.7943 (tp) cc_final: 0.7711 (tp) REVERT: B 914 THR cc_start: 0.9527 (p) cc_final: 0.9233 (p) REVERT: B 916 PHE cc_start: 0.8878 (m-10) cc_final: 0.8547 (m-10) REVERT: B 933 LEU cc_start: 0.9337 (mp) cc_final: 0.9073 (mp) REVERT: B 1019 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8562 (tttt) REVERT: B 1044 PHE cc_start: 0.8446 (t80) cc_final: 0.7838 (t80) REVERT: B 1092 LYS cc_start: 0.9253 (mmpt) cc_final: 0.8813 (tmtt) REVERT: B 1109 LEU cc_start: 0.9558 (mt) cc_final: 0.9289 (mt) REVERT: B 1145 TYR cc_start: 0.8085 (m-10) cc_final: 0.7847 (m-10) REVERT: B 1150 LEU cc_start: 0.9401 (mt) cc_final: 0.9120 (mm) REVERT: B 1208 MET cc_start: 0.9351 (ppp) cc_final: 0.9119 (ppp) REVERT: B 1248 PHE cc_start: 0.7904 (t80) cc_final: 0.7364 (t80) REVERT: B 1253 ASP cc_start: 0.8047 (m-30) cc_final: 0.7471 (m-30) REVERT: B 1299 LEU cc_start: 0.9407 (mm) cc_final: 0.9196 (mt) REVERT: B 1353 ASP cc_start: 0.8036 (m-30) cc_final: 0.7512 (p0) REVERT: B 1389 PHE cc_start: 0.8912 (m-80) cc_final: 0.8358 (m-80) REVERT: B 1431 PHE cc_start: 0.8645 (p90) cc_final: 0.8444 (p90) REVERT: C 55 ASN cc_start: 0.7088 (p0) cc_final: 0.5357 (t0) REVERT: C 121 MET cc_start: 0.9356 (pmm) cc_final: 0.9143 (pmm) REVERT: C 151 MET cc_start: 0.8991 (ttm) cc_final: 0.8183 (tpp) REVERT: C 250 VAL cc_start: 0.9112 (m) cc_final: 0.8891 (p) REVERT: C 464 MET cc_start: 0.8084 (mtt) cc_final: 0.7534 (mtt) REVERT: C 520 MET cc_start: 0.8456 (mmm) cc_final: 0.8135 (mmm) REVERT: C 931 LEU cc_start: 0.9177 (tt) cc_final: 0.8668 (mp) REVERT: C 1053 ARG cc_start: 0.9062 (mmp-170) cc_final: 0.8538 (mtt90) REVERT: C 1122 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8780 (mtp85) REVERT: C 1214 LEU cc_start: 0.6502 (tt) cc_final: 0.6129 (pp) REVERT: D 101 MET cc_start: 0.8495 (ttt) cc_final: 0.7814 (ttt) REVERT: D 223 GLU cc_start: 0.7470 (tp30) cc_final: 0.7143 (tp30) REVERT: D 318 MET cc_start: 0.7252 (ppp) cc_final: 0.6964 (ppp) REVERT: D 385 PHE cc_start: 0.8312 (m-80) cc_final: 0.8079 (m-80) REVERT: D 415 MET cc_start: 0.7198 (ttp) cc_final: 0.6217 (tmm) REVERT: D 495 PHE cc_start: 0.7475 (m-80) cc_final: 0.7210 (m-80) REVERT: D 500 MET cc_start: 0.4285 (mmm) cc_final: 0.3598 (mmt) REVERT: D 597 LEU cc_start: 0.8801 (mp) cc_final: 0.8598 (mp) REVERT: D 786 LEU cc_start: 0.7892 (tp) cc_final: 0.7653 (tp) REVERT: D 914 THR cc_start: 0.9518 (p) cc_final: 0.9202 (p) REVERT: D 916 PHE cc_start: 0.8896 (m-10) cc_final: 0.8560 (m-10) REVERT: D 933 LEU cc_start: 0.9335 (mp) cc_final: 0.9070 (mp) REVERT: D 1019 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8671 (tttt) REVERT: D 1044 PHE cc_start: 0.8499 (t80) cc_final: 0.7935 (t80) REVERT: D 1092 LYS cc_start: 0.9172 (mmpt) cc_final: 0.8905 (tmtt) REVERT: D 1109 LEU cc_start: 0.9569 (mt) cc_final: 0.9305 (mt) REVERT: D 1150 LEU cc_start: 0.9413 (mt) cc_final: 0.9150 (mm) REVERT: D 1208 MET cc_start: 0.9396 (ppp) cc_final: 0.9149 (ppp) REVERT: D 1248 PHE cc_start: 0.7922 (t80) cc_final: 0.7349 (t80) REVERT: D 1299 LEU cc_start: 0.9412 (mm) cc_final: 0.9199 (mt) REVERT: D 1389 PHE cc_start: 0.8920 (m-80) cc_final: 0.8362 (m-80) outliers start: 2 outliers final: 2 residues processed: 598 average time/residue: 0.5684 time to fit residues: 570.6694 Evaluate side-chains 470 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 0.9990 chunk 494 optimal weight: 4.9990 chunk 451 optimal weight: 9.9990 chunk 481 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 455 optimal weight: 0.7980 chunk 479 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 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 ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 43574 Z= 0.232 Angle : 0.798 12.344 59204 Z= 0.400 Chirality : 0.050 0.410 6900 Planarity : 0.006 0.062 7554 Dihedral : 7.908 59.929 6812 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.60 % Favored : 86.29 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.10), residues: 5360 helix: -0.99 (0.17), residues: 816 sheet: -2.11 (0.13), residues: 1410 loop : -3.29 (0.10), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 741 HIS 0.020 0.001 HIS D1259 PHE 0.032 0.002 PHE D 286 TYR 0.048 0.002 TYR D1216 ARG 0.010 0.001 ARG B 147 *********************** 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 579 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 578 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7112 (p0) cc_final: 0.5577 (t0) REVERT: A 151 MET cc_start: 0.9047 (ttm) cc_final: 0.8254 (tpp) REVERT: A 250 VAL cc_start: 0.9134 (m) cc_final: 0.8927 (p) REVERT: A 356 ASP cc_start: 0.9027 (t0) cc_final: 0.8792 (t0) REVERT: A 464 MET cc_start: 0.7716 (mtt) cc_final: 0.7186 (mtt) REVERT: A 520 MET cc_start: 0.8465 (mmm) cc_final: 0.8123 (mmm) REVERT: A 975 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7678 (mm-40) REVERT: A 1086 LEU cc_start: 0.6244 (tp) cc_final: 0.6013 (tp) REVERT: A 1122 ARG cc_start: 0.9009 (mtp180) cc_final: 0.8801 (mtp85) REVERT: A 1214 LEU cc_start: 0.6766 (tt) cc_final: 0.6395 (pp) REVERT: B 101 MET cc_start: 0.8530 (ttt) cc_final: 0.7827 (ttt) REVERT: B 223 GLU cc_start: 0.7440 (tp30) cc_final: 0.7225 (tp30) REVERT: B 318 MET cc_start: 0.7309 (ppp) cc_final: 0.7011 (ppp) REVERT: B 385 PHE cc_start: 0.8413 (m-80) cc_final: 0.8152 (m-80) REVERT: B 404 LEU cc_start: 0.9604 (tp) cc_final: 0.9205 (tp) REVERT: B 415 MET cc_start: 0.7348 (ttp) cc_final: 0.6735 (tmm) REVERT: B 464 MET cc_start: 0.9004 (ppp) cc_final: 0.8604 (ppp) REVERT: B 495 PHE cc_start: 0.7503 (m-80) cc_final: 0.7284 (m-80) REVERT: B 500 MET cc_start: 0.4544 (mmm) cc_final: 0.4232 (mmm) REVERT: B 520 MET cc_start: 0.5230 (tpt) cc_final: 0.5016 (tpt) REVERT: B 558 TYR cc_start: 0.9022 (m-80) cc_final: 0.8718 (m-80) REVERT: B 571 SER cc_start: 0.8998 (t) cc_final: 0.8754 (p) REVERT: B 741 TRP cc_start: 0.7428 (t60) cc_final: 0.6950 (t60) REVERT: B 786 LEU cc_start: 0.7968 (tp) cc_final: 0.7174 (mp) REVERT: B 914 THR cc_start: 0.9507 (p) cc_final: 0.9202 (p) REVERT: B 916 PHE cc_start: 0.8954 (m-10) cc_final: 0.8620 (m-10) REVERT: B 933 LEU cc_start: 0.9383 (mp) cc_final: 0.9157 (mp) REVERT: B 1044 PHE cc_start: 0.8465 (t80) cc_final: 0.7853 (t80) REVERT: B 1092 LYS cc_start: 0.9370 (mmpt) cc_final: 0.9106 (mmmt) REVERT: B 1106 THR cc_start: 0.9576 (p) cc_final: 0.9373 (p) REVERT: B 1109 LEU cc_start: 0.9594 (mt) cc_final: 0.9337 (mt) REVERT: B 1150 LEU cc_start: 0.9490 (mt) cc_final: 0.9132 (mm) REVERT: B 1208 MET cc_start: 0.9398 (ppp) cc_final: 0.9161 (ppp) REVERT: B 1248 PHE cc_start: 0.8003 (t80) cc_final: 0.7428 (t80) REVERT: B 1253 ASP cc_start: 0.8080 (m-30) cc_final: 0.7570 (m-30) REVERT: B 1299 LEU cc_start: 0.9328 (mm) cc_final: 0.9112 (mt) REVERT: B 1327 SER cc_start: 0.9445 (t) cc_final: 0.9235 (p) REVERT: B 1353 ASP cc_start: 0.8012 (m-30) cc_final: 0.7523 (p0) REVERT: B 1389 PHE cc_start: 0.8870 (m-80) cc_final: 0.8311 (m-80) REVERT: C 55 ASN cc_start: 0.7112 (p0) cc_final: 0.5574 (t0) REVERT: C 151 MET cc_start: 0.9042 (ttm) cc_final: 0.8245 (tpp) REVERT: C 250 VAL cc_start: 0.9133 (m) cc_final: 0.8926 (p) REVERT: C 464 MET cc_start: 0.7773 (mtt) cc_final: 0.7266 (mtt) REVERT: C 520 MET cc_start: 0.8451 (mmm) cc_final: 0.8112 (mmm) REVERT: C 1086 LEU cc_start: 0.6188 (tp) cc_final: 0.5899 (tp) REVERT: C 1122 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8793 (mtp85) REVERT: C 1214 LEU cc_start: 0.6770 (tt) cc_final: 0.6362 (pp) REVERT: D 101 MET cc_start: 0.8532 (ttt) cc_final: 0.7831 (ttt) REVERT: D 151 MET cc_start: 0.9138 (mpp) cc_final: 0.8732 (ttm) REVERT: D 223 GLU cc_start: 0.7437 (tp30) cc_final: 0.7217 (tp30) REVERT: D 318 MET cc_start: 0.7313 (ppp) cc_final: 0.7017 (ppp) REVERT: D 385 PHE cc_start: 0.8413 (m-80) cc_final: 0.8181 (m-80) REVERT: D 415 MET cc_start: 0.7273 (ttp) cc_final: 0.6265 (tmm) REVERT: D 495 PHE cc_start: 0.7520 (m-80) cc_final: 0.7284 (m-80) REVERT: D 500 MET cc_start: 0.4538 (mmm) cc_final: 0.4242 (mmm) REVERT: D 597 LEU cc_start: 0.8875 (mp) cc_final: 0.8675 (mp) REVERT: D 786 LEU cc_start: 0.7982 (tp) cc_final: 0.7193 (mp) REVERT: D 914 THR cc_start: 0.9509 (p) cc_final: 0.9184 (p) REVERT: D 916 PHE cc_start: 0.8973 (m-10) cc_final: 0.8638 (m-10) REVERT: D 933 LEU cc_start: 0.9382 (mp) cc_final: 0.9157 (mp) REVERT: D 1019 LYS cc_start: 0.9003 (ptpp) cc_final: 0.8702 (tttt) REVERT: D 1044 PHE cc_start: 0.8557 (t80) cc_final: 0.7964 (t80) REVERT: D 1092 LYS cc_start: 0.9237 (mmpt) cc_final: 0.8920 (tmtt) REVERT: D 1109 LEU cc_start: 0.9577 (mt) cc_final: 0.9306 (mt) REVERT: D 1145 TYR cc_start: 0.8830 (m-80) cc_final: 0.8326 (m-80) REVERT: D 1150 LEU cc_start: 0.9520 (mt) cc_final: 0.9176 (mm) REVERT: D 1208 MET cc_start: 0.9416 (ppp) cc_final: 0.9181 (ppp) REVERT: D 1248 PHE cc_start: 0.7993 (t80) cc_final: 0.7439 (t80) REVERT: D 1253 ASP cc_start: 0.8050 (m-30) cc_final: 0.7484 (m-30) REVERT: D 1299 LEU cc_start: 0.9333 (mm) cc_final: 0.9116 (mt) REVERT: D 1327 SER cc_start: 0.9451 (t) cc_final: 0.9231 (p) REVERT: D 1389 PHE cc_start: 0.8873 (m-80) cc_final: 0.8323 (m-80) REVERT: D 1431 PHE cc_start: 0.8645 (p90) cc_final: 0.8419 (p90) REVERT: D 1432 THR cc_start: 0.8266 (t) cc_final: 0.7904 (m) outliers start: 1 outliers final: 1 residues processed: 578 average time/residue: 0.5532 time to fit residues: 535.3507 Evaluate side-chains 462 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 20.0000 chunk 509 optimal weight: 0.4980 chunk 310 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 533 optimal weight: 9.9990 chunk 491 optimal weight: 10.0000 chunk 425 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 693 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN C1062 HIS ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 693 GLN ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 : 0.004 0.048 43574 Z= 0.264 Angle : 0.827 14.116 59204 Z= 0.416 Chirality : 0.051 0.415 6900 Planarity : 0.006 0.179 7554 Dihedral : 7.996 59.876 6812 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.02 % Favored : 84.87 % Rotamer: Outliers : 0.02 % Allowed : 0.51 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.10), residues: 5360 helix: -1.19 (0.16), residues: 816 sheet: -2.18 (0.13), residues: 1414 loop : -3.30 (0.10), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B1132 HIS 0.021 0.002 HIS B1259 PHE 0.033 0.002 PHE D1049 TYR 0.049 0.002 TYR B1216 ARG 0.016 0.001 ARG B1073 ********************** 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 568 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 5.567 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: A 55 ASN cc_start: 0.7131 (p0) cc_final: 0.5676 (t0) REVERT: A 99 GLU cc_start: 0.8825 (tt0) cc_final: 0.8399 (tt0) REVERT: A 151 MET cc_start: 0.9077 (ttm) cc_final: 0.8302 (tpp) REVERT: A 250 VAL cc_start: 0.9145 (m) cc_final: 0.8904 (p) REVERT: A 356 ASP cc_start: 0.8988 (t0) cc_final: 0.8758 (t0) REVERT: A 371 LEU cc_start: 0.8910 (tp) cc_final: 0.8685 (tp) REVERT: A 464 MET cc_start: 0.7761 (mtt) cc_final: 0.7217 (mtt) REVERT: A 975 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7653 (mm-40) REVERT: A 1122 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8789 (mtp85) REVERT: A 1214 LEU cc_start: 0.6929 (tt) cc_final: 0.6503 (pp) REVERT: B 101 MET cc_start: 0.8518 (ttt) cc_final: 0.7768 (ttt) REVERT: B 151 MET cc_start: 0.9255 (mpp) cc_final: 0.8715 (ttm) REVERT: B 223 GLU cc_start: 0.7479 (tp30) cc_final: 0.7209 (tp30) REVERT: B 318 MET cc_start: 0.7391 (ppp) cc_final: 0.7100 (ppp) REVERT: B 385 PHE cc_start: 0.8474 (m-80) cc_final: 0.8260 (m-80) REVERT: B 415 MET cc_start: 0.7348 (ttp) cc_final: 0.6680 (tmm) REVERT: B 464 MET cc_start: 0.9026 (ppp) cc_final: 0.8598 (ppp) REVERT: B 520 MET cc_start: 0.5334 (tpt) cc_final: 0.5117 (tpt) REVERT: B 558 TYR cc_start: 0.9070 (m-80) cc_final: 0.8676 (m-80) REVERT: B 571 SER cc_start: 0.9060 (t) cc_final: 0.8772 (p) REVERT: B 597 LEU cc_start: 0.9153 (mp) cc_final: 0.8950 (mp) REVERT: B 786 LEU cc_start: 0.8218 (tp) cc_final: 0.7932 (tp) REVERT: B 914 THR cc_start: 0.9533 (p) cc_final: 0.9241 (p) REVERT: B 916 PHE cc_start: 0.9047 (m-10) cc_final: 0.8726 (m-10) REVERT: B 933 LEU cc_start: 0.9379 (mp) cc_final: 0.9120 (mp) REVERT: B 1044 PHE cc_start: 0.8484 (t80) cc_final: 0.7898 (t80) REVERT: B 1092 LYS cc_start: 0.9414 (mmpt) cc_final: 0.9153 (mmmt) REVERT: B 1109 LEU cc_start: 0.9647 (mt) cc_final: 0.9418 (mt) REVERT: B 1150 LEU cc_start: 0.9523 (mt) cc_final: 0.9182 (mm) REVERT: B 1208 MET cc_start: 0.9424 (ppp) cc_final: 0.9186 (ppp) REVERT: B 1353 ASP cc_start: 0.8006 (m-30) cc_final: 0.7510 (p0) REVERT: B 1389 PHE cc_start: 0.8773 (m-80) cc_final: 0.8254 (m-80) REVERT: B 1431 PHE cc_start: 0.8670 (p90) cc_final: 0.8455 (p90) REVERT: B 1432 THR cc_start: 0.8356 (t) cc_final: 0.8015 (m) REVERT: C 55 ASN cc_start: 0.7131 (p0) cc_final: 0.5682 (t0) REVERT: C 99 GLU cc_start: 0.8827 (tt0) cc_final: 0.8399 (tt0) REVERT: C 151 MET cc_start: 0.9067 (ttm) cc_final: 0.8290 (tpp) REVERT: C 191 SER cc_start: 0.7480 (t) cc_final: 0.7280 (t) REVERT: C 250 VAL cc_start: 0.9166 (m) cc_final: 0.8921 (p) REVERT: C 464 MET cc_start: 0.7755 (mtt) cc_final: 0.7217 (mtt) REVERT: C 1122 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8790 (mtp85) REVERT: C 1214 LEU cc_start: 0.6925 (tt) cc_final: 0.6491 (pp) REVERT: D 101 MET cc_start: 0.8523 (ttt) cc_final: 0.7774 (ttt) REVERT: D 223 GLU cc_start: 0.7471 (tp30) cc_final: 0.7211 (tp30) REVERT: D 318 MET cc_start: 0.7403 (ppp) cc_final: 0.7105 (ppp) REVERT: D 415 MET cc_start: 0.7247 (ttp) cc_final: 0.6590 (tmm) REVERT: D 597 LEU cc_start: 0.8860 (mp) cc_final: 0.8659 (mp) REVERT: D 786 LEU cc_start: 0.8236 (tp) cc_final: 0.7954 (tp) REVERT: D 914 THR cc_start: 0.9514 (p) cc_final: 0.9202 (p) REVERT: D 916 PHE cc_start: 0.9045 (m-10) cc_final: 0.8718 (m-10) REVERT: D 933 LEU cc_start: 0.9390 (mp) cc_final: 0.9163 (mp) REVERT: D 1019 LYS cc_start: 0.9057 (ptpp) cc_final: 0.8767 (tttt) REVERT: D 1044 PHE cc_start: 0.8668 (t80) cc_final: 0.8130 (t80) REVERT: D 1092 LYS cc_start: 0.9269 (mmpt) cc_final: 0.8929 (tmtt) REVERT: D 1109 LEU cc_start: 0.9631 (mt) cc_final: 0.9381 (mt) REVERT: D 1145 TYR cc_start: 0.8792 (m-80) cc_final: 0.8287 (m-80) REVERT: D 1150 LEU cc_start: 0.9548 (mt) cc_final: 0.9220 (mm) REVERT: D 1248 PHE cc_start: 0.8029 (t80) cc_final: 0.7477 (t80) REVERT: D 1253 ASP cc_start: 0.8165 (m-30) cc_final: 0.7662 (m-30) REVERT: D 1293 ASP cc_start: 0.9131 (m-30) cc_final: 0.8931 (m-30) REVERT: D 1353 ASP cc_start: 0.8003 (m-30) cc_final: 0.7510 (p0) REVERT: D 1389 PHE cc_start: 0.8772 (m-80) cc_final: 0.8259 (m-80) REVERT: D 1431 PHE cc_start: 0.8673 (p90) cc_final: 0.8441 (p90) REVERT: D 1432 THR cc_start: 0.8315 (t) cc_final: 0.7946 (m) outliers start: 1 outliers final: 1 residues processed: 568 average time/residue: 0.5483 time to fit residues: 521.7232 Evaluate side-chains 443 residues out of total 4702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 4.9990 chunk 452 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 392 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 425 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 437 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1464 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 ** C1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN D1051 GLN ** D1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.092604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068182 restraints weight = 277839.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.070062 restraints weight = 213111.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071475 restraints weight = 173598.033| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 43574 Z= 0.228 Angle : 0.810 13.485 59204 Z= 0.405 Chirality : 0.050 0.405 6900 Planarity : 0.006 0.077 7554 Dihedral : 7.876 59.510 6812 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.62 % Favored : 86.27 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.10), residues: 5360 helix: -1.07 (0.17), residues: 812 sheet: -2.13 (0.13), residues: 1416 loop : -3.30 (0.09), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1069 HIS 0.017 0.001 HIS B1259 PHE 0.030 0.002 PHE B 286 TYR 0.049 0.002 TYR D1216 ARG 0.011 0.001 ARG A 370 =============================================================================== Job complete usr+sys time: 10334.45 seconds wall clock time: 190 minutes 48.81 seconds (11448.81 seconds total)