Starting phenix.real_space_refine on Sat Sep 12 15:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.map" model { file = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zz6_11585/09_2026/6zz6_11585.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 74 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 10387 2.51 5 N 2820 2.21 5 O 3259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16597 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2871 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3368 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 639 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Chain: "D" Number of atoms: 8264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8264 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 21, 'TRANS': 1028} Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'ASN:plan1': 8, 'GLN:plan1': 6, 'ARG:plan': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'PHE:plan': 3, 'GLU:plan': 9} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 677 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.06, per 1000 atoms: 0.18 Number of scatterers: 16597 At special positions: 0 Unit cell: (108.07, 124.12, 166.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 74 15.00 Mg 2 11.99 O 3259 8.00 N 2820 7.00 C 10387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 575.5 milliseconds 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 68.4% alpha, 6.6% beta 34 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.705A pdb=" N LEU A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 1045 through 1084 removed outlier: 3.816A pdb=" N ILE A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A1076 " --> pdb=" O SER A1072 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A1077 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1148 removed outlier: 4.109A pdb=" N TYR A1148 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1179 Processing helix chain 'A' and resid 1194 through 1198 removed outlier: 3.770A pdb=" N LYS A1197 " --> pdb=" O MET A1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.599A pdb=" N PHE B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.547A pdb=" N VAL B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.537A pdb=" N THR B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.910A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 228 removed outlier: 3.886A pdb=" N GLN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1060 removed outlier: 3.730A pdb=" N PHE B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B1008 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B1021 " --> pdb=" O SER B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1146 Processing helix chain 'B' and resid 1161 through 1176 Processing helix chain 'B' and resid 1213 through 1222 Processing helix chain 'C' and resid 69 through 103 removed outlier: 3.837A pdb=" N THR C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 520 through 538 removed outlier: 3.703A pdb=" N ALA C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 305 through 322 Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 338 through 352 removed outlier: 4.247A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 356 through 373 removed outlier: 3.516A pdb=" N THR D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 Processing helix chain 'D' and resid 409 through 420 removed outlier: 3.908A pdb=" N HIS D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 424 removed outlier: 3.525A pdb=" N LEU D 424 " --> pdb=" O ILE D 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 444 through 456 removed outlier: 3.744A pdb=" N SER D 452 " --> pdb=" O PHE D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 475 through 506 removed outlier: 3.619A pdb=" N ASN D 479 " --> pdb=" O ASP D 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN D 506 " --> pdb=" O ARG D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 524 removed outlier: 4.179A pdb=" N ILE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE D 517 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 548 removed outlier: 4.112A pdb=" N LYS D 535 " --> pdb=" O PRO D 531 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 Processing helix chain 'D' and resid 598 through 616 removed outlier: 4.215A pdb=" N PHE D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS D 603 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 604 " --> pdb=" O HIS D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 634 removed outlier: 3.637A pdb=" N THR D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 630 " --> pdb=" O TRP D 626 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 631 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 662 Processing helix chain 'D' and resid 679 through 688 removed outlier: 3.617A pdb=" N PHE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 687 " --> pdb=" O ASP D 683 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 688 " --> pdb=" O TYR D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 696 removed outlier: 3.740A pdb=" N ASN D 695 " --> pdb=" O PHE D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 709 removed outlier: 3.657A pdb=" N TYR D 700 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 709 " --> pdb=" O LEU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 730 removed outlier: 4.035A pdb=" N LYS D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 730 " --> pdb=" O LEU D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 749 removed outlier: 3.990A pdb=" N LYS D 740 " --> pdb=" O ASN D 736 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR D 742 " --> pdb=" O MET D 738 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN D 748 " --> pdb=" O HIS D 744 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 749 " --> pdb=" O ARG D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 771 through 778 removed outlier: 3.754A pdb=" N ASN D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 801 Processing helix chain 'D' and resid 803 through 817 Processing helix chain 'D' and resid 822 through 838 Processing helix chain 'D' and resid 838 through 845 removed outlier: 4.361A pdb=" N VAL D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D 845 " --> pdb=" O VAL D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 866 removed outlier: 3.536A pdb=" N ILE D 854 " --> pdb=" O LYS D 850 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 856 " --> pdb=" O LYS D 852 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 866 " --> pdb=" O MET D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 883 removed outlier: 3.556A pdb=" N TYR D 883 " --> pdb=" O PHE D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 917 removed outlier: 4.373A pdb=" N LYS D 897 " --> pdb=" O GLU D 893 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE D 898 " --> pdb=" O ALA D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 942 Processing helix chain 'D' and resid 949 through 962 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.723A pdb=" N TYR D 971 " --> pdb=" O ASP D 967 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 981 " --> pdb=" O ARG D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 1001 Processing helix chain 'D' and resid 1006 through 1022 removed outlier: 3.582A pdb=" N ILE D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP D1011 " --> pdb=" O VAL D1007 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU D1012 " --> pdb=" O ARG D1008 " (cutoff:3.500A) Proline residue: D1015 - end of helix Processing helix chain 'D' and resid 1027 through 1049 removed outlier: 4.030A pdb=" N ALA D1031 " --> pdb=" O THR D1027 " (cutoff:3.500A) Proline residue: D1043 - end of helix Processing helix chain 'D' and resid 1060 through 1075 Processing helix chain 'D' and resid 1092 through 1104 Processing helix chain 'D' and resid 1110 through 1128 Processing helix chain 'D' and resid 1129 through 1133 Processing helix chain 'D' and resid 1134 through 1147 removed outlier: 3.708A pdb=" N LEU D1138 " --> pdb=" O SER D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1175 removed outlier: 3.520A pdb=" N VAL D1155 " --> pdb=" O ASP D1151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D1156 " --> pdb=" O ILE D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1212 Processing helix chain 'D' and resid 1212 through 1221 removed outlier: 3.883A pdb=" N LEU D1221 " --> pdb=" O LEU D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1224 through 1242 Processing helix chain 'D' and resid 1245 through 1248 Processing helix chain 'D' and resid 1249 through 1258 removed outlier: 3.882A pdb=" N ALA D1258 " --> pdb=" O ILE D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1286 removed outlier: 7.915A pdb=" N THR D1281 " --> pdb=" O GLU D1277 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D1282 " --> pdb=" O LYS D1278 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1302 Processing helix chain 'D' and resid 1312 through 1320 Processing helix chain 'D' and resid 1325 through 1341 Processing helix chain 'D' and resid 1356 through 1368 removed outlier: 3.702A pdb=" N ASN D1368 " --> pdb=" O THR D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1373 through 1398 removed outlier: 3.546A pdb=" N LEU D1377 " --> pdb=" O SER D1373 " (cutoff:3.500A) Processing helix chain 'D' and resid 1414 through 1434 removed outlier: 3.518A pdb=" N TYR D1434 " --> pdb=" O LEU D1430 " (cutoff:3.500A) Processing helix chain 'D' and resid 1449 through 1454 Processing helix chain 'D' and resid 1467 through 1473 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 3.557A pdb=" N ARG A 3 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 97 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 7 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A 95 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 9 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR A 93 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 119 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 7.045A pdb=" N PHE A 28 " --> pdb=" O ALA A1200 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A1202 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER A 30 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A1204 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 32 " --> pdb=" O VAL A1204 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ARG A1206 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1096 through 1101 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 117 removed outlier: 6.600A pdb=" N GLU B 17 " --> pdb=" O THR D1180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.630A pdb=" N LYS B1196 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B1197 " --> pdb=" O VAL B1212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1067 through 1070 removed outlier: 3.783A pdb=" N GLY B1106 " --> pdb=" O HIS B1070 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 541 through 544 Processing sheet with id=AA8, first strand: chain 'D' and resid 434 through 435 983 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4816 1.34 - 1.46: 2754 1.46 - 1.58: 9186 1.58 - 1.70: 144 1.70 - 1.82: 89 Bond restraints: 16989 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C8 ATP B2000 " pdb=" N7 ATP B2000 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.16e+01 ... (remaining 16984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 23131 4.08 - 8.15: 59 8.15 - 12.23: 3 12.23 - 16.31: 1 16.31 - 20.39: 3 Bond angle restraints: 23197 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.68 19.19 1.00e+00 1.00e+00 3.68e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 119.34 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 121.32 15.51 1.00e+00 1.00e+00 2.40e+02 angle pdb=" C5 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N3 ATP A2000 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.04e+01 ... (remaining 23192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.02: 9455 27.02 - 54.03: 655 54.03 - 81.05: 91 81.05 - 108.06: 7 108.06 - 135.08: 1 Dihedral angle restraints: 10209 sinusoidal: 4559 harmonic: 5650 Sorted by residual: dihedral pdb=" CA ASP A1219 " pdb=" C ASP A1219 " pdb=" N LEU A1220 " pdb=" CA LEU A1220 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA HIS D1025 " pdb=" C HIS D1025 " pdb=" N ASP D1026 " pdb=" CA ASP D1026 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ARG D 618 " pdb=" C ARG D 618 " pdb=" N ARG D 619 " pdb=" CA ARG D 619 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 10206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2409 0.065 - 0.129: 272 0.129 - 0.194: 22 0.194 - 0.258: 2 0.258 - 0.323: 1 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CB ILE D 474 " pdb=" CA ILE D 474 " pdb=" CG1 ILE D 474 " pdb=" CG2 ILE D 474 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ILE A 110 " pdb=" N ILE A 110 " pdb=" C ILE A 110 " pdb=" CB ILE A 110 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS A 63 " pdb=" N LYS A 63 " pdb=" C LYS A 63 " pdb=" CB LYS A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2703 not shown) Planarity restraints: 2674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 121 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ARG B 121 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG B 121 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 527 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO D 528 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 528 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 528 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 11 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C PHE B 11 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 11 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 12 " 0.010 2.00e-02 2.50e+03 ... (remaining 2671 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 134 2.61 - 3.18: 14469 3.18 - 3.76: 26542 3.76 - 4.33: 34499 4.33 - 4.90: 56551 Nonbonded interactions: 132195 Sorted by model distance: nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb=" OG SER A 40 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLN A 151 " pdb="MG MG A2001 " model vdw 2.068 2.170 nonbonded pdb=" OG SER A1130 " pdb=" O1B ATP B2000 " model vdw 2.104 3.040 ... (remaining 132190 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 15.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.004 0.083 16989 Z= 0.309 Angle : 0.685 20.387 23197 Z= 0.522 Chirality : 0.041 0.323 2706 Planarity : 0.003 0.052 2674 Dihedral : 16.956 135.081 6513 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.61 % Allowed : 0.12 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1858 helix: 2.56 (0.15), residues: 1213 sheet: 0.76 (0.44), residues: 163 loop : -1.40 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 792 TYR 0.016 0.001 TYR D1094 PHE 0.023 0.001 PHE B 47 TRP 0.008 0.001 TRP D 837 HIS 0.005 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.31 (16989) covalent geometry : angle 0.68528 / 0.52 (23197) hydrogen bonds : bond 0.11494 / 7.59 ( 1051) hydrogen bonds : angle 4.52933 / 3.25 ( 3043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.548 Fit side-chains REVERT: A 1196 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6761 (mm-30) REVERT: B 1003 LYS cc_start: 0.5831 (ptmm) cc_final: 0.5572 (pttm) REVERT: C 102 MET cc_start: 0.5157 (tpp) cc_final: 0.4332 (ttm) REVERT: D 607 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 780 ASN cc_start: 0.7485 (t0) cc_final: 0.7059 (t0) REVERT: D 993 ASP cc_start: 0.7108 (m-30) cc_final: 0.6887 (m-30) outliers start: 10 outliers final: 2 residues processed: 245 average time/residue: 0.1197 time to fit residues: 45.6893 Evaluate side-chains 162 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain D residue 890 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN B 16 ASN ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125018 restraints weight = 21973.013| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.95 r_work: 0.3418 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16989 Z= 0.201 Angle : 0.626 8.398 23197 Z= 0.342 Chirality : 0.042 0.212 2706 Planarity : 0.004 0.060 2674 Dihedral : 16.882 135.382 2858 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 7.58 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.20), residues: 1858 helix: 2.41 (0.15), residues: 1227 sheet: 0.87 (0.44), residues: 161 loop : -1.65 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.020 0.002 TYR B 116 PHE 0.019 0.002 PHE A1195 TRP 0.016 0.001 TRP D 626 HIS 0.008 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (16989) covalent geometry : angle 0.62640 / 0.34 (23197) hydrogen bonds : bond 0.04602 / 2.97 ( 1051) hydrogen bonds : angle 3.72786 / 2.62 ( 3043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.618 Fit side-chains REVERT: A 177 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.4918 (pm20) REVERT: A 1078 ILE cc_start: 0.8526 (mt) cc_final: 0.8234 (mm) REVERT: B 88 SER cc_start: 0.7654 (m) cc_final: 0.7422 (t) REVERT: C 102 MET cc_start: 0.5873 (tpp) cc_final: 0.4776 (ttm) REVERT: D 412 PHE cc_start: 0.8007 (t80) cc_final: 0.7673 (t80) REVERT: D 993 ASP cc_start: 0.7843 (m-30) cc_final: 0.7558 (m-30) REVERT: D 1147 SER cc_start: 0.8460 (m) cc_final: 0.8246 (m) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.1200 time to fit residues: 37.2381 Evaluate side-chains 179 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1288 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN B 28 ASN ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124759 restraints weight = 22061.023| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.86 r_work: 0.3413 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16989 Z= 0.158 Angle : 0.563 7.737 23197 Z= 0.310 Chirality : 0.040 0.210 2706 Planarity : 0.004 0.043 2674 Dihedral : 17.248 137.317 2856 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.64 % Allowed : 10.86 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1858 helix: 2.49 (0.15), residues: 1220 sheet: 0.81 (0.44), residues: 161 loop : -1.73 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.023 0.002 TYR B 116 PHE 0.020 0.002 PHE D 624 TRP 0.005 0.001 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16989) covalent geometry : angle 0.56327 / 0.31 (23197) hydrogen bonds : bond 0.04208 / 2.77 ( 1051) hydrogen bonds : angle 3.58141 / 2.53 ( 3043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.504 Fit side-chains REVERT: A 42 MET cc_start: 0.8362 (tpp) cc_final: 0.7870 (ttm) REVERT: A 191 LYS cc_start: 0.8046 (tttp) cc_final: 0.7597 (mmtm) REVERT: B 28 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8508 (p0) REVERT: B 88 SER cc_start: 0.7940 (m) cc_final: 0.7680 (t) REVERT: B 1118 ASN cc_start: 0.8240 (t0) cc_final: 0.7943 (t0) REVERT: B 1146 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6405 (p0) REVERT: D 412 PHE cc_start: 0.7889 (t80) cc_final: 0.7663 (t80) REVERT: D 993 ASP cc_start: 0.8082 (m-30) cc_final: 0.7738 (m-30) REVERT: D 1147 SER cc_start: 0.8505 (m) cc_final: 0.8247 (m) outliers start: 27 outliers final: 20 residues processed: 202 average time/residue: 0.1155 time to fit residues: 36.3624 Evaluate side-chains 182 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 1107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN A1167 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124512 restraints weight = 21906.236| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.82 r_work: 0.3410 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16989 Z= 0.142 Angle : 0.546 7.905 23197 Z= 0.301 Chirality : 0.039 0.198 2706 Planarity : 0.004 0.045 2674 Dihedral : 17.369 137.707 2856 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.55 % Allowed : 11.28 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1858 helix: 2.57 (0.15), residues: 1220 sheet: 0.75 (0.43), residues: 161 loop : -1.74 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.019 0.001 TYR B 116 PHE 0.021 0.002 PHE A1154 TRP 0.004 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16989) covalent geometry : angle 0.54602 / 0.30 (23197) hydrogen bonds : bond 0.03996 / 2.62 ( 1051) hydrogen bonds : angle 3.52962 / 2.48 ( 3043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.572 Fit side-chains REVERT: A 42 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8057 (ttm) REVERT: A 177 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5129 (pm20) REVERT: A 191 LYS cc_start: 0.7863 (tttp) cc_final: 0.7365 (mmtm) REVERT: B 88 SER cc_start: 0.7998 (m) cc_final: 0.7734 (t) REVERT: B 106 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7660 (ttm110) REVERT: B 210 MET cc_start: 0.7501 (tpp) cc_final: 0.7271 (ttm) REVERT: B 1118 ASN cc_start: 0.8203 (t0) cc_final: 0.7965 (t0) REVERT: B 1146 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6217 (p0) REVERT: D 412 PHE cc_start: 0.7944 (t80) cc_final: 0.7697 (t80) REVERT: D 993 ASP cc_start: 0.8079 (m-30) cc_final: 0.7724 (m-30) REVERT: D 1147 SER cc_start: 0.8524 (m) cc_final: 0.8257 (m) outliers start: 42 outliers final: 26 residues processed: 198 average time/residue: 0.1126 time to fit residues: 35.0520 Evaluate side-chains 182 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 123 optimal weight: 0.2980 chunk 194 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN D 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126042 restraints weight = 21795.725| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.72 r_work: 0.3449 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16989 Z= 0.137 Angle : 0.537 8.030 23197 Z= 0.295 Chirality : 0.039 0.209 2706 Planarity : 0.003 0.046 2674 Dihedral : 17.450 137.631 2856 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.67 % Allowed : 11.83 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.20), residues: 1858 helix: 2.59 (0.15), residues: 1223 sheet: 0.60 (0.42), residues: 166 loop : -1.74 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 106 TYR 0.020 0.001 TYR B 116 PHE 0.014 0.001 PHE D 624 TRP 0.009 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (16989) covalent geometry : angle 0.53691 / 0.30 (23197) hydrogen bonds : bond 0.03921 / 2.58 ( 1051) hydrogen bonds : angle 3.45231 / 2.43 ( 3043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.478 Fit side-chains REVERT: A 42 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: A 177 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5170 (pm20) REVERT: A 191 LYS cc_start: 0.7935 (tttp) cc_final: 0.7444 (mmtm) REVERT: B 88 SER cc_start: 0.7864 (m) cc_final: 0.7658 (t) REVERT: B 128 ILE cc_start: 0.7665 (mt) cc_final: 0.7350 (mm) REVERT: D 993 ASP cc_start: 0.7896 (m-30) cc_final: 0.7598 (m-30) REVERT: D 1147 SER cc_start: 0.8475 (m) cc_final: 0.8243 (m) outliers start: 44 outliers final: 28 residues processed: 199 average time/residue: 0.1141 time to fit residues: 36.0137 Evaluate side-chains 183 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1288 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 112 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 67 optimal weight: 0.0030 chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A1096 ASN A1146 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121223 restraints weight = 21914.445| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.84 r_work: 0.3403 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16989 Z= 0.129 Angle : 0.528 7.823 23197 Z= 0.291 Chirality : 0.038 0.198 2706 Planarity : 0.003 0.045 2674 Dihedral : 17.454 137.637 2856 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.61 % Allowed : 12.25 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1858 helix: 2.66 (0.15), residues: 1222 sheet: 0.53 (0.42), residues: 166 loop : -1.72 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 106 TYR 0.018 0.001 TYR D 959 PHE 0.014 0.001 PHE A1195 TRP 0.008 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16989) covalent geometry : angle 0.52781 / 0.29 (23197) hydrogen bonds : bond 0.03820 / 2.51 ( 1051) hydrogen bonds : angle 3.40018 / 2.39 ( 3043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.623 Fit side-chains REVERT: A 42 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: A 177 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.5317 (pm20) REVERT: A 191 LYS cc_start: 0.7899 (tttp) cc_final: 0.7383 (mmtm) REVERT: B 88 SER cc_start: 0.8030 (m) cc_final: 0.7796 (t) REVERT: B 128 ILE cc_start: 0.7821 (mt) cc_final: 0.7447 (mm) REVERT: B 191 GLN cc_start: 0.6613 (tm-30) cc_final: 0.6382 (tm-30) REVERT: B 198 LYS cc_start: 0.6950 (pptt) cc_final: 0.6724 (pttp) REVERT: C 95 ASP cc_start: 0.7913 (m-30) cc_final: 0.7679 (m-30) REVERT: C 102 MET cc_start: 0.5833 (tpp) cc_final: 0.4918 (ttm) REVERT: D 993 ASP cc_start: 0.8114 (m-30) cc_final: 0.7736 (m-30) outliers start: 43 outliers final: 32 residues processed: 199 average time/residue: 0.1127 time to fit residues: 35.4640 Evaluate side-chains 190 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 HIS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN B 141 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 748 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125276 restraints weight = 21755.312| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.72 r_work: 0.3431 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16989 Z= 0.139 Angle : 0.539 7.951 23197 Z= 0.296 Chirality : 0.039 0.245 2706 Planarity : 0.003 0.047 2674 Dihedral : 17.495 137.832 2856 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.61 % Allowed : 13.04 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1858 helix: 2.67 (0.15), residues: 1222 sheet: 0.47 (0.42), residues: 166 loop : -1.71 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 106 TYR 0.020 0.001 TYR B 116 PHE 0.015 0.001 PHE A1195 TRP 0.008 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16989) covalent geometry : angle 0.53908 / 0.30 (23197) hydrogen bonds : bond 0.03893 / 2.57 ( 1051) hydrogen bonds : angle 3.39781 / 2.39 ( 3043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.634 Fit side-chains REVERT: A 42 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8065 (ttm) REVERT: A 177 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5209 (pm20) REVERT: A 191 LYS cc_start: 0.7939 (tttp) cc_final: 0.7461 (mmtm) REVERT: B 198 LYS cc_start: 0.7075 (pptt) cc_final: 0.6861 (pttp) REVERT: B 1146 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6190 (p0) REVERT: C 95 ASP cc_start: 0.7860 (m-30) cc_final: 0.7548 (m-30) REVERT: D 365 TYR cc_start: 0.7436 (t80) cc_final: 0.7031 (m-80) REVERT: D 453 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: D 993 ASP cc_start: 0.7909 (m-30) cc_final: 0.7585 (m-30) outliers start: 43 outliers final: 33 residues processed: 191 average time/residue: 0.1130 time to fit residues: 33.9554 Evaluate side-chains 188 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 HIS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 453 MET Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 127 optimal weight: 0.0570 chunk 184 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 165 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.161002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124637 restraints weight = 21956.185| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.82 r_work: 0.3415 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16989 Z= 0.113 Angle : 0.516 9.201 23197 Z= 0.285 Chirality : 0.038 0.198 2706 Planarity : 0.003 0.043 2674 Dihedral : 17.482 138.082 2856 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.76 % Allowed : 14.13 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.20), residues: 1858 helix: 2.79 (0.15), residues: 1220 sheet: 0.43 (0.42), residues: 166 loop : -1.68 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 106 TYR 0.016 0.001 TYR B 14 PHE 0.014 0.001 PHE A1195 TRP 0.014 0.001 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16989) covalent geometry : angle 0.51642 / 0.28 (23197) hydrogen bonds : bond 0.03677 / 2.42 ( 1051) hydrogen bonds : angle 3.31324 / 2.33 ( 3043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.635 Fit side-chains REVERT: A 42 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8148 (ttm) REVERT: A 177 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5398 (pm20) REVERT: A 191 LYS cc_start: 0.7902 (tttp) cc_final: 0.7409 (mmtm) REVERT: B 128 ILE cc_start: 0.7849 (mt) cc_final: 0.7444 (mm) REVERT: C 95 ASP cc_start: 0.7919 (m-30) cc_final: 0.7696 (m-30) REVERT: C 102 MET cc_start: 0.5770 (tpp) cc_final: 0.4878 (ttm) REVERT: D 365 TYR cc_start: 0.7352 (t80) cc_final: 0.6930 (m-80) REVERT: D 993 ASP cc_start: 0.8069 (m-30) cc_final: 0.7684 (m-30) REVERT: D 1396 MET cc_start: 0.7133 (mmm) cc_final: 0.6848 (mmm) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.1143 time to fit residues: 34.7561 Evaluate side-chains 182 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 137 optimal weight: 0.0270 chunk 96 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122269 restraints weight = 22109.939| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.90 r_work: 0.3368 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16989 Z= 0.138 Angle : 0.541 8.568 23197 Z= 0.295 Chirality : 0.039 0.194 2706 Planarity : 0.003 0.047 2674 Dihedral : 17.519 138.332 2856 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.82 % Allowed : 14.43 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.20), residues: 1858 helix: 2.73 (0.15), residues: 1222 sheet: 0.37 (0.42), residues: 166 loop : -1.68 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.018 0.001 TYR B 116 PHE 0.012 0.001 PHE A1195 TRP 0.018 0.001 TRP D 626 HIS 0.006 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (16989) covalent geometry : angle 0.54094 / 0.29 (23197) hydrogen bonds : bond 0.03874 / 2.57 ( 1051) hydrogen bonds : angle 3.35550 / 2.36 ( 3043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.500 Fit side-chains REVERT: A 177 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5357 (pm20) REVERT: A 191 LYS cc_start: 0.7874 (tttp) cc_final: 0.7397 (mmtm) REVERT: B 198 LYS cc_start: 0.6402 (pttp) cc_final: 0.6130 (pttp) REVERT: C 95 ASP cc_start: 0.7961 (m-30) cc_final: 0.7663 (m-30) REVERT: C 102 MET cc_start: 0.5720 (tpp) cc_final: 0.4825 (ttm) REVERT: D 365 TYR cc_start: 0.7434 (t80) cc_final: 0.6990 (m-80) REVERT: D 453 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8365 (ttp) REVERT: D 993 ASP cc_start: 0.8156 (m-30) cc_final: 0.7768 (m-30) outliers start: 30 outliers final: 26 residues processed: 181 average time/residue: 0.1129 time to fit residues: 32.0570 Evaluate side-chains 179 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 453 MET Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 109 optimal weight: 0.0020 chunk 183 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 0.0010 chunk 167 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126043 restraints weight = 21709.180| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.71 r_work: 0.3458 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16989 Z= 0.118 Angle : 0.526 8.744 23197 Z= 0.289 Chirality : 0.038 0.194 2706 Planarity : 0.003 0.045 2674 Dihedral : 17.477 138.558 2856 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.88 % Allowed : 14.86 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.20), residues: 1858 helix: 2.78 (0.15), residues: 1220 sheet: 0.36 (0.41), residues: 166 loop : -1.67 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.016 0.001 TYR B 14 PHE 0.017 0.001 PHE D 387 TRP 0.029 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16989) covalent geometry : angle 0.52610 / 0.29 (23197) hydrogen bonds : bond 0.03728 / 2.46 ( 1051) hydrogen bonds : angle 3.32247 / 2.34 ( 3043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7301 (mmm160) REVERT: A 177 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5295 (pm20) REVERT: A 191 LYS cc_start: 0.7911 (tttp) cc_final: 0.7453 (mmtm) REVERT: B 128 ILE cc_start: 0.7851 (mt) cc_final: 0.7465 (mm) REVERT: C 80 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7511 (ttp-110) REVERT: C 95 ASP cc_start: 0.7904 (m-30) cc_final: 0.7693 (m-30) REVERT: C 102 MET cc_start: 0.5649 (tpp) cc_final: 0.4769 (ttm) REVERT: D 365 TYR cc_start: 0.7489 (t80) cc_final: 0.7072 (m-80) REVERT: D 453 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8306 (ttp) REVERT: D 993 ASP cc_start: 0.7945 (m-30) cc_final: 0.7595 (m-30) outliers start: 31 outliers final: 26 residues processed: 182 average time/residue: 0.1147 time to fit residues: 33.2391 Evaluate side-chains 176 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 453 MET Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 112 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN D 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121009 restraints weight = 22034.696| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.11 r_work: 0.3336 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16989 Z= 0.145 Angle : 0.560 11.810 23197 Z= 0.302 Chirality : 0.039 0.269 2706 Planarity : 0.004 0.047 2674 Dihedral : 17.505 138.715 2856 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.18 % Allowed : 14.86 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.20), residues: 1858 helix: 2.71 (0.15), residues: 1222 sheet: 0.31 (0.41), residues: 166 loop : -1.64 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 113 TYR 0.019 0.001 TYR B 116 PHE 0.015 0.001 PHE D 338 TRP 0.024 0.002 TRP D 626 HIS 0.006 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (16989) covalent geometry : angle 0.55950 / 0.30 (23197) hydrogen bonds : bond 0.03935 / 2.60 ( 1051) hydrogen bonds : angle 3.37158 / 2.37 ( 3043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.01 seconds wall clock time: 63 minutes 51.67 seconds (3831.67 seconds total)