Starting phenix.real_space_refine on Fri Jul 3 22:41:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zz6_11585/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.map" model { file = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_2026/6zz6_11585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zz6_11585/07_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-dev-6108/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: 3.94, per 1000 atoms: 0.24 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: 1.85 Conformation dependent library (CDL) restraints added in 689.1 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: 2.55 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: 4.22 Time building geometry restraints manager: 2.33 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.560 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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 : 0.684 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 0.68433 / 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 : 0.564 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: 0.1310 time to fit residues: 49.5835 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 : 0.711 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 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: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.164644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126748 restraints weight = 21948.627| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.98 r_work: 0.3436 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16989 Z= 0.187 Angle : 0.606 8.300 23197 Z= 0.331 Chirality : 0.041 0.211 2706 Planarity : 0.004 0.056 2674 Dihedral : 16.854 135.302 2858 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.33 % Allowed : 7.52 % Favored : 91.15 % 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: 2.07 (0.20), residues: 1858 helix: 2.47 (0.15), residues: 1227 sheet: 0.91 (0.44), residues: 161 loop : -1.60 (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 D 970 PHE 0.018 0.002 PHE B1150 TRP 0.013 0.001 TRP D 626 HIS 0.007 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16989) covalent geometry : angle 0.60555 / 0.33 (23197) hydrogen bonds : bond 0.04433 / 2.86 ( 1051) hydrogen bonds : angle 3.68796 / 2.59 ( 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 209 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.597 Fit side-chains REVERT: A 177 GLN cc_start: 0.5782 (OUTLIER) cc_final: 0.4784 (pm20) REVERT: A 191 LYS cc_start: 0.7847 (tttp) cc_final: 0.7367 (mmtm) REVERT: A 1078 ILE cc_start: 0.8513 (mt) cc_final: 0.8222 (mm) REVERT: C 102 MET cc_start: 0.5779 (tpp) cc_final: 0.4692 (ttm) REVERT: D 412 PHE cc_start: 0.7995 (t80) cc_final: 0.7652 (t80) REVERT: D 993 ASP cc_start: 0.7784 (m-30) cc_final: 0.7521 (m-30) REVERT: D 1147 SER cc_start: 0.8445 (m) cc_final: 0.8238 (m) outliers start: 22 outliers final: 14 residues processed: 200 average time/residue: 0.1235 time to fit residues: 38.7146 Evaluate side-chains 178 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN 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 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: 7.9990 chunk 44 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 439 GLN ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120393 restraints weight = 22103.813| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.92 r_work: 0.3374 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16989 Z= 0.187 Angle : 0.604 9.754 23197 Z= 0.328 Chirality : 0.042 0.225 2706 Planarity : 0.004 0.046 2674 Dihedral : 17.357 137.667 2856 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.43 % Allowed : 9.95 % Favored : 87.63 % 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: 1.91 (0.20), residues: 1858 helix: 2.42 (0.15), residues: 1219 sheet: 0.70 (0.43), residues: 166 loop : -1.74 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.029 0.002 TYR B 116 PHE 0.022 0.002 PHE D 624 TRP 0.004 0.001 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16989) covalent geometry : angle 0.60398 / 0.33 (23197) hydrogen bonds : bond 0.04384 / 2.90 ( 1051) hydrogen bonds : angle 3.64440 / 2.57 ( 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 223 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.442 Fit side-chains REVERT: A 42 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: A 191 LYS cc_start: 0.8045 (tttp) cc_final: 0.7589 (mmtm) REVERT: B 106 ARG cc_start: 0.7966 (ttt90) cc_final: 0.7596 (ttm110) REVERT: B 128 ILE cc_start: 0.7841 (mt) cc_final: 0.7484 (mm) REVERT: B 1118 ASN cc_start: 0.8319 (t0) cc_final: 0.8038 (t0) REVERT: B 1146 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6478 (p0) REVERT: D 412 PHE cc_start: 0.7957 (t80) cc_final: 0.7705 (t80) REVERT: D 993 ASP cc_start: 0.8107 (m-30) cc_final: 0.7762 (m-30) REVERT: D 1147 SER cc_start: 0.8520 (m) cc_final: 0.8258 (m) outliers start: 40 outliers final: 24 residues processed: 210 average time/residue: 0.1281 time to fit residues: 42.1391 Evaluate side-chains 179 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 1100 THR Chi-restraints excluded: chain A residue 1146 ASN 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 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 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 630 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 184 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1096 ASN A1167 ASN D 439 GLN D 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.159916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123251 restraints weight = 22092.983| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.83 r_work: 0.3400 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16989 Z= 0.136 Angle : 0.543 8.005 23197 Z= 0.299 Chirality : 0.039 0.192 2706 Planarity : 0.004 0.045 2674 Dihedral : 17.447 137.521 2856 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.43 % Allowed : 11.52 % Favored : 86.05 % 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: 2.05 (0.20), residues: 1858 helix: 2.53 (0.15), residues: 1223 sheet: 0.72 (0.43), residues: 165 loop : -1.72 (0.28), residues: 470 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 0.024 0.002 PHE A1154 TRP 0.005 0.001 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (16989) covalent geometry : angle 0.54279 / 0.30 (23197) hydrogen bonds : bond 0.03986 / 2.62 ( 1051) hydrogen bonds : angle 3.51448 / 2.47 ( 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 212 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.637 Fit side-chains REVERT: A 42 MET cc_start: 0.8343 (tpp) cc_final: 0.7883 (ttm) REVERT: A 177 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5236 (pm20) REVERT: A 191 LYS cc_start: 0.7924 (tttp) cc_final: 0.7392 (mmtm) REVERT: B 106 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7614 (ttm110) REVERT: B 128 ILE cc_start: 0.7766 (mt) cc_final: 0.7416 (mm) REVERT: B 1118 ASN cc_start: 0.8259 (t0) cc_final: 0.8059 (t0) REVERT: B 1146 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6205 (p0) REVERT: D 344 LEU cc_start: 0.7851 (mp) cc_final: 0.7624 (tt) REVERT: D 412 PHE cc_start: 0.7985 (t80) cc_final: 0.7736 (t80) REVERT: D 993 ASP cc_start: 0.8082 (m-30) cc_final: 0.7729 (m-30) REVERT: D 1147 SER cc_start: 0.8521 (m) cc_final: 0.8245 (m) REVERT: D 1396 MET cc_start: 0.7077 (mmm) cc_final: 0.6822 (mmm) outliers start: 40 outliers final: 26 residues processed: 196 average time/residue: 0.1231 time to fit residues: 38.1778 Evaluate side-chains 187 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 ASN Chi-restraints excluded: chain B residue 1105 THR 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 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 890 HIS Chi-restraints excluded: chain D residue 1107 ASP 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: 0.1980 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A1146 ASN D 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125468 restraints weight = 21922.601| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.91 r_work: 0.3406 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2117 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= 0.119 Angle : 0.517 7.762 23197 Z= 0.287 Chirality : 0.038 0.200 2706 Planarity : 0.003 0.044 2674 Dihedral : 17.454 137.604 2856 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 11.95 % Favored : 85.57 % 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: 2.19 (0.20), residues: 1858 helix: 2.66 (0.15), residues: 1221 sheet: 0.69 (0.43), residues: 165 loop : -1.71 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.015 0.001 TYR B 116 PHE 0.014 0.001 PHE D 624 TRP 0.019 0.002 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (16989) covalent geometry : angle 0.51702 / 0.29 (23197) hydrogen bonds : bond 0.03787 / 2.49 ( 1051) hydrogen bonds : angle 3.41300 / 2.40 ( 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 214 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.653 Fit side-chains REVERT: A 42 MET cc_start: 0.8398 (tpp) cc_final: 0.8050 (ttm) REVERT: A 177 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5189 (pm20) REVERT: A 191 LYS cc_start: 0.7908 (tttp) cc_final: 0.7384 (mmtm) REVERT: B 106 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7661 (ttm110) REVERT: B 128 ILE cc_start: 0.7800 (mt) cc_final: 0.7446 (mm) REVERT: C 95 ASP cc_start: 0.7883 (m-30) cc_final: 0.7656 (m-30) REVERT: C 102 MET cc_start: 0.5874 (tpp) cc_final: 0.4928 (ttm) REVERT: D 344 LEU cc_start: 0.7862 (mp) cc_final: 0.7627 (tt) REVERT: D 993 ASP cc_start: 0.8087 (m-30) cc_final: 0.7733 (m-30) REVERT: D 1426 LEU cc_start: 0.7293 (tp) cc_final: 0.6906 (tt) outliers start: 41 outliers final: 28 residues processed: 204 average time/residue: 0.1238 time to fit residues: 39.7851 Evaluate side-chains 191 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1193 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 112 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 90 GLN A1096 ASN B 141 ASN B1039 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 748 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110214 restraints weight = 22315.576| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.92 r_work: 0.3218 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 16989 Z= 0.285 Angle : 0.726 8.273 23197 Z= 0.389 Chirality : 0.046 0.227 2706 Planarity : 0.005 0.057 2674 Dihedral : 17.782 137.568 2856 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.40 % Allowed : 12.01 % Favored : 84.60 % 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: 1.32 (0.20), residues: 1858 helix: 2.01 (0.14), residues: 1212 sheet: 0.24 (0.41), residues: 165 loop : -1.93 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 58 TYR 0.049 0.003 TYR B 116 PHE 0.022 0.003 PHE B 47 TRP 0.016 0.002 TRP D 626 HIS 0.009 0.002 HIS D 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.29 (16989) covalent geometry : angle 0.72605 / 0.39 (23197) hydrogen bonds : bond 0.05260 / 3.49 ( 1051) hydrogen bonds : angle 3.91659 / 2.74 ( 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 231 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8039 (ttm) REVERT: A 146 ASN cc_start: 0.8325 (p0) cc_final: 0.7976 (p0) REVERT: A 191 LYS cc_start: 0.7848 (tttp) cc_final: 0.7363 (mmtm) REVERT: B 2 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 106 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7762 (ttt90) REVERT: B 141 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (m-40) REVERT: B 198 LYS cc_start: 0.7144 (pptt) cc_final: 0.6644 (pttp) REVERT: B 1146 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6843 (p0) REVERT: B 1190 MET cc_start: 0.7565 (pmm) cc_final: 0.6768 (ptm) REVERT: C 95 ASP cc_start: 0.8059 (m-30) cc_final: 0.7800 (m-30) REVERT: D 365 TYR cc_start: 0.7614 (t80) cc_final: 0.7028 (m-80) REVERT: D 407 ASP cc_start: 0.7863 (m-30) cc_final: 0.7553 (t0) REVERT: D 993 ASP cc_start: 0.8148 (m-30) cc_final: 0.7774 (m-30) REVERT: D 1396 MET cc_start: 0.7080 (mmm) cc_final: 0.6862 (mmm) outliers start: 56 outliers final: 37 residues processed: 212 average time/residue: 0.1208 time to fit residues: 39.9369 Evaluate side-chains 194 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 A residue 1212 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 30 ILE 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 141 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 342 LEU 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 518 VAL Chi-restraints excluded: chain D residue 520 ASP 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 930 LYS 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: 0.9990 chunk 104 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 129 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1158 GLN B1120 GLN C 550 ASN D 439 GLN D 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116174 restraints weight = 21952.148| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.99 r_work: 0.3275 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16989 Z= 0.137 Angle : 0.564 7.782 23197 Z= 0.311 Chirality : 0.039 0.188 2706 Planarity : 0.004 0.049 2674 Dihedral : 17.736 137.662 2856 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.24 % Allowed : 14.13 % Favored : 83.63 % 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: 1.77 (0.20), residues: 1858 helix: 2.36 (0.15), residues: 1220 sheet: 0.36 (0.42), residues: 165 loop : -1.84 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1008 TYR 0.015 0.001 TYR B 14 PHE 0.016 0.001 PHE A1195 TRP 0.023 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (16989) covalent geometry : angle 0.56393 / 0.31 (23197) hydrogen bonds : bond 0.04164 / 2.76 ( 1051) hydrogen bonds : angle 3.58967 / 2.52 ( 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 194 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.604 Fit side-chains REVERT: A 42 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7770 (ttm) REVERT: A 146 ASN cc_start: 0.8127 (p0) cc_final: 0.7778 (p0) REVERT: A 177 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5259 (pm20) REVERT: A 191 LYS cc_start: 0.7911 (tttp) cc_final: 0.7413 (mmtm) REVERT: B 106 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7446 (ttm110) REVERT: B 139 MET cc_start: 0.8031 (mmm) cc_final: 0.7739 (mmt) REVERT: B 198 LYS cc_start: 0.7090 (pptt) cc_final: 0.6689 (pttp) REVERT: B 1190 MET cc_start: 0.7412 (pmm) cc_final: 0.6652 (ptp) REVERT: C 95 ASP cc_start: 0.7861 (m-30) cc_final: 0.7621 (m-30) REVERT: C 102 MET cc_start: 0.5964 (tpp) cc_final: 0.4976 (ttm) REVERT: D 365 TYR cc_start: 0.7388 (t80) cc_final: 0.6883 (m-80) REVERT: D 993 ASP cc_start: 0.7854 (m-30) cc_final: 0.7474 (m-30) outliers start: 37 outliers final: 29 residues processed: 180 average time/residue: 0.1276 time to fit residues: 35.7560 Evaluate side-chains 176 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 1193 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 421 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 127 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0040 chunk 55 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 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 = 0.3971 r_free = 0.3971 target = 0.153677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114902 restraints weight = 22067.621| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.83 r_work: 0.3301 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2871 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= 0.139 Angle : 0.552 8.439 23197 Z= 0.303 Chirality : 0.039 0.228 2706 Planarity : 0.004 0.047 2674 Dihedral : 17.738 138.338 2856 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.49 % Allowed : 14.74 % Favored : 82.78 % 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: 1.93 (0.20), residues: 1858 helix: 2.49 (0.15), residues: 1220 sheet: 0.40 (0.42), residues: 165 loop : -1.80 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1199 TYR 0.015 0.001 TYR B 116 PHE 0.015 0.001 PHE A1195 TRP 0.032 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16989) covalent geometry : angle 0.55159 / 0.30 (23197) hydrogen bonds : bond 0.04079 / 2.70 ( 1051) hydrogen bonds : angle 3.50794 / 2.46 ( 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 191 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.606 Fit side-chains REVERT: A 42 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: A 177 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: A 191 LYS cc_start: 0.7903 (tttp) cc_final: 0.7437 (mmtm) REVERT: B 106 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7682 (ttm110) REVERT: B 1190 MET cc_start: 0.7407 (pmm) cc_final: 0.6864 (ptm) REVERT: C 95 ASP cc_start: 0.7994 (m-30) cc_final: 0.7748 (m-30) REVERT: C 102 MET cc_start: 0.6031 (tpp) cc_final: 0.5055 (ttm) REVERT: D 365 TYR cc_start: 0.7495 (t80) cc_final: 0.6928 (m-80) REVERT: D 993 ASP cc_start: 0.8025 (m-30) cc_final: 0.7634 (m-30) REVERT: D 1396 MET cc_start: 0.7149 (mmm) cc_final: 0.6829 (mmm) outliers start: 41 outliers final: 32 residues processed: 178 average time/residue: 0.1187 time to fit residues: 33.0347 Evaluate side-chains 177 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 165 LEU 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 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 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 137 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117800 restraints weight = 22116.212| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.87 r_work: 0.3310 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2902 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= 0.130 Angle : 0.549 9.454 23197 Z= 0.300 Chirality : 0.039 0.212 2706 Planarity : 0.004 0.046 2674 Dihedral : 17.697 138.588 2856 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.06 % Allowed : 15.40 % Favored : 82.53 % 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: 2.55 (0.15), residues: 1221 sheet: 0.40 (0.42), residues: 163 loop : -1.76 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 113 TYR 0.015 0.001 TYR B 14 PHE 0.014 0.001 PHE A1195 TRP 0.045 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16989) covalent geometry : angle 0.54903 / 0.30 (23197) hydrogen bonds : bond 0.03968 / 2.63 ( 1051) hydrogen bonds : angle 3.44769 / 2.42 ( 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 177 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.614 Fit side-chains REVERT: A 42 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: A 177 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: A 191 LYS cc_start: 0.7884 (tttp) cc_final: 0.7429 (mmtm) REVERT: B 106 ARG cc_start: 0.7954 (ttt90) cc_final: 0.7697 (ttm110) REVERT: B 1190 MET cc_start: 0.7219 (pmm) cc_final: 0.6941 (ptm) REVERT: C 95 ASP cc_start: 0.7918 (m-30) cc_final: 0.7691 (m-30) REVERT: C 102 MET cc_start: 0.6015 (tpp) cc_final: 0.5049 (ttm) REVERT: D 365 TYR cc_start: 0.7493 (t80) cc_final: 0.6929 (m-80) REVERT: D 868 MET cc_start: 0.8040 (ppp) cc_final: 0.7727 (ppp) REVERT: D 993 ASP cc_start: 0.8035 (m-30) cc_final: 0.7645 (m-30) REVERT: D 1396 MET cc_start: 0.7002 (mmm) cc_final: 0.6784 (mmm) outliers start: 34 outliers final: 28 residues processed: 166 average time/residue: 0.1236 time to fit residues: 31.9348 Evaluate side-chains 168 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 1125 ASP Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE 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 1193 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114614 restraints weight = 22046.439| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.93 r_work: 0.3283 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3004 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= 0.151 Angle : 0.565 8.564 23197 Z= 0.309 Chirality : 0.040 0.191 2706 Planarity : 0.004 0.049 2674 Dihedral : 17.720 138.832 2856 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.30 % Allowed : 15.22 % Favored : 82.47 % 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: 1.93 (0.20), residues: 1858 helix: 2.51 (0.15), residues: 1223 sheet: 0.28 (0.42), residues: 165 loop : -1.85 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.017 0.001 TYR B 116 PHE 0.013 0.001 PHE B 47 TRP 0.043 0.002 TRP D 626 HIS 0.007 0.001 HIS D 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16989) covalent geometry : angle 0.56470 / 0.31 (23197) hydrogen bonds : bond 0.04112 / 2.72 ( 1051) hydrogen bonds : angle 3.47607 / 2.44 ( 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 176 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.569 Fit side-chains REVERT: A 42 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: A 191 LYS cc_start: 0.7880 (tttp) cc_final: 0.7431 (mmtm) REVERT: B 106 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7705 (ttm110) REVERT: B 1190 MET cc_start: 0.7218 (pmm) cc_final: 0.6995 (ptm) REVERT: C 95 ASP cc_start: 0.8001 (m-30) cc_final: 0.7744 (m-30) REVERT: C 102 MET cc_start: 0.5935 (tpp) cc_final: 0.4967 (ttm) REVERT: D 365 TYR cc_start: 0.7541 (t80) cc_final: 0.6958 (m-80) REVERT: D 868 MET cc_start: 0.8028 (ppp) cc_final: 0.7713 (ppp) REVERT: D 993 ASP cc_start: 0.8056 (m-30) cc_final: 0.7664 (m-30) REVERT: D 1396 MET cc_start: 0.7071 (mmm) cc_final: 0.6815 (mmm) outliers start: 38 outliers final: 31 residues processed: 166 average time/residue: 0.1119 time to fit residues: 28.9071 Evaluate side-chains 169 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 30 ILE 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 111 LEU 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 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain C residue 543 SER 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 547 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 112 optimal weight: 0.8980 chunk 114 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116328 restraints weight = 22011.963| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.77 r_work: 0.3329 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16989 Z= 0.122 Angle : 0.543 8.972 23197 Z= 0.297 Chirality : 0.039 0.275 2706 Planarity : 0.004 0.045 2674 Dihedral : 17.672 139.012 2856 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.00 % Allowed : 15.34 % Favored : 82.66 % 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: 2.00 (0.20), residues: 1858 helix: 2.57 (0.15), residues: 1226 sheet: 0.31 (0.43), residues: 163 loop : -1.84 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.017 0.001 TYR A 178 PHE 0.016 0.001 PHE D 338 TRP 0.042 0.002 TRP D 626 HIS 0.008 0.001 HIS A1115 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16989) covalent geometry : angle 0.54328 / 0.30 (23197) hydrogen bonds : bond 0.03898 / 2.57 ( 1051) hydrogen bonds : angle 3.41087 / 2.40 ( 3043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.74 seconds wall clock time: 69 minutes 1.27 seconds (4141.27 seconds total)