Starting phenix.real_space_refine on Sat Feb 7 00:25:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujn_64218/02_2026/9ujn_64218.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.044 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 94 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17758 2.51 5 N 5068 2.21 5 O 5521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28516 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1772 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "B" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1776 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "C" Number of atoms: 8783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 Chain: "D" Number of atoms: 10729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10729 Classifications: {'peptide': 1360} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1291} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "F" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain breaks: 1 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 903 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' ZN': 2, 'C5P%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20155 SG CYS D1112 22.259 60.468 120.216 1.00 73.50 S ATOM 20799 SG CYS D1194 26.061 60.416 119.419 1.00 49.17 S ATOM 20855 SG CYS D1201 24.709 61.866 122.671 1.00 55.50 S ATOM 20879 SG CYS D1204 24.944 58.619 122.575 1.00 69.46 S ATOM 12800 SG CYS D 58 54.542 104.471 83.930 1.00 94.84 S ATOM 12811 SG CYS D 60 55.317 104.370 80.739 1.00 85.70 S ATOM 12922 SG CYS D 73 52.171 104.704 80.702 1.00 84.64 S ATOM 12948 SG CYS D 76 54.006 101.408 81.103 1.00 87.08 S Time building chain proxies: 5.75, per 1000 atoms: 0.20 Number of scatterers: 28516 At special positions: 0 Unit cell: (130.196, 158.172, 206.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 94 15.00 Mg 3 11.99 O 5521 8.00 N 5068 7.00 C 17758 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " Number of angles added : 12 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6206 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 50 sheets defined 43.4% alpha, 17.4% beta 27 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.075A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.302A pdb=" N GLN C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.706A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 228' Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 removed outlier: 3.886A pdb=" N ALA C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 360 removed outlier: 3.799A pdb=" N LEU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.780A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.557A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.661A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.528A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.737A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 removed outlier: 3.537A pdb=" N VAL C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.840A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 872 through 876 Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 933 removed outlier: 3.683A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.560A pdb=" N LYS C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.785A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.134A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.086A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.870A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.545A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.551A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 922 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.612A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.256A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.682A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.671A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.140A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 removed outlier: 3.532A pdb=" N GLU D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.185A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1490 through 1498 removed outlier: 3.653A pdb=" N ILE D1495 " --> pdb=" O THR D1491 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D1498 " --> pdb=" O ALA D1494 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.626A pdb=" N THR E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 165 removed outlier: 3.502A pdb=" N VAL F 156 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.170A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.748A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.791A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.663A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.706A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 361 removed outlier: 3.644A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 373 Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 removed outlier: 3.764A pdb=" N ILE F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 3.639A pdb=" N TYR A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS A 194 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 181 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR A 196 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 179 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 198 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 177 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP A 200 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.295A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.647A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.530A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.077A pdb=" N GLU C 2 " --> pdb=" O ARG C 900 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE C 902 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS C 4 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.752A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.299A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.948A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.358A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 removed outlier: 3.531A pdb=" N ASP C 533 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.938A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.673A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.807A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.197A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 6.310A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.716A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.720A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD3, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.712A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.367A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.748A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.534A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 342 through 346 removed outlier: 6.921A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 353 Processing sheet with id=AE1, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.696A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.023A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.544A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 626 through 633 removed outlier: 7.634A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1303 Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.829A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 1235 hydrogen bonds defined for protein. 3438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4693 1.31 - 1.43: 7493 1.43 - 1.56: 16715 1.56 - 1.68: 188 1.68 - 1.81: 127 Bond restraints: 29216 Sorted by residual: bond pdb=" O5' C5P D1605 " pdb=" P C5P D1605 " ideal model delta sigma weight residual 1.709 1.591 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C GLN D1441 " pdb=" O GLN D1441 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.09e-02 8.42e+03 1.26e+01 bond pdb=" C ASP D 579 " pdb=" O ASP D 579 " ideal model delta sigma weight residual 1.236 1.196 0.041 1.26e-02 6.30e+03 1.04e+01 bond pdb=" C23 1N7 B 401 " pdb=" C24 1N7 B 401 " ideal model delta sigma weight residual 1.512 1.574 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" CA TYR D 128 " pdb=" CB TYR D 128 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.46e-02 4.69e+03 9.21e+00 ... (remaining 29211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 38881 1.30 - 2.60: 802 2.60 - 3.91: 195 3.91 - 5.21: 34 5.21 - 6.51: 9 Bond angle restraints: 39921 Sorted by residual: angle pdb=" PA ATP G 101 " pdb=" O3A ATP G 101 " pdb=" PB ATP G 101 " ideal model delta sigma weight residual 136.83 130.38 6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" PB ATP G 101 " pdb=" O3B ATP G 101 " pdb=" PG ATP G 101 " ideal model delta sigma weight residual 139.87 135.48 4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" N VAL E 39 " pdb=" CA VAL E 39 " pdb=" C VAL E 39 " ideal model delta sigma weight residual 112.83 108.98 3.85 9.90e-01 1.02e+00 1.51e+01 angle pdb=" C GLN D1441 " pdb=" N ASN D1442 " pdb=" CA ASN D1442 " ideal model delta sigma weight residual 122.36 127.17 -4.81 1.42e+00 4.96e-01 1.15e+01 angle pdb=" C ASP D 579 " pdb=" CA ASP D 579 " pdb=" CB ASP D 579 " ideal model delta sigma weight residual 110.67 117.14 -6.47 1.92e+00 2.71e-01 1.13e+01 ... (remaining 39916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16111 17.95 - 35.90: 1154 35.90 - 53.85: 386 53.85 - 71.80: 129 71.80 - 89.74: 23 Dihedral angle restraints: 17803 sinusoidal: 8160 harmonic: 9643 Sorted by residual: dihedral pdb=" CB GLU D 122 " pdb=" CG GLU D 122 " pdb=" CD GLU D 122 " pdb=" OE1 GLU D 122 " ideal model delta sinusoidal sigma weight residual 0.00 -89.74 89.74 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 189 " pdb=" CD ARG B 189 " pdb=" NE ARG B 189 " pdb=" CZ ARG B 189 " ideal model delta sinusoidal sigma weight residual 90.00 134.09 -44.09 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " pdb=" CG ASP C 124 " pdb=" OD1 ASP C 124 " ideal model delta sinusoidal sigma weight residual -30.00 -84.38 54.38 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 17800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3581 0.047 - 0.094: 691 0.094 - 0.142: 220 0.142 - 0.189: 6 0.189 - 0.236: 3 Chirality restraints: 4501 Sorted by residual: chirality pdb=" C1' C5P D1605 " pdb=" C2' C5P D1605 " pdb=" N1 C5P D1605 " pdb=" O4' C5P D1605 " both_signs ideal model delta sigma weight residual False 2.22 2.46 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ASP D 579 " pdb=" N ASP D 579 " pdb=" C ASP D 579 " pdb=" CB ASP D 579 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA TYR D1207 " pdb=" N TYR D1207 " pdb=" C TYR D1207 " pdb=" CB TYR D1207 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 4498 not shown) Planarity restraints: 4890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 34 " 0.008 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR D 34 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 34 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 34 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR D 34 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 34 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 34 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 723 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C GLY D 723 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY D 723 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN D 724 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP G 101 " 0.024 2.00e-02 2.50e+03 1.00e-02 2.77e+00 pdb=" C2 ATP G 101 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ATP G 101 " -0.003 2.00e-02 2.50e+03 pdb=" C5 ATP G 101 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ATP G 101 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ATP G 101 " -0.006 2.00e-02 2.50e+03 pdb=" N1 ATP G 101 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ATP G 101 " -0.007 2.00e-02 2.50e+03 pdb=" N6 ATP G 101 " 0.013 2.00e-02 2.50e+03 pdb=" N7 ATP G 101 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ATP G 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 4887 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 235 2.59 - 3.17: 22963 3.17 - 3.75: 45077 3.75 - 4.32: 66202 4.32 - 4.90: 108646 Nonbonded interactions: 243123 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.014 2.170 nonbonded pdb="MG MG D1603 " pdb=" O3' C5P D1605 " model vdw 2.030 2.170 nonbonded pdb="MG MG D1603 " pdb=" O HOH D1701 " model vdw 2.048 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.066 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.078 2.170 ... (remaining 243118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 229) selection = (chain 'B' and resid 6 through 229) } 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=0.05 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.003 0.118 29225 Z= 0.153 Angle : 0.553 23.356 39933 Z= 0.275 Chirality : 0.041 0.236 4501 Planarity : 0.004 0.047 4890 Dihedral : 14.990 89.744 11597 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.99 (0.14), residues: 3332 helix: 1.10 (0.14), residues: 1287 sheet: 0.35 (0.26), residues: 434 loop : 0.55 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 546 TYR 0.024 0.001 TYR D 34 PHE 0.017 0.001 PHE D 740 TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00296 (29216) covalent geometry : angle 0.49568 (39921) hydrogen bonds : bond 0.21748 ( 1295) hydrogen bonds : angle 7.44546 ( 3562) metal coordination : bond 0.01491 ( 8) metal coordination : angle 14.18134 ( 12) Misc. bond : bond 0.05050 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8214 (ttm110) REVERT: D 661 MET cc_start: 0.8743 (mtp) cc_final: 0.8509 (mtp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 1.0890 time to fit residues: 244.3454 Evaluate side-chains 102 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN C 575 GLN D 976 GLN D1441 GLN ** F 170 HIS ** 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 = 0.3123 r_free = 0.3123 target = 0.052598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.038258 restraints weight = 101890.971| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.84 r_work: 0.2522 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29225 Z= 0.244 Angle : 0.588 8.591 39933 Z= 0.312 Chirality : 0.044 0.143 4501 Planarity : 0.005 0.047 4890 Dihedral : 15.460 79.316 4862 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.74 % Allowed : 5.46 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.39 (0.15), residues: 3332 helix: 1.58 (0.14), residues: 1306 sheet: 0.33 (0.26), residues: 423 loop : 0.70 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 434 TYR 0.017 0.001 TYR C 925 PHE 0.016 0.001 PHE C 778 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00554 (29216) covalent geometry : angle 0.58463 (39921) hydrogen bonds : bond 0.05452 ( 1295) hydrogen bonds : angle 5.25636 ( 3562) metal coordination : bond 0.01227 ( 8) metal coordination : angle 3.90629 ( 12) Misc. bond : bond 0.00175 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8867 (mt0) cc_final: 0.8607 (pt0) REVERT: C 420 ARG cc_start: 0.9027 (ttm110) cc_final: 0.8693 (ttp-110) REVERT: C 771 GLU cc_start: 0.8927 (tt0) cc_final: 0.8310 (tp30) REVERT: D 980 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8818 (mpp) REVERT: E 12 MET cc_start: 0.9108 (mtp) cc_final: 0.8810 (mtp) REVERT: E 86 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8526 (tm-30) REVERT: E 87 LYS cc_start: 0.9371 (mmpt) cc_final: 0.9014 (mmpt) REVERT: F 410 TYR cc_start: 0.8987 (m-10) cc_final: 0.8775 (m-10) outliers start: 21 outliers final: 7 residues processed: 116 average time/residue: 0.9688 time to fit residues: 127.7368 Evaluate side-chains 102 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain E residue 36 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038930 restraints weight = 101172.584| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.85 r_work: 0.2545 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29225 Z= 0.138 Angle : 0.509 8.131 39933 Z= 0.271 Chirality : 0.041 0.137 4501 Planarity : 0.004 0.049 4890 Dihedral : 15.417 78.426 4862 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.84 % Allowed : 6.23 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.47 (0.15), residues: 3332 helix: 1.69 (0.15), residues: 1312 sheet: 0.43 (0.27), residues: 396 loop : 0.67 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 557 TYR 0.011 0.001 TYR C 925 PHE 0.013 0.001 PHE C 922 TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00311 (29216) covalent geometry : angle 0.50781 (39921) hydrogen bonds : bond 0.04120 ( 1295) hydrogen bonds : angle 4.81180 ( 3562) metal coordination : bond 0.00599 ( 8) metal coordination : angle 2.08344 ( 12) Misc. bond : bond 0.00152 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8894 (mt0) cc_final: 0.8653 (pt0) REVERT: A 47 SER cc_start: 0.9521 (m) cc_final: 0.9172 (p) REVERT: A 64 GLU cc_start: 0.8927 (pt0) cc_final: 0.8477 (pt0) REVERT: C 184 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (tmm) REVERT: C 384 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8744 (tm-30) REVERT: C 771 GLU cc_start: 0.8937 (tt0) cc_final: 0.8357 (tm-30) REVERT: D 661 MET cc_start: 0.9356 (mtp) cc_final: 0.9017 (mtp) REVERT: D 980 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8722 (mpp) REVERT: E 12 MET cc_start: 0.9141 (mtp) cc_final: 0.8796 (mtp) REVERT: E 41 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8693 (mm-30) REVERT: E 43 GLU cc_start: 0.9383 (mp0) cc_final: 0.9169 (pm20) REVERT: E 44 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8552 (pt0) REVERT: E 86 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8237 (tm-30) REVERT: E 87 LYS cc_start: 0.9342 (mmpt) cc_final: 0.8972 (mmmt) REVERT: F 410 TYR cc_start: 0.8920 (m-10) cc_final: 0.8586 (m-10) outliers start: 24 outliers final: 8 residues processed: 113 average time/residue: 0.9478 time to fit residues: 121.7347 Evaluate side-chains 102 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 980 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 17 optimal weight: 0.0670 chunk 319 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 180 GLN C 670 GLN D 762 GLN ** F 170 HIS ** 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 = 0.3131 r_free = 0.3131 target = 0.052640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.038466 restraints weight = 101050.184| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.80 r_work: 0.2533 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29225 Z= 0.158 Angle : 0.497 8.532 39933 Z= 0.263 Chirality : 0.041 0.135 4501 Planarity : 0.004 0.043 4890 Dihedral : 15.357 77.531 4862 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.67 % Allowed : 7.29 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.56 (0.15), residues: 3332 helix: 1.81 (0.15), residues: 1316 sheet: 0.39 (0.27), residues: 399 loop : 0.71 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.020 0.001 TYR D 158 PHE 0.012 0.001 PHE D 502 TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00362 (29216) covalent geometry : angle 0.49575 (39921) hydrogen bonds : bond 0.03862 ( 1295) hydrogen bonds : angle 4.57140 ( 3562) metal coordination : bond 0.00657 ( 8) metal coordination : angle 1.87316 ( 12) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8854 (mt0) cc_final: 0.8602 (pt0) REVERT: A 47 SER cc_start: 0.9489 (m) cc_final: 0.9189 (p) REVERT: C 1 MET cc_start: 0.8003 (tmm) cc_final: 0.7786 (tpt) REVERT: C 184 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8592 (tmm) REVERT: C 361 MET cc_start: 0.8022 (pp-130) cc_final: 0.7567 (pp-130) REVERT: C 384 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 771 GLU cc_start: 0.8926 (tt0) cc_final: 0.8377 (tm-30) REVERT: D 678 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8503 (mp0) REVERT: D 980 MET cc_start: 0.8989 (mpp) cc_final: 0.8732 (mpp) REVERT: E 12 MET cc_start: 0.9192 (mtp) cc_final: 0.8961 (mtp) REVERT: E 41 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8684 (mm-30) REVERT: E 43 GLU cc_start: 0.9385 (mp0) cc_final: 0.9184 (pm20) REVERT: E 44 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8579 (pt0) REVERT: E 86 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 87 LYS cc_start: 0.9346 (mmpt) cc_final: 0.8904 (mmmt) REVERT: E 90 GLU cc_start: 0.8784 (pp20) cc_final: 0.8442 (pp20) REVERT: F 410 TYR cc_start: 0.8916 (m-10) cc_final: 0.8597 (m-10) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 0.9267 time to fit residues: 116.1863 Evaluate side-chains 101 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 241 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 976 GLN ** F 170 HIS ** 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 = 0.3124 r_free = 0.3124 target = 0.052421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.038201 restraints weight = 101664.215| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.81 r_work: 0.2528 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29225 Z= 0.165 Angle : 0.492 8.555 39933 Z= 0.260 Chirality : 0.041 0.136 4501 Planarity : 0.004 0.040 4890 Dihedral : 15.362 76.993 4862 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.84 % Allowed : 7.71 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.60 (0.15), residues: 3332 helix: 1.87 (0.14), residues: 1316 sheet: 0.34 (0.26), residues: 405 loop : 0.73 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.012 0.001 TYR D 128 PHE 0.011 0.001 PHE D 502 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00378 (29216) covalent geometry : angle 0.49097 (39921) hydrogen bonds : bond 0.03732 ( 1295) hydrogen bonds : angle 4.50106 ( 3562) metal coordination : bond 0.00670 ( 8) metal coordination : angle 1.49503 ( 12) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8791 (mt0) cc_final: 0.8542 (pt0) REVERT: A 47 SER cc_start: 0.9467 (m) cc_final: 0.9180 (p) REVERT: C 1 MET cc_start: 0.7973 (tmm) cc_final: 0.7761 (tpt) REVERT: C 184 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8550 (tmm) REVERT: C 361 MET cc_start: 0.8166 (pp-130) cc_final: 0.7787 (ppp) REVERT: C 384 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 1052 MET cc_start: 0.9439 (mmm) cc_final: 0.8894 (mtm) REVERT: D 661 MET cc_start: 0.9397 (mtp) cc_final: 0.9133 (mtp) REVERT: D 678 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8505 (mp0) REVERT: D 980 MET cc_start: 0.8998 (mpp) cc_final: 0.8778 (mpp) REVERT: E 12 MET cc_start: 0.9195 (mtp) cc_final: 0.8932 (mtp) REVERT: E 41 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8705 (mm-30) REVERT: E 44 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8569 (pt0) REVERT: E 86 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 87 LYS cc_start: 0.9342 (mmpt) cc_final: 0.8900 (mmmt) REVERT: E 90 GLU cc_start: 0.8866 (pp20) cc_final: 0.8591 (pp20) REVERT: F 410 TYR cc_start: 0.8924 (m-10) cc_final: 0.8588 (m-10) outliers start: 24 outliers final: 7 residues processed: 110 average time/residue: 0.8982 time to fit residues: 112.9532 Evaluate side-chains 101 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 5 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 0.0170 chunk 308 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D1359 GLN ** F 170 HIS ** 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 = 0.3096 r_free = 0.3096 target = 0.051285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.037087 restraints weight = 102029.322| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.80 r_work: 0.2489 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 29225 Z= 0.250 Angle : 0.543 8.933 39933 Z= 0.283 Chirality : 0.043 0.138 4501 Planarity : 0.004 0.039 4890 Dihedral : 15.435 76.350 4862 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 8.55 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.56 (0.15), residues: 3332 helix: 1.85 (0.14), residues: 1317 sheet: 0.13 (0.26), residues: 417 loop : 0.75 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.015 0.001 TYR D 128 PHE 0.016 0.001 PHE D 502 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00577 (29216) covalent geometry : angle 0.54215 (39921) hydrogen bonds : bond 0.04106 ( 1295) hydrogen bonds : angle 4.55167 ( 3562) metal coordination : bond 0.01078 ( 8) metal coordination : angle 1.93281 ( 12) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8754 (mt0) cc_final: 0.8542 (pt0) REVERT: A 47 SER cc_start: 0.9474 (m) cc_final: 0.9194 (p) REVERT: A 201 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8976 (p) REVERT: C 1 MET cc_start: 0.8117 (tmm) cc_final: 0.7803 (tpt) REVERT: C 361 MET cc_start: 0.8305 (pp-130) cc_final: 0.7904 (ppp) REVERT: C 384 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8659 (tm-30) REVERT: C 629 TYR cc_start: 0.7992 (t80) cc_final: 0.7469 (t80) REVERT: C 1052 MET cc_start: 0.9468 (mmm) cc_final: 0.8799 (mtm) REVERT: D 980 MET cc_start: 0.8989 (mpp) cc_final: 0.8768 (mpp) REVERT: D 1207 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: E 44 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8486 (pt0) REVERT: E 86 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8380 (tm-30) REVERT: E 87 LYS cc_start: 0.9367 (mmpt) cc_final: 0.8972 (mmmt) REVERT: E 90 GLU cc_start: 0.8928 (pp20) cc_final: 0.8703 (pp20) REVERT: F 410 TYR cc_start: 0.8951 (m-10) cc_final: 0.8595 (m-10) outliers start: 23 outliers final: 9 residues processed: 107 average time/residue: 0.8784 time to fit residues: 107.6251 Evaluate side-chains 103 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 148 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1047 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.038570 restraints weight = 100957.032| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.81 r_work: 0.2541 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29225 Z= 0.111 Angle : 0.477 8.845 39933 Z= 0.253 Chirality : 0.041 0.142 4501 Planarity : 0.004 0.041 4890 Dihedral : 15.326 75.634 4862 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.53 % Allowed : 9.04 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.65 (0.15), residues: 3332 helix: 1.96 (0.14), residues: 1319 sheet: 0.35 (0.27), residues: 392 loop : 0.71 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.011 0.001 TYR C 925 PHE 0.011 0.001 PHE C 922 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00253 (29216) covalent geometry : angle 0.47681 (39921) hydrogen bonds : bond 0.03404 ( 1295) hydrogen bonds : angle 4.37043 ( 3562) metal coordination : bond 0.00330 ( 8) metal coordination : angle 1.19738 ( 12) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9444 (m) cc_final: 0.9230 (p) REVERT: A 64 GLU cc_start: 0.8838 (pt0) cc_final: 0.8348 (pt0) REVERT: C 1 MET cc_start: 0.8139 (tmm) cc_final: 0.7769 (tpt) REVERT: C 361 MET cc_start: 0.8406 (pp-130) cc_final: 0.8013 (ppp) REVERT: C 384 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8752 (tm-30) REVERT: C 420 ARG cc_start: 0.9122 (ttp-110) cc_final: 0.8870 (ttp-110) REVERT: C 629 TYR cc_start: 0.7962 (t80) cc_final: 0.7685 (t80) REVERT: C 1052 MET cc_start: 0.9417 (mmm) cc_final: 0.8787 (mtm) REVERT: D 661 MET cc_start: 0.9398 (mtp) cc_final: 0.9167 (mtp) REVERT: D 678 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8619 (mt-10) REVERT: D 1207 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: E 41 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8731 (mm-30) REVERT: E 44 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8581 (pt0) REVERT: E 83 ASP cc_start: 0.9474 (p0) cc_final: 0.9244 (p0) REVERT: E 86 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8616 (tm-30) REVERT: E 87 LYS cc_start: 0.9380 (mmpt) cc_final: 0.9164 (mtmm) REVERT: F 410 TYR cc_start: 0.8923 (m-10) cc_final: 0.8558 (m-10) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.7677 time to fit residues: 92.8012 Evaluate side-chains 100 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 162 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 324 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN D1441 GLN ** F 170 HIS ** 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 = 0.3134 r_free = 0.3134 target = 0.052632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.038489 restraints weight = 101626.112| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.81 r_work: 0.2539 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29225 Z= 0.125 Angle : 0.479 9.332 39933 Z= 0.252 Chirality : 0.041 0.143 4501 Planarity : 0.004 0.040 4890 Dihedral : 15.290 75.071 4862 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.63 % Allowed : 9.28 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.71 (0.15), residues: 3332 helix: 1.99 (0.14), residues: 1318 sheet: 0.38 (0.27), residues: 392 loop : 0.75 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.011 0.001 TYR D 128 PHE 0.010 0.001 PHE C 922 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00286 (29216) covalent geometry : angle 0.47840 (39921) hydrogen bonds : bond 0.03411 ( 1295) hydrogen bonds : angle 4.31508 ( 3562) metal coordination : bond 0.00414 ( 8) metal coordination : angle 1.18070 ( 12) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8129 (tmm) cc_final: 0.7759 (tpt) REVERT: C 361 MET cc_start: 0.8467 (pp-130) cc_final: 0.8030 (ppp) REVERT: C 384 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8660 (tm-30) REVERT: C 629 TYR cc_start: 0.7910 (t80) cc_final: 0.7623 (t80) REVERT: C 771 GLU cc_start: 0.8931 (tt0) cc_final: 0.8356 (tm-30) REVERT: D 661 MET cc_start: 0.9401 (mtp) cc_final: 0.9180 (mtp) REVERT: D 1207 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: E 41 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8723 (mm-30) REVERT: E 44 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8590 (pt0) REVERT: E 86 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8375 (tm-30) REVERT: E 87 LYS cc_start: 0.9371 (mmpt) cc_final: 0.9055 (mmmt) REVERT: F 410 TYR cc_start: 0.8904 (m-10) cc_final: 0.8564 (m-10) outliers start: 18 outliers final: 8 residues processed: 106 average time/residue: 0.8493 time to fit residues: 102.7571 Evaluate side-chains 100 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 71 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 331 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 80 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038685 restraints weight = 101062.277| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.81 r_work: 0.2548 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29225 Z= 0.122 Angle : 0.477 11.075 39933 Z= 0.251 Chirality : 0.041 0.138 4501 Planarity : 0.004 0.046 4890 Dihedral : 15.216 74.625 4862 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.42 % Allowed : 9.53 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.74 (0.15), residues: 3332 helix: 2.02 (0.14), residues: 1320 sheet: 0.40 (0.27), residues: 392 loop : 0.77 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1087 TYR 0.010 0.001 TYR D 128 PHE 0.013 0.001 PHE F 389 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00279 (29216) covalent geometry : angle 0.47695 (39921) hydrogen bonds : bond 0.03314 ( 1295) hydrogen bonds : angle 4.27150 ( 3562) metal coordination : bond 0.00398 ( 8) metal coordination : angle 1.08794 ( 12) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8894 (pt0) cc_final: 0.8422 (pt0) REVERT: C 1 MET cc_start: 0.8016 (tmm) cc_final: 0.7739 (tpt) REVERT: C 361 MET cc_start: 0.8538 (pp-130) cc_final: 0.8095 (ppp) REVERT: C 384 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 629 TYR cc_start: 0.7892 (t80) cc_final: 0.7605 (t80) REVERT: C 771 GLU cc_start: 0.8938 (tt0) cc_final: 0.8332 (tm-30) REVERT: D 678 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8488 (mp0) REVERT: D 1207 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: E 41 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8736 (mm-30) REVERT: E 44 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8533 (pt0) REVERT: E 83 ASP cc_start: 0.9473 (p0) cc_final: 0.9239 (p0) REVERT: E 86 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8629 (tm-30) REVERT: E 87 LYS cc_start: 0.9360 (mmpt) cc_final: 0.9138 (mtmm) REVERT: F 410 TYR cc_start: 0.8930 (m-10) cc_final: 0.8588 (m-10) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.8696 time to fit residues: 102.2807 Evaluate side-chains 99 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 1207 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 48 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 326 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.052373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.038187 restraints weight = 101066.499| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.80 r_work: 0.2528 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29225 Z= 0.156 Angle : 0.495 11.972 39933 Z= 0.258 Chirality : 0.041 0.153 4501 Planarity : 0.004 0.043 4890 Dihedral : 15.204 74.157 4862 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.46 % Allowed : 9.56 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.74 (0.15), residues: 3332 helix: 2.04 (0.14), residues: 1315 sheet: 0.29 (0.27), residues: 398 loop : 0.79 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1087 TYR 0.011 0.001 TYR D 128 PHE 0.013 0.001 PHE F 389 TRP 0.008 0.001 TRP D 688 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00359 (29216) covalent geometry : angle 0.49420 (39921) hydrogen bonds : bond 0.03482 ( 1295) hydrogen bonds : angle 4.30568 ( 3562) metal coordination : bond 0.00591 ( 8) metal coordination : angle 1.27217 ( 12) Misc. bond : bond 0.00022 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6664 Ramachandran restraints generated. 3332 Oldfield, 0 Emsley, 3332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8128 (tmm) cc_final: 0.7820 (tpt) REVERT: C 361 MET cc_start: 0.8613 (pp-130) cc_final: 0.8161 (ppp) REVERT: C 384 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8667 (tm-30) REVERT: C 629 TYR cc_start: 0.7908 (t80) cc_final: 0.7620 (t80) REVERT: C 1052 MET cc_start: 0.9378 (mmm) cc_final: 0.8810 (mtm) REVERT: D 678 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8487 (mp0) REVERT: D 1207 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: E 41 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8794 (mm-30) REVERT: E 44 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8586 (pt0) REVERT: E 86 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8668 (tm-30) REVERT: F 410 TYR cc_start: 0.8932 (m-10) cc_final: 0.8587 (m-10) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.8430 time to fit residues: 94.1876 Evaluate side-chains 98 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 1207 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 225 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 303 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 244 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.038362 restraints weight = 101108.904| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.87 r_work: 0.2542 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29225 Z= 0.126 Angle : 0.481 12.381 39933 Z= 0.252 Chirality : 0.041 0.169 4501 Planarity : 0.004 0.043 4890 Dihedral : 15.172 73.852 4862 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.53 % Allowed : 9.74 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.76 (0.15), residues: 3332 helix: 2.07 (0.14), residues: 1315 sheet: 0.31 (0.27), residues: 397 loop : 0.78 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1087 TYR 0.010 0.001 TYR D 128 PHE 0.013 0.001 PHE F 389 TRP 0.010 0.001 TRP D 688 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00290 (29216) covalent geometry : angle 0.48104 (39921) hydrogen bonds : bond 0.03317 ( 1295) hydrogen bonds : angle 4.26681 ( 3562) metal coordination : bond 0.00419 ( 8) metal coordination : angle 1.06717 ( 12) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7287.11 seconds wall clock time: 125 minutes 26.72 seconds (7526.72 seconds total)