Starting phenix.real_space_refine on Sun Jul 5 17:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujn_64218/07_2026/9ujn_64218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujn_64218/07_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_64218/07_2026/9ujn_64218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujn_64218/07_2026/9ujn_64218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ujn_64218/07_2026/9ujn_64218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujn_64218/07_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-dev-6108/lib/python3.11/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: 5.37, per 1000 atoms: 0.19 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 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: 2.73 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: 6.77 Time building geometry restraints manager: 2.49 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=" C3' DA H 10 " pdb=" C2' DA H 10 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC H 24 " pdb=" C2' DC H 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+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 ... (remaining 29211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 38620 1.30 - 2.60: 1057 2.60 - 3.91: 201 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=" N3 DT G 4 " pdb=" C4 DT G 4 " pdb=" O4 DT G 4 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT H 3 " pdb=" C4 DT H 3 " pdb=" O4 DT H 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT H 2 " pdb=" C4 DT H 2 " pdb=" O4 DT H 2 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+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: 3486 0.047 - 0.094: 770 0.094 - 0.142: 236 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: 1.810 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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= 0.232 Angle : 0.583 23.356 39933 Z= 0.349 Chirality : 0.043 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/Z covalent geometry : bond 0.00336 / 0.23 (29216) covalent geometry : angle 0.52820 / 0.35 (39921) hydrogen bonds : bond 0.21748 / 14.45 ( 1295) hydrogen bonds : angle 7.44546 / 5.10 ( 3562) metal coordination : bond 0.01491 / 0.78 ( 8) metal coordination : angle 14.18134 / 7.04 ( 12) Misc. bond : bond 0.05050 / 2.66 ( 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 : 1.215 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: 1.0030 time to fit residues: 225.9861 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 : 1.101 ------------------------------------------------------------------------------- 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... 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 = 0.3126 r_free = 0.3126 target = 0.052727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.038291 restraints weight = 101685.647| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.85 r_work: 0.2524 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 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 = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29225 Z= 0.238 Angle : 0.620 8.650 39933 Z= 0.328 Chirality : 0.045 0.190 4501 Planarity : 0.005 0.051 4890 Dihedral : 15.626 79.044 4862 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.97 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: 1.32 (0.15), residues: 3332 helix: 1.49 (0.14), residues: 1306 sheet: 0.40 (0.27), residues: 395 loop : 0.66 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 406 TYR 0.024 0.001 TYR F 410 PHE 0.014 0.002 PHE D1008 TRP 0.014 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (29216) covalent geometry : angle 0.61605 / 0.33 (39921) hydrogen bonds : bond 0.05737 / 3.85 ( 1295) hydrogen bonds : angle 5.32408 / 3.71 ( 3562) metal coordination : bond 0.01136 / 0.53 ( 8) metal coordination : angle 4.05226 / 2.01 ( 12) Misc. bond : bond 0.00283 / 0.15 ( 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 131 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8777 (ttp-110) REVERT: C 771 GLU cc_start: 0.8924 (tt0) cc_final: 0.8379 (tm-30) REVERT: D 980 MET cc_start: 0.9026 (mpp) cc_final: 0.8781 (mpp) REVERT: E 12 MET cc_start: 0.9085 (mtp) cc_final: 0.8784 (mtp) REVERT: E 86 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8573 (tm-30) REVERT: E 87 LYS cc_start: 0.9371 (mmpt) cc_final: 0.9006 (mmmt) outliers start: 21 outliers final: 7 residues processed: 117 average time/residue: 0.8784 time to fit residues: 116.9074 Evaluate side-chains 102 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 25 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN C 670 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 = 0.3114 r_free = 0.3114 target = 0.052127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.037827 restraints weight = 101910.506| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.81 r_work: 0.2508 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 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 = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29225 Z= 0.217 Angle : 0.556 8.901 39933 Z= 0.295 Chirality : 0.043 0.163 4501 Planarity : 0.004 0.046 4890 Dihedral : 15.802 78.103 4862 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.09 % Allowed : 6.80 % Favored : 92.12 % 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: 1.65 (0.14), residues: 1312 sheet: 0.27 (0.26), residues: 397 loop : 0.64 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 406 TYR 0.016 0.001 TYR F 410 PHE 0.014 0.001 PHE D 502 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (29216) covalent geometry : angle 0.55431 / 0.30 (39921) hydrogen bonds : bond 0.04717 / 3.15 ( 1295) hydrogen bonds : angle 4.88525 / 3.41 ( 3562) metal coordination : bond 0.00968 / 0.48 ( 8) metal coordination : angle 2.33653 / 1.14 ( 12) Misc. bond : bond 0.00241 / 0.13 ( 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 132 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9522 (m) cc_final: 0.9176 (p) REVERT: C 1 MET cc_start: 0.7987 (tmm) cc_final: 0.7774 (tpt) REVERT: C 184 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8661 (tmm) REVERT: C 384 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8647 (pp20) REVERT: C 771 GLU cc_start: 0.8925 (tt0) cc_final: 0.8337 (tm-30) REVERT: C 1052 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8850 (mmm) REVERT: D 661 MET cc_start: 0.9331 (mtp) cc_final: 0.8976 (mtp) REVERT: E 12 MET cc_start: 0.9168 (mtp) cc_final: 0.8851 (mtp) REVERT: E 41 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8724 (mm-30) REVERT: E 44 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8595 (pt0) REVERT: E 86 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8485 (tm-30) REVERT: E 87 LYS cc_start: 0.9377 (mmpt) cc_final: 0.9112 (mmpt) REVERT: F 410 TYR cc_start: 0.8978 (m-10) cc_final: 0.8688 (m-10) outliers start: 31 outliers final: 8 residues processed: 112 average time/residue: 0.8368 time to fit residues: 106.6472 Evaluate side-chains 103 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 34 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain E residue 36 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 17 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 262 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3142 r_free = 0.3142 target = 0.053149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.038981 restraints weight = 100325.747| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.79 r_work: 0.2549 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29225 Z= 0.112 Angle : 0.499 7.847 39933 Z= 0.268 Chirality : 0.042 0.145 4501 Planarity : 0.004 0.048 4890 Dihedral : 15.660 78.117 4862 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.81 % Allowed : 7.22 % Favored : 91.98 % 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: 1.47 (0.15), residues: 3332 helix: 1.75 (0.14), residues: 1314 sheet: 0.41 (0.28), residues: 372 loop : 0.61 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 406 TYR 0.020 0.001 TYR D 158 PHE 0.010 0.001 PHE D 129 TRP 0.011 0.001 TRP B 200 HIS 0.008 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (29216) covalent geometry : angle 0.49841 / 0.27 (39921) hydrogen bonds : bond 0.03803 / 2.56 ( 1295) hydrogen bonds : angle 4.64772 / 3.26 ( 3562) metal coordination : bond 0.00331 / 0.15 ( 8) metal coordination : angle 1.58590 / 0.73 ( 12) Misc. bond : bond 0.00074 / 0.04 ( 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 126 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9508 (m) cc_final: 0.9195 (p) REVERT: A 64 GLU cc_start: 0.8899 (pt0) cc_final: 0.8397 (pt0) REVERT: C 1 MET cc_start: 0.8087 (tmm) cc_final: 0.7671 (tpt) REVERT: C 184 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8543 (tmm) REVERT: C 384 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8470 (pp20) REVERT: C 771 GLU cc_start: 0.8942 (tt0) cc_final: 0.8374 (tm-30) REVERT: D 661 MET cc_start: 0.9348 (mtp) cc_final: 0.8999 (mtp) REVERT: D 678 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8494 (mp0) REVERT: D 980 MET cc_start: 0.9024 (mpp) cc_final: 0.8777 (mpp) REVERT: E 12 MET cc_start: 0.9201 (mtp) cc_final: 0.8966 (mtp) REVERT: E 41 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8715 (mm-30) REVERT: E 44 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8601 (pt0) REVERT: E 86 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8642 (tm-30) REVERT: E 87 LYS cc_start: 0.9338 (mmpt) cc_final: 0.9126 (mtmm) REVERT: F 410 TYR cc_start: 0.8925 (m-10) cc_final: 0.8681 (m-10) outliers start: 23 outliers final: 7 residues processed: 115 average time/residue: 0.8427 time to fit residues: 110.6913 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 : 1.040 ------------------------------------------------------------------------------- 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 118 ILE 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 575 GLN Chi-restraints excluded: chain D residue 692 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 241 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN D 442 ASN D 762 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.036212 restraints weight = 103362.777| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.80 r_work: 0.2457 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 29225 Z= 0.405 Angle : 0.656 8.810 39933 Z= 0.337 Chirality : 0.046 0.152 4501 Planarity : 0.005 0.043 4890 Dihedral : 15.866 77.475 4862 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.95 % Allowed : 7.71 % Favored : 91.35 % 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: 1.40 (0.15), residues: 3332 helix: 1.73 (0.14), residues: 1306 sheet: 0.09 (0.26), residues: 405 loop : 0.63 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 237 TYR 0.017 0.001 TYR D 128 PHE 0.019 0.002 PHE D 502 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS C 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00924 / 0.41 (29216) covalent geometry : angle 0.65465 / 0.34 (39921) hydrogen bonds : bond 0.04880 / 3.26 ( 1295) hydrogen bonds : angle 4.82318 / 3.37 ( 3562) metal coordination : bond 0.01922 / 0.99 ( 8) metal coordination : angle 2.73754 / 1.44 ( 12) Misc. bond : bond 0.00068 / 0.04 ( 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 120 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9489 (m) cc_final: 0.9161 (p) REVERT: A 201 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 1 MET cc_start: 0.8111 (tmm) cc_final: 0.7741 (tpt) REVERT: C 361 MET cc_start: 0.7978 (pp-130) cc_final: 0.7600 (pp-130) REVERT: C 384 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8792 (tm-30) REVERT: D 980 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8689 (mpp) REVERT: E 41 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8749 (mm-30) REVERT: E 44 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8537 (pt0) REVERT: E 86 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8288 (tm-30) REVERT: E 87 LYS cc_start: 0.9337 (mmpt) cc_final: 0.8990 (mmmt) REVERT: F 410 TYR cc_start: 0.8957 (m-10) cc_final: 0.8718 (m-10) outliers start: 27 outliers final: 14 residues processed: 108 average time/residue: 0.7984 time to fit residues: 99.2677 Evaluate side-chains 104 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain C residue 121 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 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain E residue 36 LYS 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: 3.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1441 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 = 0.3119 r_free = 0.3119 target = 0.052127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.037821 restraints weight = 100803.206| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.85 r_work: 0.2519 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 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 = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2246 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= 0.127 Angle : 0.505 9.047 39933 Z= 0.270 Chirality : 0.042 0.140 4501 Planarity : 0.004 0.042 4890 Dihedral : 15.687 77.259 4862 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.84 % Allowed : 8.44 % Favored : 90.72 % 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: 1.45 (0.15), residues: 3332 helix: 1.80 (0.14), residues: 1315 sheet: 0.22 (0.27), residues: 377 loop : 0.59 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.014 0.001 TYR D 132 PHE 0.013 0.001 PHE D 129 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (29216) covalent geometry : angle 0.50440 / 0.27 (39921) hydrogen bonds : bond 0.03793 / 2.55 ( 1295) hydrogen bonds : angle 4.58329 / 3.22 ( 3562) metal coordination : bond 0.00376 / 0.20 ( 8) metal coordination : angle 1.43250 / 0.67 ( 12) Misc. bond : bond 0.00004 / 0.00 ( 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 121 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9491 (m) cc_final: 0.9189 (p) REVERT: A 64 GLU cc_start: 0.8830 (pt0) cc_final: 0.8343 (pt0) REVERT: C 1 MET cc_start: 0.8225 (tmm) cc_final: 0.7724 (tpt) REVERT: C 384 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8492 (pp20) REVERT: D 980 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8790 (mpp) REVERT: E 41 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8664 (mm-30) REVERT: E 43 GLU cc_start: 0.9357 (mp0) cc_final: 0.9145 (pm20) REVERT: E 44 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8404 (pt0) REVERT: E 86 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8638 (tm-30) REVERT: E 87 LYS cc_start: 0.9326 (mmpt) cc_final: 0.9085 (mtmm) REVERT: F 410 TYR cc_start: 0.8932 (m-10) cc_final: 0.8605 (m-10) outliers start: 24 outliers final: 8 residues processed: 109 average time/residue: 0.7945 time to fit residues: 99.2596 Evaluate side-chains 101 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 980 MET 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: 1.9990 chunk 102 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 0.0020 chunk 319 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN D 976 GLN D1359 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 = 0.3132 r_free = 0.3132 target = 0.052594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.038362 restraints weight = 100703.340| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.85 r_work: 0.2538 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 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 = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29225 Z= 0.117 Angle : 0.487 8.954 39933 Z= 0.260 Chirality : 0.041 0.139 4501 Planarity : 0.004 0.042 4890 Dihedral : 15.487 76.896 4862 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.70 % Allowed : 8.86 % 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: 1.56 (0.15), residues: 3332 helix: 1.87 (0.14), residues: 1318 sheet: 0.22 (0.27), residues: 392 loop : 0.69 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 416 TYR 0.011 0.001 TYR D 128 PHE 0.011 0.001 PHE C 922 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (29216) covalent geometry : angle 0.48685 / 0.26 (39921) hydrogen bonds : bond 0.03568 / 2.40 ( 1295) hydrogen bonds : angle 4.44363 / 3.13 ( 3562) metal coordination : bond 0.00351 / 0.18 ( 8) metal coordination : angle 1.35868 / 0.63 ( 12) Misc. bond : bond 0.00005 / 0.00 ( 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 116 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9462 (m) cc_final: 0.9228 (p) REVERT: A 64 GLU cc_start: 0.8823 (pt0) cc_final: 0.8341 (pt0) REVERT: C 1 MET cc_start: 0.8151 (tmm) cc_final: 0.7683 (tpt) REVERT: C 361 MET cc_start: 0.8088 (pp-130) cc_final: 0.7824 (ppp) REVERT: C 384 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8740 (tm-30) REVERT: C 629 TYR cc_start: 0.7971 (t80) cc_final: 0.7512 (t80) REVERT: C 1052 MET cc_start: 0.9366 (mmm) cc_final: 0.8919 (mtm) REVERT: D 661 MET cc_start: 0.9401 (mtp) cc_final: 0.9162 (mtp) REVERT: D 678 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8508 (mp0) REVERT: D 980 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: D 1207 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: E 41 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8747 (mm-30) REVERT: E 44 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8472 (pt0) REVERT: E 86 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8216 (tm-30) REVERT: E 87 LYS cc_start: 0.9356 (mmpt) cc_final: 0.8973 (mmmt) REVERT: E 90 GLU cc_start: 0.8837 (pp20) cc_final: 0.8505 (pp20) REVERT: F 410 TYR cc_start: 0.8929 (m-10) cc_final: 0.8571 (m-10) outliers start: 20 outliers final: 8 residues processed: 104 average time/residue: 0.7786 time to fit residues: 93.2827 Evaluate side-chains 104 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 980 MET 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: 0.7980 chunk 324 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 316 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3136 r_free = 0.3136 target = 0.052744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.038576 restraints weight = 101223.965| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.82 r_work: 0.2540 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- 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 = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (28 function evaluations) r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29225 Z= 0.117 Angle : 0.488 10.365 39933 Z= 0.258 Chirality : 0.041 0.163 4501 Planarity : 0.004 0.040 4890 Dihedral : 15.399 76.737 4862 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.74 % Allowed : 8.93 % Favored : 90.33 % 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: 1.63 (0.15), residues: 3332 helix: 1.94 (0.14), residues: 1317 sheet: 0.28 (0.27), residues: 380 loop : 0.73 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 416 TYR 0.010 0.001 TYR D 128 PHE 0.011 0.001 PHE D 129 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (29216) covalent geometry : angle 0.48723 / 0.26 (39921) hydrogen bonds : bond 0.03448 / 2.31 ( 1295) hydrogen bonds : angle 4.36741 / 3.07 ( 3562) metal coordination : bond 0.00362 / 0.18 ( 8) metal coordination : angle 1.16049 / 0.56 ( 12) Misc. bond : bond 0.00006 / 0.00 ( 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 117 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.9443 (m) cc_final: 0.9238 (p) REVERT: C 1 MET cc_start: 0.8138 (tmm) cc_final: 0.7658 (tpt) REVERT: C 361 MET cc_start: 0.8231 (pp-130) cc_final: 0.7959 (ppp) REVERT: C 384 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8744 (tm-30) REVERT: C 629 TYR cc_start: 0.7954 (t80) cc_final: 0.7550 (t80) REVERT: C 1052 MET cc_start: 0.9388 (mmm) cc_final: 0.8918 (mtm) REVERT: D 661 MET cc_start: 0.9382 (mtp) cc_final: 0.9135 (mtp) REVERT: D 980 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: D 1207 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: E 41 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8682 (mm-30) REVERT: E 44 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8406 (pt0) REVERT: E 86 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8631 (tm-30) REVERT: F 410 TYR cc_start: 0.8905 (m-10) cc_final: 0.8600 (m-10) outliers start: 21 outliers final: 9 residues processed: 106 average time/residue: 0.7890 time to fit residues: 96.1299 Evaluate side-chains 101 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 980 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: 3.9990 chunk 252 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3140 r_free = 0.3140 target = 0.052913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038655 restraints weight = 100692.670| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.84 r_work: 0.2545 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29225 Z= 0.111 Angle : 0.489 10.794 39933 Z= 0.259 Chirality : 0.041 0.166 4501 Planarity : 0.004 0.042 4890 Dihedral : 15.342 76.583 4862 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.63 % Allowed : 9.35 % Favored : 90.02 % 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: 1.68 (0.15), residues: 3332 helix: 1.97 (0.14), residues: 1317 sheet: 0.31 (0.27), residues: 380 loop : 0.75 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 396 TYR 0.010 0.001 TYR D 128 PHE 0.012 0.001 PHE F 389 TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (29216) covalent geometry : angle 0.48864 / 0.26 (39921) hydrogen bonds : bond 0.03373 / 2.26 ( 1295) hydrogen bonds : angle 4.32526 / 3.05 ( 3562) metal coordination : bond 0.00301 / 0.15 ( 8) metal coordination : angle 1.09345 / 0.52 ( 12) Misc. bond : bond 0.00009 / 0.00 ( 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 112 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8087 (tmm) cc_final: 0.7607 (tpt) REVERT: C 361 MET cc_start: 0.8330 (pp-130) cc_final: 0.8036 (ppp) REVERT: C 384 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8750 (tm-30) REVERT: C 629 TYR cc_start: 0.7953 (t80) cc_final: 0.7571 (t80) REVERT: C 1052 MET cc_start: 0.9368 (mmm) cc_final: 0.8908 (mtm) REVERT: D 678 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8470 (mp0) REVERT: D 980 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7943 (mpp) REVERT: D 1207 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: E 41 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8756 (mm-30) REVERT: E 44 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8506 (pt0) REVERT: E 86 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8567 (tm-30) REVERT: F 410 TYR cc_start: 0.8910 (m-10) cc_final: 0.8576 (m-10) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.8068 time to fit residues: 98.3342 Evaluate side-chains 104 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 48 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 336 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 240 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3121 r_free = 0.3121 target = 0.052162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037960 restraints weight = 101077.030| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.80 r_work: 0.2522 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29225 Z= 0.173 Angle : 0.513 12.053 39933 Z= 0.269 Chirality : 0.042 0.192 4501 Planarity : 0.004 0.044 4890 Dihedral : 15.401 76.237 4862 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.60 % Allowed : 9.35 % 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: 1.68 (0.15), residues: 3332 helix: 1.99 (0.14), residues: 1319 sheet: 0.20 (0.27), residues: 386 loop : 0.76 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1087 TYR 0.012 0.001 TYR D 128 PHE 0.014 0.001 PHE F 389 TRP 0.007 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (29216) covalent geometry : angle 0.51273 / 0.27 (39921) hydrogen bonds : bond 0.03629 / 2.43 ( 1295) hydrogen bonds : angle 4.36340 / 3.07 ( 3562) metal coordination : bond 0.00664 / 0.34 ( 8) metal coordination : angle 1.37506 / 0.70 ( 12) Misc. bond : bond 0.00017 / 0.01 ( 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 106 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8162 (tmm) cc_final: 0.7653 (tpt) REVERT: C 361 MET cc_start: 0.8403 (pp-130) cc_final: 0.8116 (ppp) REVERT: C 384 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8653 (tm-30) REVERT: C 629 TYR cc_start: 0.8001 (t80) cc_final: 0.7604 (t80) REVERT: C 1052 MET cc_start: 0.9399 (mmm) cc_final: 0.8832 (mtm) REVERT: D 678 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8501 (mp0) REVERT: D 980 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: D 1207 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: E 41 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8769 (mm-30) REVERT: E 44 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8548 (pt0) REVERT: F 410 TYR cc_start: 0.8921 (m-10) cc_final: 0.8554 (m-10) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.7638 time to fit residues: 87.5103 Evaluate side-chains 101 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 992 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 225 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3130 r_free = 0.3130 target = 0.052513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.038340 restraints weight = 101134.935| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.81 r_work: 0.2534 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 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 = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29225 Z= 0.127 Angle : 0.495 12.251 39933 Z= 0.260 Chirality : 0.041 0.137 4501 Planarity : 0.004 0.042 4890 Dihedral : 15.387 76.072 4862 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.53 % Allowed : 9.39 % 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: 1.69 (0.15), residues: 3332 helix: 2.00 (0.14), residues: 1318 sheet: 0.22 (0.27), residues: 385 loop : 0.76 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1087 TYR 0.011 0.001 TYR D 128 PHE 0.014 0.001 PHE F 389 TRP 0.009 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (29216) covalent geometry : angle 0.49461 / 0.26 (39921) hydrogen bonds : bond 0.03431 / 2.30 ( 1295) hydrogen bonds : angle 4.32539 / 3.04 ( 3562) metal coordination : bond 0.00415 / 0.22 ( 8) metal coordination : angle 1.13092 / 0.53 ( 12) Misc. bond : bond 0.00010 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6786.69 seconds wall clock time: 116 minutes 52.71 seconds (7012.71 seconds total)