Starting phenix.real_space_refine on Thu Mar 5 22:08:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r9b_4769/03_2026/6r9b_4769.map" } resolution = 3.8 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 16142 2.51 5 N 4503 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25880 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1790 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1648 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10260 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 7, 'PHE:plan': 7, 'ARG:plan': 15, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 186 Chain: "D" Number of atoms: 9901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 9901 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 54, 'TRANS': 1268} Chain breaks: 6 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 4, 'ARG:plan': 25, 'PHE:plan': 7, 'TYR:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 266 Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 567 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Time building chain proxies: 5.66, per 1000 atoms: 0.22 Number of scatterers: 25880 At special positions: 0 Unit cell: (135.04, 168.8, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 5122 8.00 N 4503 7.00 C 16142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 814 " - pdb=" SG CYS D 895 " distance=2.87 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 29 sheets defined 37.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.621A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.588A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.664A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 35 through 48 removed outlier: 3.528A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.812A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.187A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.751A pdb=" N GLN C 86 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.875A pdb=" N ARG C 201 " --> pdb=" O ILE C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.644A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 4.175A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.466A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.735A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.973A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.698A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.608A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 4.106A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 524 " --> pdb=" O PRO C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.583A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.663A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.673A pdb=" N GLY C 792 " --> pdb=" O THR C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 4.128A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 899 through 906 Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.671A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 Processing helix chain 'C' and resid 1005 through 1039 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.770A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1169 through 1176 Processing helix chain 'C' and resid 1192 through 1202 removed outlier: 4.514A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.652A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.734A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1322 through 1331 Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.192A pdb=" N ILE D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.605A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.647A pdb=" N GLY D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.299A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 229 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.534A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.530A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.500A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 539 removed outlier: 4.335A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.547A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.803A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 5.015A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.580A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 700 Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.610A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.658A pdb=" N ALA D 741 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 787 Processing helix chain 'D' and resid 788 through 803 removed outlier: 3.751A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.521A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.618A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.527A pdb=" N ASP D 891 " --> pdb=" O CYS D 888 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 892 " --> pdb=" O ASP D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 888 through 892' Processing helix chain 'D' and resid 914 through 922 removed outlier: 3.683A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 936 removed outlier: 3.530A pdb=" N PHE D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 931 through 936' Processing helix chain 'D' and resid 1063 through 1068 Processing helix chain 'D' and resid 1134 through 1138 removed outlier: 3.770A pdb=" N LEU D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1134 through 1138' Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.902A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.611A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1286 removed outlier: 3.862A pdb=" N LYS D1286 " --> pdb=" O TYR D1282 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.566A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.083A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.720A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 29 through 43 removed outlier: 4.055A pdb=" N ASP F 35 " --> pdb=" O ASP F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 76 through 96 removed outlier: 3.767A pdb=" N ILE F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 4.073A pdb=" N ASN F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL F 108 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 26 removed outlier: 4.037A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.855A pdb=" N ILE G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.763A pdb=" N PHE G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.927A pdb=" N LEU G 70 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 71' Processing helix chain 'G' and resid 76 through 108 removed outlier: 3.751A pdb=" N ILE G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 108 " --> pdb=" O TYR G 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.526A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.062A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.940A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.723A pdb=" N VAL B 26 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.602A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 70 Processing sheet with id=AA7, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.050A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.723A pdb=" N GLY C 154 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 187 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 195 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 204 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB1, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.551A pdb=" N LYS C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.844A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 604 through 605 removed outlier: 3.839A pdb=" N HIS C 604 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.795A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 724 through 728 removed outlier: 6.787A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AB8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.904A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 831 through 835 removed outlier: 7.750A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 838 through 839 Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AC3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.068A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 352 " --> pdb=" O HIS C1244 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C1246 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.529A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 105 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 369 removed outlier: 6.518A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 548 through 552 removed outlier: 3.983A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 843 through 844 removed outlier: 4.381A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 950 through 951 removed outlier: 7.074A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.703A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 965 through 967 removed outlier: 4.238A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1264 through 1265 867 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7923 1.34 - 1.46: 3827 1.46 - 1.58: 14294 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26242 Sorted by residual: bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.335 1.377 -0.042 8.70e-03 1.32e+04 2.30e+01 bond pdb=" C LYS D 749 " pdb=" N PRO D 750 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.20e-02 6.94e+03 1.95e+01 bond pdb=" C ARG D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.37e+00 bond pdb=" CA CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sigma weight residual 1.530 1.497 0.033 1.69e-02 3.50e+03 3.88e+00 bond pdb=" CA CYS D 895 " pdb=" C CYS D 895 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.34e-02 5.57e+03 3.78e+00 ... (remaining 26237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 35132 3.16 - 6.32: 327 6.32 - 9.48: 67 9.48 - 12.64: 11 12.64 - 15.80: 4 Bond angle restraints: 35541 Sorted by residual: angle pdb=" C GLY C1318 " pdb=" N MET C1319 " pdb=" CA MET C1319 " ideal model delta sigma weight residual 120.67 136.47 -15.80 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N SER D 143 " pdb=" CA SER D 143 " pdb=" C SER D 143 " ideal model delta sigma weight residual 111.17 121.16 -9.99 1.41e+00 5.03e-01 5.02e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 106.72 117.23 -10.51 1.59e+00 3.96e-01 4.37e+01 angle pdb=" C GLY C1102 " pdb=" N VAL C1103 " pdb=" CA VAL C1103 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" N TYR D 144 " pdb=" CA TYR D 144 " pdb=" C TYR D 144 " ideal model delta sigma weight residual 110.80 124.35 -13.55 2.13e+00 2.20e-01 4.04e+01 ... (remaining 35536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 15360 15.17 - 30.34: 576 30.34 - 45.52: 150 45.52 - 60.69: 25 60.69 - 75.86: 21 Dihedral angle restraints: 16132 sinusoidal: 6347 harmonic: 9785 Sorted by residual: dihedral pdb=" C VAL D 886 " pdb=" N VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual -122.00 -142.71 20.71 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CA VAL D 886 " pdb=" CB VAL D 886 " ideal model delta harmonic sigma weight residual 123.40 143.29 -19.89 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" CB CYS D 814 " pdb=" SG CYS D 814 " pdb=" SG CYS D 895 " pdb=" CB CYS D 895 " ideal model delta sinusoidal sigma weight residual 93.00 26.32 66.68 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 4078 0.169 - 0.337: 27 0.337 - 0.506: 4 0.506 - 0.674: 1 0.674 - 0.843: 1 Chirality restraints: 4111 Sorted by residual: chirality pdb=" CA VAL D 886 " pdb=" N VAL D 886 " pdb=" C VAL D 886 " pdb=" CB VAL D 886 " both_signs ideal model delta sigma weight residual False 2.44 1.60 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA TYR D 144 " pdb=" N TYR D 144 " pdb=" C TYR D 144 " pdb=" CB TYR D 144 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA VAL D 501 " pdb=" N VAL D 501 " pdb=" C VAL D 501 " pdb=" CB VAL D 501 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 4108 not shown) Planarity restraints: 4712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 925 " 0.057 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO D 926 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 926 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 926 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 923 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE D 923 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE D 923 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY D 924 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 427 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.036 5.00e-02 4.00e+02 ... (remaining 4709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7196 2.82 - 3.34: 22113 3.34 - 3.86: 39480 3.86 - 4.38: 43068 4.38 - 4.90: 75038 Nonbonded interactions: 186895 Sorted by model distance: nonbonded pdb=" OG SER C 815 " pdb=" O VAL C1075 " model vdw 2.296 3.040 nonbonded pdb=" O ARG D 425 " pdb=" OG1 THR D 428 " model vdw 2.303 3.040 nonbonded pdb=" OG SER D1032 " pdb=" O ILE D1115 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR F 7 " pdb=" OD2 ASP F 92 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP A 15 " pdb=" OG1 THR A 27 " model vdw 2.324 3.040 ... (remaining 186890 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 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 60 or (resid 61 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 70 or (resi \ d 71 and (name N or name CA or name C or name O or name CB )) or resid 72 throug \ h 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or re \ sid 79 through 116 or (resid 117 and (name N or name CA or name C or name O or n \ ame CB )) or resid 118 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or n \ ame C or name O or name CB )) or resid 126 through 131 or (resid 132 and (name N \ or name CA or name C or name O or name CB )) or resid 133 through 141 or (resid \ 142 through 143 and (name N or name CA or name C or name O or name CB )) or res \ id 144 through 159 or resid 172 through 176 or (resid 177 and (name N or name CA \ or name C or name O or name CB )) or resid 178 through 234 or (resid 235 and (n \ ame N or name CA or name C or name O or name CB )) or resid 236 through 237)) selection = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 5 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 108)) } 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=0.00 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.250 Find NCS groups from input model: 0.190 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 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 : 0.006 0.835 26243 Z= 0.327 Angle : 0.880 15.800 35543 Z= 0.502 Chirality : 0.057 0.843 4111 Planarity : 0.006 0.085 4712 Dihedral : 9.765 75.860 9817 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 0.70 % Allowed : 2.57 % Favored : 96.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -4.57 (0.11), residues: 3373 helix: -2.95 (0.10), residues: 1172 sheet: -1.61 (0.31), residues: 233 loop : -3.42 (0.11), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 592 TYR 0.022 0.001 TYR C 215 PHE 0.022 0.002 PHE D 620 TRP 0.011 0.001 TRP C1276 HIS 0.015 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00337 (26242) covalent geometry : angle 0.87939 (35541) SS BOND : bond 0.83459 ( 1) SS BOND : angle 2.93733 ( 2) hydrogen bonds : bond 0.15697 ( 867) hydrogen bonds : angle 6.80004 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 742 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 330 HIS cc_start: 0.5248 (m-70) cc_final: 0.5042 (m-70) REVERT: C 611 GLU cc_start: 0.5726 (pt0) cc_final: 0.5400 (pp20) REVERT: C 704 MET cc_start: 0.5480 (mmp) cc_final: 0.4783 (ppp) REVERT: C 735 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8559 (tptm) REVERT: C 755 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7143 (mtpp) REVERT: C 767 GLN cc_start: 0.7252 (mm110) cc_final: 0.6915 (mm-40) REVERT: C 782 VAL cc_start: 0.7528 (p) cc_final: 0.7325 (m) REVERT: D 29 MET cc_start: 0.7671 (ttp) cc_final: 0.7410 (tpp) REVERT: D 475 GLU cc_start: 0.7058 (pm20) cc_final: 0.6810 (mp0) REVERT: F 38 HIS cc_start: 0.6427 (m-70) cc_final: 0.6082 (m90) REVERT: G 5 MET cc_start: 0.3567 (mmp) cc_final: 0.3000 (mmt) outliers start: 19 outliers final: 4 residues processed: 754 average time/residue: 0.1928 time to fit residues: 218.8777 Evaluate side-chains 387 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 383 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 885 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 117 HIS B 41 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN C 767 GLN C 932 GLN C 952 GLN C1080 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1244 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN D 702 GLN D 805 GLN D1268 ASN D1350 ASN F 9 ASN F 13 HIS F 43 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.222493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.201802 restraints weight = 42001.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.200617 restraints weight = 60972.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.200696 restraints weight = 55336.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.200073 restraints weight = 40006.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.200531 restraints weight = 35464.922| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26243 Z= 0.127 Angle : 0.650 11.856 35543 Z= 0.335 Chirality : 0.045 0.359 4111 Planarity : 0.005 0.055 4712 Dihedral : 5.020 56.869 3669 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 2.68 % Allowed : 10.57 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -3.19 (0.13), residues: 3373 helix: -1.09 (0.14), residues: 1190 sheet: -1.51 (0.35), residues: 199 loop : -3.00 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 378 TYR 0.042 0.002 TYR F 15 PHE 0.026 0.001 PHE F 11 TRP 0.021 0.001 TRP D 580 HIS 0.016 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00277 (26242) covalent geometry : angle 0.65037 (35541) SS BOND : bond 0.02027 ( 1) SS BOND : angle 0.94315 ( 2) hydrogen bonds : bond 0.03672 ( 867) hydrogen bonds : angle 4.65027 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7445 (p) cc_final: 0.6459 (m) REVERT: B 215 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6614 (tm-30) REVERT: C 454 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6869 (mtp85) REVERT: C 604 HIS cc_start: 0.6780 (p-80) cc_final: 0.6523 (p90) REVERT: C 704 MET cc_start: 0.5194 (mmp) cc_final: 0.4852 (ppp) REVERT: C 755 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7418 (mtpp) REVERT: C 1107 MET cc_start: 0.7128 (mtt) cc_final: 0.6838 (mtm) REVERT: C 1285 TYR cc_start: 0.5690 (t80) cc_final: 0.5350 (t80) REVERT: D 475 GLU cc_start: 0.7614 (pm20) cc_final: 0.7325 (mp0) REVERT: D 638 SER cc_start: 0.6452 (t) cc_final: 0.6048 (p) REVERT: G 5 MET cc_start: 0.4200 (mmp) cc_final: 0.2419 (mmt) outliers start: 73 outliers final: 33 residues processed: 452 average time/residue: 0.1808 time to fit residues: 125.5589 Evaluate side-chains 340 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain F residue 18 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 143 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 292 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 181 optimal weight: 0.1980 chunk 211 optimal weight: 9.9990 chunk 333 optimal weight: 0.0770 chunk 20 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 84 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 725 GLN C 832 HIS C 932 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1367 GLN G 21 ASN G 38 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.217299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.195219 restraints weight = 41672.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.193913 restraints weight = 74300.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.195004 restraints weight = 69826.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.195228 restraints weight = 45046.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.195581 restraints weight = 44994.972| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26243 Z= 0.132 Angle : 0.644 12.918 35543 Z= 0.328 Chirality : 0.045 0.332 4111 Planarity : 0.004 0.055 4712 Dihedral : 4.870 58.512 3669 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.56 % Favored : 92.38 % Rotamer: Outliers : 2.94 % Allowed : 12.15 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3373 helix: -0.29 (0.15), residues: 1192 sheet: -1.24 (0.34), residues: 214 loop : -2.77 (0.12), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 883 TYR 0.038 0.002 TYR F 15 PHE 0.044 0.002 PHE C 405 TRP 0.019 0.001 TRP D 236 HIS 0.014 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00294 (26242) covalent geometry : angle 0.64421 (35541) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.20424 ( 2) hydrogen bonds : bond 0.03479 ( 867) hydrogen bonds : angle 4.30655 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 342 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7502 (p) cc_final: 0.6814 (m) REVERT: B 215 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6717 (tp30) REVERT: C 185 ASP cc_start: 0.6941 (t70) cc_final: 0.6740 (t70) REVERT: C 704 MET cc_start: 0.5437 (mmp) cc_final: 0.4823 (ppp) REVERT: C 796 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7101 (pp) REVERT: C 1285 TYR cc_start: 0.5983 (t80) cc_final: 0.5647 (t80) REVERT: D 448 GLN cc_start: 0.5759 (pm20) cc_final: 0.5460 (pm20) REVERT: D 475 GLU cc_start: 0.7756 (pm20) cc_final: 0.7521 (mp0) REVERT: D 638 SER cc_start: 0.7038 (t) cc_final: 0.6477 (p) REVERT: D 697 MET cc_start: 0.7159 (ppp) cc_final: 0.6683 (ttp) REVERT: D 698 MET cc_start: 0.4407 (mmm) cc_final: 0.3971 (mmm) REVERT: D 747 MET cc_start: 0.3409 (tpp) cc_final: 0.3095 (ttm) REVERT: D 837 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.5076 (p0) REVERT: G 5 MET cc_start: 0.4071 (mmp) cc_final: 0.2547 (mmt) outliers start: 80 outliers final: 45 residues processed: 397 average time/residue: 0.1713 time to fit residues: 106.0421 Evaluate side-chains 334 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 52 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 159 optimal weight: 2.9990 chunk 227 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 247 optimal weight: 0.0070 chunk 174 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 204 optimal weight: 30.0000 chunk 208 optimal weight: 20.0000 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 84 ASN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C1108 ASN C1111 GLN C1136 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.214003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.191779 restraints weight = 41526.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.191183 restraints weight = 70406.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.191833 restraints weight = 65267.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.191712 restraints weight = 42623.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.191931 restraints weight = 44105.694| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26243 Z= 0.132 Angle : 0.631 12.197 35543 Z= 0.320 Chirality : 0.045 0.240 4111 Planarity : 0.004 0.053 4712 Dihedral : 4.675 58.191 3666 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 2.97 % Allowed : 12.78 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3373 helix: 0.04 (0.15), residues: 1206 sheet: -1.20 (0.33), residues: 236 loop : -2.65 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 148 TYR 0.034 0.002 TYR F 15 PHE 0.024 0.001 PHE G 11 TRP 0.034 0.002 TRP D 236 HIS 0.014 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00295 (26242) covalent geometry : angle 0.63120 (35541) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.71981 ( 2) hydrogen bonds : bond 0.03383 ( 867) hydrogen bonds : angle 4.25278 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 336 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7443 (p) cc_final: 0.6881 (m) REVERT: B 88 LEU cc_start: 0.7344 (mm) cc_final: 0.7069 (mm) REVERT: B 215 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6672 (tp30) REVERT: C 130 MET cc_start: 0.5556 (tpp) cc_final: 0.4967 (ttm) REVERT: C 704 MET cc_start: 0.5618 (mmp) cc_final: 0.5021 (ppp) REVERT: C 741 MET cc_start: 0.6423 (mmm) cc_final: 0.6100 (mpp) REVERT: C 796 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7234 (pp) REVERT: C 822 VAL cc_start: 0.6858 (t) cc_final: 0.6306 (p) REVERT: C 1180 MET cc_start: 0.8485 (tmm) cc_final: 0.8176 (tmm) REVERT: C 1235 LEU cc_start: 0.7585 (mt) cc_final: 0.7313 (mt) REVERT: C 1285 TYR cc_start: 0.6022 (t80) cc_final: 0.5739 (t80) REVERT: D 448 GLN cc_start: 0.5812 (pm20) cc_final: 0.3778 (mt0) REVERT: D 490 ILE cc_start: 0.5024 (mp) cc_final: 0.4764 (mt) REVERT: D 591 ILE cc_start: 0.4786 (pt) cc_final: 0.4349 (pt) REVERT: D 638 SER cc_start: 0.7428 (t) cc_final: 0.6804 (p) REVERT: D 697 MET cc_start: 0.7431 (ppp) cc_final: 0.6845 (ttp) REVERT: D 698 MET cc_start: 0.4774 (mmm) cc_final: 0.4369 (mmm) REVERT: D 837 ASP cc_start: 0.5304 (OUTLIER) cc_final: 0.5061 (p0) REVERT: G 5 MET cc_start: 0.4131 (mmp) cc_final: 0.2078 (mmt) outliers start: 81 outliers final: 50 residues processed: 394 average time/residue: 0.1578 time to fit residues: 100.0879 Evaluate side-chains 353 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 777 HIS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 95 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 303 optimal weight: 0.0370 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.214784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.192570 restraints weight = 41320.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.191799 restraints weight = 70766.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.192584 restraints weight = 68205.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.192550 restraints weight = 41513.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.193070 restraints weight = 38874.306| |-----------------------------------------------------------------------------| r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26243 Z= 0.108 Angle : 0.613 11.433 35543 Z= 0.308 Chirality : 0.045 0.256 4111 Planarity : 0.004 0.059 4712 Dihedral : 4.397 54.993 3665 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 2.31 % Allowed : 14.02 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -1.95 (0.14), residues: 3373 helix: 0.32 (0.15), residues: 1208 sheet: -1.18 (0.34), residues: 228 loop : -2.52 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 150 TYR 0.033 0.001 TYR F 15 PHE 0.032 0.001 PHE C 405 TRP 0.025 0.001 TRP D 236 HIS 0.013 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00238 (26242) covalent geometry : angle 0.61260 (35541) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.49498 ( 2) hydrogen bonds : bond 0.03161 ( 867) hydrogen bonds : angle 4.11730 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 330 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7398 (p) cc_final: 0.6883 (m) REVERT: B 88 LEU cc_start: 0.7393 (mm) cc_final: 0.7182 (mm) REVERT: B 215 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6122 (tm-30) REVERT: C 130 MET cc_start: 0.5674 (tpp) cc_final: 0.5013 (ttt) REVERT: C 704 MET cc_start: 0.5174 (mmp) cc_final: 0.4933 (ppp) REVERT: C 796 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7157 (pp) REVERT: C 822 VAL cc_start: 0.7071 (t) cc_final: 0.6627 (p) REVERT: C 1285 TYR cc_start: 0.6054 (t80) cc_final: 0.5736 (t80) REVERT: C 1290 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6978 (tmm) REVERT: C 1305 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6478 (m-10) REVERT: D 448 GLN cc_start: 0.5844 (pm20) cc_final: 0.3856 (mt0) REVERT: D 490 ILE cc_start: 0.5419 (mp) cc_final: 0.5165 (mt) REVERT: D 638 SER cc_start: 0.7474 (t) cc_final: 0.6905 (p) REVERT: D 822 MET cc_start: 0.6804 (mmm) cc_final: 0.6591 (mmt) REVERT: F 5 MET cc_start: 0.4542 (ppp) cc_final: 0.4015 (ppp) REVERT: G 5 MET cc_start: 0.4071 (mmp) cc_final: 0.2250 (mmt) outliers start: 63 outliers final: 44 residues processed: 373 average time/residue: 0.1623 time to fit residues: 96.3781 Evaluate side-chains 350 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 117 HIS B 75 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 832 HIS C 932 GLN C1116 HIS C1313 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 593 ASN D 805 GLN D 910 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.202841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.182754 restraints weight = 42117.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.183093 restraints weight = 84028.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.182333 restraints weight = 61918.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.182094 restraints weight = 49808.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.182285 restraints weight = 39870.291| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 26243 Z= 0.242 Angle : 0.792 16.846 35543 Z= 0.403 Chirality : 0.050 0.282 4111 Planarity : 0.006 0.063 4712 Dihedral : 5.241 55.324 3665 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 3.41 % Allowed : 13.91 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3373 helix: 0.08 (0.15), residues: 1208 sheet: -1.28 (0.31), residues: 257 loop : -2.66 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 368 TYR 0.032 0.003 TYR C 810 PHE 0.028 0.003 PHE A 231 TRP 0.023 0.002 TRP D 236 HIS 0.013 0.002 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00560 (26242) covalent geometry : angle 0.79143 (35541) SS BOND : bond 0.00541 ( 1) SS BOND : angle 1.75959 ( 2) hydrogen bonds : bond 0.04166 ( 867) hydrogen bonds : angle 4.72399 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 343 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: A 131 CYS cc_start: 0.7574 (p) cc_final: 0.7195 (m) REVERT: B 39 LEU cc_start: 0.7593 (mp) cc_final: 0.7385 (mt) REVERT: B 88 LEU cc_start: 0.7518 (mm) cc_final: 0.7304 (mm) REVERT: B 215 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6592 (tm-30) REVERT: C 11 ILE cc_start: 0.8810 (mm) cc_final: 0.8520 (mt) REVERT: C 309 LEU cc_start: 0.5381 (tp) cc_final: 0.4973 (pp) REVERT: C 704 MET cc_start: 0.6198 (mmp) cc_final: 0.5752 (ppp) REVERT: D 442 ILE cc_start: 0.8578 (mt) cc_final: 0.8004 (pt) REVERT: D 448 GLN cc_start: 0.6528 (pm20) cc_final: 0.6308 (pm20) REVERT: D 582 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7167 (mt) REVERT: D 638 SER cc_start: 0.8139 (t) cc_final: 0.7460 (p) REVERT: D 770 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7294 (mp) REVERT: D 1254 GLU cc_start: 0.6917 (tt0) cc_final: 0.6464 (mt-10) REVERT: F 5 MET cc_start: 0.4415 (ppp) cc_final: 0.4036 (ppp) REVERT: G 5 MET cc_start: 0.4129 (mmp) cc_final: 0.2625 (mmt) outliers start: 93 outliers final: 53 residues processed: 407 average time/residue: 0.1659 time to fit residues: 107.6377 Evaluate side-chains 365 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1195 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1223 LEU Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 184 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 226 optimal weight: 0.0870 chunk 173 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 192 optimal weight: 7.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS C 604 HIS C 613 ASN C 767 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.204253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.183883 restraints weight = 41893.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.183422 restraints weight = 85719.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.183571 restraints weight = 72762.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.182963 restraints weight = 51344.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.183146 restraints weight = 49651.786| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26243 Z= 0.155 Angle : 0.691 12.623 35543 Z= 0.348 Chirality : 0.047 0.382 4111 Planarity : 0.004 0.063 4712 Dihedral : 4.911 52.151 3665 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 2.31 % Allowed : 15.82 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -1.99 (0.14), residues: 3373 helix: 0.25 (0.15), residues: 1217 sheet: -1.22 (0.32), residues: 259 loop : -2.54 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.029 0.002 TYR F 15 PHE 0.034 0.002 PHE C 405 TRP 0.017 0.002 TRP D 236 HIS 0.012 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00356 (26242) covalent geometry : angle 0.69056 (35541) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.61602 ( 2) hydrogen bonds : bond 0.03562 ( 867) hydrogen bonds : angle 4.48346 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 324 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7461 (p) cc_final: 0.7095 (m) REVERT: B 185 TYR cc_start: 0.6855 (p90) cc_final: 0.6542 (p90) REVERT: C 11 ILE cc_start: 0.8778 (mm) cc_final: 0.8425 (mt) REVERT: C 684 ASN cc_start: 0.8161 (p0) cc_final: 0.7901 (p0) REVERT: C 704 MET cc_start: 0.6295 (mmp) cc_final: 0.5592 (ppp) REVERT: C 767 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: C 796 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7147 (pp) REVERT: D 582 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7106 (mt) REVERT: D 651 HIS cc_start: 0.5028 (t-90) cc_final: 0.4820 (t-90) REVERT: F 5 MET cc_start: 0.4249 (ppp) cc_final: 0.3985 (ppp) REVERT: F 23 ARG cc_start: 0.6916 (tpp80) cc_final: 0.6517 (mmm-85) REVERT: G 5 MET cc_start: 0.4147 (mmp) cc_final: 0.2596 (mmt) outliers start: 63 outliers final: 45 residues processed: 368 average time/residue: 0.1598 time to fit residues: 93.9780 Evaluate side-chains 349 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 24 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 204 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 chunk 295 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 117 HIS A 132 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 659 GLN C 767 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.194847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.174205 restraints weight = 42392.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.172756 restraints weight = 96157.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.171249 restraints weight = 64658.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.169953 restraints weight = 63631.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.170113 restraints weight = 59570.971| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 26243 Z= 0.318 Angle : 0.924 17.172 35543 Z= 0.474 Chirality : 0.054 0.333 4111 Planarity : 0.006 0.064 4712 Dihedral : 5.996 57.856 3665 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.70 % Favored : 89.18 % Rotamer: Outliers : 2.90 % Allowed : 16.26 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.14), residues: 3373 helix: -0.31 (0.15), residues: 1223 sheet: -1.63 (0.29), residues: 291 loop : -2.75 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 220 TYR 0.032 0.003 TYR C 810 PHE 0.034 0.003 PHE C 514 TRP 0.018 0.003 TRP D 236 HIS 0.018 0.003 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00745 (26242) covalent geometry : angle 0.92425 (35541) SS BOND : bond 0.00609 ( 1) SS BOND : angle 1.59876 ( 2) hydrogen bonds : bond 0.04842 ( 867) hydrogen bonds : angle 5.22544 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: A 131 CYS cc_start: 0.7478 (p) cc_final: 0.7161 (m) REVERT: D 493 PRO cc_start: 0.6327 (Cg_exo) cc_final: 0.6009 (Cg_endo) REVERT: D 651 HIS cc_start: 0.5114 (t-90) cc_final: 0.4911 (t-90) REVERT: G 5 MET cc_start: 0.4117 (mmp) cc_final: 0.3452 (tpp) outliers start: 79 outliers final: 57 residues processed: 394 average time/residue: 0.1537 time to fit residues: 97.3884 Evaluate side-chains 349 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1195 ILE Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 310 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 241 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D 875 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4709 r_free = 0.4709 target = 0.200708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.179745 restraints weight = 41663.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.178492 restraints weight = 82942.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.178772 restraints weight = 70456.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.177865 restraints weight = 52374.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.178157 restraints weight = 51103.016| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26243 Z= 0.145 Angle : 0.759 13.484 35543 Z= 0.380 Chirality : 0.047 0.350 4111 Planarity : 0.008 0.444 4712 Dihedral : 5.544 101.207 3665 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 1.98 % Allowed : 18.50 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3373 helix: 0.11 (0.15), residues: 1214 sheet: -1.45 (0.30), residues: 275 loop : -2.56 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 23 TYR 0.040 0.002 TYR D 795 PHE 0.037 0.002 PHE C 405 TRP 0.047 0.002 TRP D 236 HIS 0.018 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00328 (26242) covalent geometry : angle 0.75882 (35541) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.57758 ( 2) hydrogen bonds : bond 0.03768 ( 867) hydrogen bonds : angle 4.70269 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7509 (p) cc_final: 0.7200 (m) REVERT: B 185 TYR cc_start: 0.6671 (p90) cc_final: 0.6139 (p90) REVERT: C 183 TRP cc_start: 0.4734 (OUTLIER) cc_final: 0.2564 (m-10) REVERT: C 681 MET cc_start: 0.6803 (tpt) cc_final: 0.6450 (tpt) REVERT: C 685 MET cc_start: 0.8348 (tpp) cc_final: 0.7537 (tpp) REVERT: C 796 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7108 (pp) REVERT: D 127 LEU cc_start: 0.4789 (mt) cc_final: 0.4328 (mt) REVERT: D 493 PRO cc_start: 0.5695 (Cg_exo) cc_final: 0.5473 (Cg_endo) REVERT: D 582 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7126 (mt) REVERT: D 651 HIS cc_start: 0.4822 (t-90) cc_final: 0.4600 (t-90) REVERT: G 5 MET cc_start: 0.4166 (mmp) cc_final: 0.2873 (mmt) outliers start: 54 outliers final: 41 residues processed: 362 average time/residue: 0.1566 time to fit residues: 90.3332 Evaluate side-chains 341 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 141 optimal weight: 9.9990 chunk 186 optimal weight: 50.0000 chunk 84 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 155 optimal weight: 0.0000 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D1244 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4694 r_free = 0.4694 target = 0.199227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.177681 restraints weight = 41794.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.176555 restraints weight = 90086.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.177069 restraints weight = 83046.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.176727 restraints weight = 55176.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.177024 restraints weight = 50434.577| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26243 Z= 0.173 Angle : 0.780 13.363 35543 Z= 0.387 Chirality : 0.048 0.316 4111 Planarity : 0.008 0.445 4712 Dihedral : 5.419 86.992 3665 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 1.91 % Allowed : 18.98 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.14), residues: 3373 helix: 0.19 (0.15), residues: 1208 sheet: -1.40 (0.30), residues: 280 loop : -2.52 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 23 TYR 0.036 0.002 TYR C 578 PHE 0.024 0.002 PHE G 11 TRP 0.047 0.002 TRP D 236 HIS 0.015 0.002 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00404 (26242) covalent geometry : angle 0.77991 (35541) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.79263 ( 2) hydrogen bonds : bond 0.03795 ( 867) hydrogen bonds : angle 4.69169 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: A 131 CYS cc_start: 0.7542 (p) cc_final: 0.7267 (m) REVERT: C 11 ILE cc_start: 0.8839 (mm) cc_final: 0.8489 (mt) REVERT: C 183 TRP cc_start: 0.4861 (OUTLIER) cc_final: 0.2690 (m-10) REVERT: C 741 MET cc_start: 0.5441 (mmm) cc_final: 0.4535 (mmm) REVERT: C 796 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7137 (pp) REVERT: D 127 LEU cc_start: 0.4891 (mt) cc_final: 0.4511 (mt) REVERT: D 582 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7271 (mt) REVERT: D 651 HIS cc_start: 0.4988 (t-90) cc_final: 0.4761 (t-90) REVERT: G 5 MET cc_start: 0.4148 (mmp) cc_final: 0.2854 (mmt) outliers start: 52 outliers final: 40 residues processed: 341 average time/residue: 0.1574 time to fit residues: 86.6240 Evaluate side-chains 338 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1305 TYR Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 814 CYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 979 ASN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 71 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 156 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 115 optimal weight: 0.1980 chunk 171 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 191 optimal weight: 40.0000 chunk 164 optimal weight: 6.9990 chunk 188 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** F 82 GLN ** 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 = 0.4718 r_free = 0.4718 target = 0.201466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.181190 restraints weight = 41789.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.180777 restraints weight = 82544.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180131 restraints weight = 68610.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.179078 restraints weight = 54141.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.179373 restraints weight = 48919.642| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26243 Z= 0.140 Angle : 0.742 13.918 35543 Z= 0.368 Chirality : 0.047 0.331 4111 Planarity : 0.008 0.428 4712 Dihedral : 5.134 76.626 3665 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 1.65 % Allowed : 19.49 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.03 % 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: -1.88 (0.14), residues: 3373 helix: 0.34 (0.15), residues: 1210 sheet: -1.61 (0.29), residues: 301 loop : -2.39 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 23 TYR 0.035 0.002 TYR C 578 PHE 0.037 0.002 PHE C 405 TRP 0.041 0.002 TRP D 236 HIS 0.015 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00322 (26242) covalent geometry : angle 0.74223 (35541) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.45610 ( 2) hydrogen bonds : bond 0.03526 ( 867) hydrogen bonds : angle 4.54565 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.00 seconds wall clock time: 61 minutes 49.24 seconds (3709.24 seconds total)