Starting phenix.real_space_refine on Mon Sep 14 10:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szk_25571/09_2026/7szk_25571.map" } resolution = 2.94 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= 0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 18547 2.51 5 N 5260 2.21 5 O 5785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29759 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 4, 'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3799 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 14, 'TRANS': 451} Chain breaks: 3 Chain: "X" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "Y" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 82 Unusual residues: {'D9X': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14615 SG CYS D 70 43.056 116.702 81.360 1.00141.16 S ATOM 14629 SG CYS D 72 43.095 117.516 85.168 1.00154.90 S ATOM 14737 SG CYS D 85 42.223 120.160 82.792 1.00153.37 S ATOM 14761 SG CYS D 88 45.709 118.966 82.987 1.00148.93 S ATOM 20449 SG CYS D 814 80.257 95.912 27.490 1.00 56.35 S ATOM 21014 SG CYS D 888 81.014 95.978 31.119 1.00 53.92 S ATOM 21065 SG CYS D 895 78.939 93.224 29.725 1.00 45.54 S ATOM 21086 SG CYS D 898 82.576 93.415 28.949 1.00 47.58 S Time building chain proxies: 6.05, per 1000 atoms: 0.20 Number of scatterers: 29759 At special positions: 0 Unit cell: (173.6, 191.52, 165.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 36 15.00 Mg 1 11.99 O 5785 8.00 N 5260 7.00 C 18547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 47 sheets defined 44.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.134A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.840A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.753A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.419A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.827A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.662A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.839A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.372A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.354A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.764A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.897A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.943A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.748A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.937A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.591A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.977A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (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 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 539 through 543 removed outlier: 4.052A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 614 removed outlier: 4.248A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 removed outlier: 4.012A pdb=" N VAL C 650 " --> pdb=" O ARG C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.747A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.939A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.197A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.969A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.556A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.872A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.506A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.513A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.596A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.959A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.733A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.579A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.006A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.622A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.691A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.683A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.865A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.510A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 4.050A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.038A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.551A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.579A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.943A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.631A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 4.061A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.477A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.546A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.817A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.685A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.532A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 removed outlier: 3.640A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.593A pdb=" N TYR F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 Processing helix chain 'F' and resid 214 through 234 Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.441A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 352 removed outlier: 4.132A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 3.659A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.104A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 492 through 500 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.875A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 600 removed outlier: 4.293A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 611 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 3.752A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.467A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.628A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 17 removed outlier: 4.503A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 105 removed outlier: 8.023A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.920A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.997A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.904A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.904A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.585A pdb=" N PHE C 186 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.522A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.696A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.567A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.549A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.852A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.529A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ALA D 446 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.832A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 347 " --> pdb=" O GLN C1268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.578A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.724A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.018A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AE5, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.732A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.098A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE8, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.586A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1187 through 1188 Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AF2, first strand: chain 'F' and resid 162 through 165 removed outlier: 5.574A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 1308 hydrogen bonds defined for protein. 3708 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: 6.69 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5130 1.31 - 1.43: 7109 1.43 - 1.56: 17723 1.56 - 1.68: 87 1.68 - 1.81: 225 Bond restraints: 30274 Sorted by residual: bond pdb=" C05 D9X C3001 " pdb=" C43 D9X C3001 " ideal model delta sigma weight residual 1.391 1.624 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C02 D9X C3001 " pdb=" C03 D9X C3001 " ideal model delta sigma weight residual 1.383 1.598 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C75 D9X C3001 " pdb=" C76 D9X C3001 " ideal model delta sigma weight residual 1.387 1.559 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C47 D9X C3001 " pdb=" C63 D9X C3001 " ideal model delta sigma weight residual 1.387 1.555 -0.168 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C46 D9X C3001 " pdb=" C47 D9X C3001 " ideal model delta sigma weight residual 1.424 1.592 -0.168 2.00e-02 2.50e+03 7.04e+01 ... (remaining 30269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 40824 2.71 - 5.41: 187 5.41 - 8.12: 10 8.12 - 10.82: 3 10.82 - 13.53: 3 Bond angle restraints: 41027 Sorted by residual: angle pdb=" C79 D9X C3001 " pdb=" C78 D9X C3001 " pdb=" O77 D9X C3001 " ideal model delta sigma weight residual 103.83 117.36 -13.53 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C81 D9X C3001 " pdb=" C79 D9X C3001 " pdb=" N80 D9X C3001 " ideal model delta sigma weight residual 111.45 124.28 -12.83 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N3 DT Y 16 " pdb=" C4 DT Y 16 " pdb=" O4 DT Y 16 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT X 63 " pdb=" C4 DT X 63 " pdb=" O4 DT X 63 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT X 75 " pdb=" C4 DT X 75 " pdb=" O4 DT X 75 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 41022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16663 17.90 - 35.80: 1575 35.80 - 53.70: 307 53.70 - 71.61: 95 71.61 - 89.51: 27 Dihedral angle restraints: 18667 sinusoidal: 8063 harmonic: 10604 Sorted by residual: dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 142.94 37.06 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" CA ASP C1160 " pdb=" C ASP C1160 " pdb=" N LEU C1161 " pdb=" CA LEU C1161 " ideal model delta harmonic sigma weight residual 0.00 26.69 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 18664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.532: 4672 0.532 - 1.064: 0 1.064 - 1.596: 0 1.596 - 2.128: 0 2.128 - 2.660: 2 Chirality restraints: 4674 Sorted by residual: chirality pdb=" C78 D9X C3001 " pdb=" C44 D9X C3001 " pdb=" C79 D9X C3001 " pdb=" O77 D9X C3001 " both_signs ideal model delta sigma weight residual False -2.66 -0.00 -2.66 2.00e-01 2.50e+01 1.77e+02 chirality pdb=" C79 D9X C3001 " pdb=" C78 D9X C3001 " pdb=" C81 D9X C3001 " pdb=" N80 D9X C3001 " both_signs ideal model delta sigma weight residual False 2.52 0.04 2.48 2.00e-01 2.50e+01 1.54e+02 chirality pdb=" C11 D9X C3001 " pdb=" C10 D9X C3001 " pdb=" C12 D9X C3001 " pdb=" O36 D9X C3001 " both_signs ideal model delta sigma weight residual False -2.68 -2.48 -0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 4671 not shown) Planarity restraints: 5242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 697 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO C 698 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 10 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO B 11 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " -0.023 5.00e-02 4.00e+02 ... (remaining 5239 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 276 2.57 - 3.15: 25222 3.15 - 3.73: 43691 3.73 - 4.32: 60239 4.32 - 4.90: 103043 Nonbonded interactions: 232471 Sorted by model distance: nonbonded pdb=" O LEU F 250 " pdb=" OG SER F 253 " model vdw 1.985 3.040 nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 2.006 3.040 nonbonded pdb=" OE1 GLU D 811 " pdb=" OG1 THR D 890 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLN D1044 " pdb=" OG1 THR D1045 " model vdw 2.034 3.040 nonbonded pdb=" O LYS F 418 " pdb=" OH TYR F 430 " model vdw 2.041 3.040 ... (remaining 232466 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 7 through 235) selection = (chain 'B' and resid 7 through 235) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 31.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.005 0.233 30282 Z= 0.270 Angle : 0.499 13.529 41039 Z= 0.283 Chirality : 0.066 2.660 4674 Planarity : 0.003 0.056 5242 Dihedral : 14.725 89.507 11831 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.28 (0.14), residues: 3661 helix: 2.25 (0.14), residues: 1465 sheet: -0.31 (0.27), residues: 417 loop : -1.56 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 220 TYR 0.011 0.001 TYR C1281 PHE 0.017 0.001 PHE F 221 TRP 0.010 0.001 TRP D 33 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.27 (30274) covalent geometry : angle 0.49855 / 0.28 (41027) hydrogen bonds : bond 0.16338 / 11.12 ( 1298) hydrogen bonds : angle 6.21839 / 4.35 ( 3708) metal coordination : bond 0.06599 / 3.39 ( 8) metal coordination : angle 0.78978 / 0.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.256 Fit side-chains REVERT: C 473 ARG cc_start: 0.7456 (tmt-80) cc_final: 0.7041 (tmt-80) REVERT: C 853 ASP cc_start: 0.7939 (t0) cc_final: 0.7562 (p0) REVERT: D 133 ARG cc_start: 0.6658 (mpt180) cc_final: 0.5768 (ttm-80) REVERT: D 1314 LEU cc_start: 0.7458 (tt) cc_final: 0.7252 (tt) REVERT: D 1325 PHE cc_start: 0.6917 (p90) cc_final: 0.6694 (p90) REVERT: F 456 MET cc_start: 0.6778 (mmm) cc_final: 0.6159 (tpp) REVERT: F 545 HIS cc_start: 0.7377 (t-170) cc_final: 0.7034 (t-170) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.7861 time to fit residues: 316.8273 Evaluate side-chains 255 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS C 83 GLN C 327 GLN C 894 GLN C1324 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN F 455 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.185825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114222 restraints weight = 38973.749| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.54 r_work: 0.3199 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30282 Z= 0.162 Angle : 0.647 8.603 41039 Z= 0.337 Chirality : 0.045 0.175 4674 Planarity : 0.005 0.046 5242 Dihedral : 11.077 83.089 4552 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.62 % Allowed : 9.60 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.11 (0.14), residues: 3661 helix: 1.91 (0.14), residues: 1484 sheet: -0.16 (0.26), residues: 422 loop : -1.57 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 245 TYR 0.016 0.001 TYR D1186 PHE 0.023 0.002 PHE C 514 TRP 0.012 0.001 TRP D1020 HIS 0.009 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (30274) covalent geometry : angle 0.64337 / 0.34 (41027) hydrogen bonds : bond 0.05343 / 3.72 ( 1298) hydrogen bonds : angle 4.96087 / 3.48 ( 3708) metal coordination : bond 0.00807 / 0.41 ( 8) metal coordination : angle 3.99158 / 1.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: B 95 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8207 (mtmp) REVERT: C 122 VAL cc_start: 0.7743 (m) cc_final: 0.7515 (p) REVERT: C 315 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.5232 (mtm) REVERT: C 473 ARG cc_start: 0.7713 (tmt-80) cc_final: 0.7350 (tmt-80) REVERT: C 687 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7728 (mtm180) REVERT: C 1236 ASN cc_start: 0.8670 (t0) cc_final: 0.8461 (t0) REVERT: D 188 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6180 (mt) REVERT: D 388 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8369 (mtp-110) REVERT: D 873 GLU cc_start: 0.7887 (tp30) cc_final: 0.6757 (mt-10) REVERT: D 1020 TRP cc_start: 0.5555 (p-90) cc_final: 0.5294 (p-90) REVERT: D 1215 GLU cc_start: 0.7346 (pm20) cc_final: 0.6634 (pt0) REVERT: D 1279 GLN cc_start: 0.8225 (mp10) cc_final: 0.7820 (mm-40) REVERT: D 1325 PHE cc_start: 0.6870 (p90) cc_final: 0.6588 (p90) REVERT: D 1370 MET cc_start: 0.6786 (tmm) cc_final: 0.6481 (ttm) REVERT: E 55 GLU cc_start: 0.7045 (tt0) cc_final: 0.6716 (pt0) REVERT: F 100 MET cc_start: 0.5148 (mtt) cc_final: 0.4779 (mpp) REVERT: F 430 TYR cc_start: 0.3799 (OUTLIER) cc_final: 0.3589 (t80) REVERT: F 456 MET cc_start: 0.6868 (mmm) cc_final: 0.6184 (tpp) REVERT: F 476 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7314 (ptt180) REVERT: F 477 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5122 (pp20) REVERT: F 502 LYS cc_start: 0.4199 (tttp) cc_final: 0.3676 (tttm) REVERT: F 545 HIS cc_start: 0.7250 (t-170) cc_final: 0.6940 (t-170) REVERT: F 567 MET cc_start: 0.6149 (mtm) cc_final: 0.5662 (ptp) outliers start: 51 outliers final: 12 residues processed: 304 average time/residue: 0.7293 time to fit residues: 257.7250 Evaluate side-chains 270 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 950 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 228 optimal weight: 0.1980 chunk 167 optimal weight: 0.5980 chunk 361 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 360 optimal weight: 0.9990 chunk 282 optimal weight: 30.0000 chunk 146 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C 327 GLN D 45 ASN D1098 GLN E 43 ASN E 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.186611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112800 restraints weight = 38901.873| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.27 r_work: 0.3226 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30282 Z= 0.126 Angle : 0.571 8.678 41039 Z= 0.298 Chirality : 0.042 0.161 4674 Planarity : 0.004 0.057 5242 Dihedral : 10.923 87.713 4552 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.38 % Allowed : 12.34 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.15 (0.14), residues: 3661 helix: 1.95 (0.14), residues: 1485 sheet: -0.07 (0.26), residues: 417 loop : -1.57 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 903 TYR 0.032 0.001 TYR D 46 PHE 0.019 0.001 PHE C 514 TRP 0.009 0.001 TRP D 33 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (30274) covalent geometry : angle 0.56729 / 0.30 (41027) hydrogen bonds : bond 0.04580 / 3.21 ( 1298) hydrogen bonds : angle 4.60670 / 3.25 ( 3708) metal coordination : bond 0.00529 / 0.27 ( 8) metal coordination : angle 3.72156 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: B 95 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8182 (mtmp) REVERT: C 122 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7467 (p) REVERT: C 172 TYR cc_start: 0.7210 (m-80) cc_final: 0.6928 (m-80) REVERT: C 549 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: C 687 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7712 (mtm180) REVERT: C 1265 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6702 (m-10) REVERT: D 75 TYR cc_start: 0.7316 (m-10) cc_final: 0.7072 (m-80) REVERT: D 180 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4530 (tpp) REVERT: D 188 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6215 (mt) REVERT: D 873 GLU cc_start: 0.7892 (tp30) cc_final: 0.6743 (mt-10) REVERT: D 1020 TRP cc_start: 0.5686 (p-90) cc_final: 0.5405 (p-90) REVERT: D 1215 GLU cc_start: 0.7223 (pm20) cc_final: 0.6660 (pt0) REVERT: D 1325 PHE cc_start: 0.6847 (p90) cc_final: 0.6607 (p90) REVERT: D 1370 MET cc_start: 0.6784 (tmm) cc_final: 0.6423 (ttp) REVERT: D 1371 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6049 (ptm160) REVERT: E 55 GLU cc_start: 0.7135 (tt0) cc_final: 0.6587 (pt0) REVERT: F 100 MET cc_start: 0.5094 (mtt) cc_final: 0.4786 (mpp) REVERT: F 266 PHE cc_start: 0.4019 (m-80) cc_final: 0.3795 (m-80) REVERT: F 276 MET cc_start: 0.2208 (OUTLIER) cc_final: 0.1971 (tpt) REVERT: F 430 TYR cc_start: 0.3811 (OUTLIER) cc_final: 0.3585 (t80) REVERT: F 502 LYS cc_start: 0.4192 (tttp) cc_final: 0.3650 (tttm) REVERT: F 545 HIS cc_start: 0.7284 (t-170) cc_final: 0.6972 (t-170) REVERT: F 567 MET cc_start: 0.5885 (mtm) cc_final: 0.5684 (mtm) outliers start: 75 outliers final: 23 residues processed: 313 average time/residue: 0.7584 time to fit residues: 276.4117 Evaluate side-chains 275 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 39 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 0.0980 chunk 238 optimal weight: 0.0980 chunk 251 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C 406 ASN C 799 ASN C1324 ASN D 45 ASN D 94 GLN E 43 ASN E 62 GLN E 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.187107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113177 restraints weight = 38695.610| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.26 r_work: 0.3234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30282 Z= 0.121 Angle : 0.558 8.096 41039 Z= 0.292 Chirality : 0.042 0.159 4674 Planarity : 0.004 0.059 5242 Dihedral : 10.881 89.525 4552 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.19 % Allowed : 13.70 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.15 (0.14), residues: 3661 helix: 1.93 (0.14), residues: 1485 sheet: 0.02 (0.26), residues: 416 loop : -1.59 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1034 TYR 0.012 0.001 TYR C1281 PHE 0.017 0.001 PHE C 514 TRP 0.009 0.001 TRP F 315 HIS 0.004 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (30274) covalent geometry : angle 0.55465 / 0.29 (41027) hydrogen bonds : bond 0.04287 / 3.02 ( 1298) hydrogen bonds : angle 4.46680 / 3.16 ( 3708) metal coordination : bond 0.00521 / 0.26 ( 8) metal coordination : angle 3.56614 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8254 (ttm-80) REVERT: B 95 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7957 (mtmt) REVERT: C 122 VAL cc_start: 0.7545 (m) cc_final: 0.7334 (p) REVERT: C 370 MET cc_start: 0.6991 (tpt) cc_final: 0.6666 (mmp) REVERT: C 687 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7819 (mtm180) REVERT: C 899 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: C 1236 ASN cc_start: 0.8600 (t0) cc_final: 0.8340 (t0) REVERT: C 1265 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: D 45 ASN cc_start: 0.7353 (t0) cc_final: 0.7097 (t0) REVERT: D 75 TYR cc_start: 0.7308 (m-10) cc_final: 0.7041 (m-80) REVERT: D 83 VAL cc_start: 0.8272 (p) cc_final: 0.8067 (m) REVERT: D 724 MET cc_start: 0.8861 (mtp) cc_final: 0.8129 (mtp) REVERT: D 747 MET cc_start: 0.8357 (mmp) cc_final: 0.8127 (mmm) REVERT: D 873 GLU cc_start: 0.7871 (tp30) cc_final: 0.6726 (mt-10) REVERT: D 1020 TRP cc_start: 0.5693 (p-90) cc_final: 0.5387 (p-90) REVERT: D 1215 GLU cc_start: 0.7216 (pm20) cc_final: 0.6727 (pt0) REVERT: D 1325 PHE cc_start: 0.7003 (p90) cc_final: 0.6619 (p90) REVERT: D 1370 MET cc_start: 0.6685 (tmm) cc_final: 0.6458 (ttp) REVERT: D 1371 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6127 (ptm160) REVERT: E 55 GLU cc_start: 0.7197 (tt0) cc_final: 0.6572 (pt0) REVERT: F 100 MET cc_start: 0.5078 (mtt) cc_final: 0.4775 (mpp) REVERT: F 276 MET cc_start: 0.2141 (OUTLIER) cc_final: 0.1799 (tpt) REVERT: F 430 TYR cc_start: 0.3788 (OUTLIER) cc_final: 0.3560 (t80) REVERT: F 502 LYS cc_start: 0.4148 (tttp) cc_final: 0.3747 (tmtm) REVERT: F 545 HIS cc_start: 0.7304 (t-170) cc_final: 0.7011 (t-170) REVERT: F 551 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4155 (tp) outliers start: 69 outliers final: 28 residues processed: 309 average time/residue: 0.7115 time to fit residues: 256.8703 Evaluate side-chains 281 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 687 ARG Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 205 optimal weight: 4.9990 chunk 259 optimal weight: 0.1980 chunk 322 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 342 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN D 45 ASN E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.184859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112414 restraints weight = 38841.720| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.57 r_work: 0.3184 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30282 Z= 0.170 Angle : 0.604 9.593 41039 Z= 0.314 Chirality : 0.043 0.160 4674 Planarity : 0.004 0.065 5242 Dihedral : 10.949 89.044 4552 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.67 % Allowed : 14.09 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.02 (0.14), residues: 3661 helix: 1.84 (0.14), residues: 1484 sheet: 0.02 (0.26), residues: 411 loop : -1.69 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 388 TYR 0.019 0.002 TYR C1149 PHE 0.023 0.001 PHE C 514 TRP 0.009 0.001 TRP F 315 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (30274) covalent geometry : angle 0.60091 / 0.31 (41027) hydrogen bonds : bond 0.04961 / 3.49 ( 1298) hydrogen bonds : angle 4.45874 / 3.15 ( 3708) metal coordination : bond 0.00570 / 0.29 ( 8) metal coordination : angle 3.71137 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 259 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8262 (ttm-80) REVERT: B 95 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7922 (mtmt) REVERT: B 202 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8529 (t) REVERT: C 370 MET cc_start: 0.7021 (tpt) cc_final: 0.6680 (mmp) REVERT: C 624 ASP cc_start: 0.8280 (p0) cc_final: 0.8032 (p0) REVERT: C 626 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: C 799 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8341 (m110) REVERT: C 1158 LYS cc_start: 0.7634 (mptt) cc_final: 0.7417 (mptt) REVERT: C 1265 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6798 (m-10) REVERT: D 75 TYR cc_start: 0.7410 (m-10) cc_final: 0.7161 (m-80) REVERT: D 156 ARG cc_start: 0.6054 (tmt170) cc_final: 0.5840 (tmm-80) REVERT: D 545 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.6223 (p90) REVERT: D 724 MET cc_start: 0.8966 (mtp) cc_final: 0.8293 (mtp) REVERT: D 747 MET cc_start: 0.8404 (mmp) cc_final: 0.8192 (mmm) REVERT: D 873 GLU cc_start: 0.7857 (tp30) cc_final: 0.6716 (mt-10) REVERT: D 1015 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6868 (pp20) REVERT: D 1020 TRP cc_start: 0.5716 (p-90) cc_final: 0.5392 (p-90) REVERT: D 1195 GLN cc_start: 0.7156 (pm20) cc_final: 0.6725 (pp30) REVERT: D 1215 GLU cc_start: 0.7216 (pm20) cc_final: 0.6809 (pt0) REVERT: D 1325 PHE cc_start: 0.7094 (p90) cc_final: 0.6725 (p90) REVERT: D 1371 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6107 (ptm160) REVERT: D 1372 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5778 (tpp-160) REVERT: E 55 GLU cc_start: 0.7357 (tt0) cc_final: 0.6733 (pt0) REVERT: F 100 MET cc_start: 0.5192 (mtt) cc_final: 0.4920 (mpp) REVERT: F 102 MET cc_start: 0.5160 (mtt) cc_final: 0.4954 (mmm) REVERT: F 276 MET cc_start: 0.2099 (OUTLIER) cc_final: 0.1749 (tpt) REVERT: F 430 TYR cc_start: 0.4150 (OUTLIER) cc_final: 0.3861 (t80) REVERT: F 502 LYS cc_start: 0.4174 (tttp) cc_final: 0.3568 (tttp) REVERT: F 545 HIS cc_start: 0.7257 (t-170) cc_final: 0.6991 (t-170) REVERT: F 551 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.4226 (tp) outliers start: 84 outliers final: 43 residues processed: 318 average time/residue: 0.7318 time to fit residues: 270.8840 Evaluate side-chains 302 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 228 optimal weight: 0.3980 chunk 287 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C 799 ASN D 45 ASN E 43 ASN E 62 GLN E 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.185604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114193 restraints weight = 38622.674| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.73 r_work: 0.3174 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30282 Z= 0.138 Angle : 0.571 9.365 41039 Z= 0.298 Chirality : 0.042 0.154 4674 Planarity : 0.004 0.068 5242 Dihedral : 10.924 89.762 4552 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.83 % Allowed : 14.66 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.06 (0.14), residues: 3661 helix: 1.88 (0.14), residues: 1483 sheet: 0.02 (0.27), residues: 405 loop : -1.65 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1034 TYR 0.014 0.001 TYR C1281 PHE 0.018 0.001 PHE C 514 TRP 0.008 0.001 TRP F 315 HIS 0.012 0.001 HIS F 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (30274) covalent geometry : angle 0.56808 / 0.30 (41027) hydrogen bonds : bond 0.04593 / 3.24 ( 1298) hydrogen bonds : angle 4.37658 / 3.09 ( 3708) metal coordination : bond 0.00500 / 0.26 ( 8) metal coordination : angle 3.49976 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8290 (ttm-80) REVERT: B 95 LYS cc_start: 0.8294 (mtpt) cc_final: 0.8045 (mtmt) REVERT: C 44 GLU cc_start: 0.8305 (mp0) cc_final: 0.8002 (mp0) REVERT: C 370 MET cc_start: 0.6994 (tpt) cc_final: 0.6671 (mmp) REVERT: C 623 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8102 (mt) REVERT: C 624 ASP cc_start: 0.8338 (p0) cc_final: 0.8063 (p0) REVERT: C 626 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6455 (mt-10) REVERT: C 1265 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: D 45 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7109 (t0) REVERT: D 75 TYR cc_start: 0.7422 (m-10) cc_final: 0.7170 (m-80) REVERT: D 83 VAL cc_start: 0.8217 (p) cc_final: 0.7978 (m) REVERT: D 545 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.6245 (p90) REVERT: D 663 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6603 (pt0) REVERT: D 724 MET cc_start: 0.8991 (mtp) cc_final: 0.8370 (mtp) REVERT: D 873 GLU cc_start: 0.7893 (tp30) cc_final: 0.6771 (mt-10) REVERT: D 1015 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: D 1020 TRP cc_start: 0.5704 (p-90) cc_final: 0.5399 (p-90) REVERT: D 1195 GLN cc_start: 0.7153 (pm20) cc_final: 0.6803 (pp30) REVERT: D 1198 VAL cc_start: 0.5693 (OUTLIER) cc_final: 0.5475 (t) REVERT: D 1215 GLU cc_start: 0.7081 (pm20) cc_final: 0.6743 (pt0) REVERT: D 1243 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7995 (tt) REVERT: D 1325 PHE cc_start: 0.7161 (p90) cc_final: 0.6768 (p90) REVERT: D 1371 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6208 (ptm160) REVERT: D 1372 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5823 (tpp-160) REVERT: E 55 GLU cc_start: 0.7369 (tt0) cc_final: 0.6738 (pt0) REVERT: F 100 MET cc_start: 0.5188 (mtt) cc_final: 0.4928 (mpp) REVERT: F 276 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.2089 (tpt) REVERT: F 430 TYR cc_start: 0.4167 (OUTLIER) cc_final: 0.3846 (t80) REVERT: F 476 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7372 (ptt180) REVERT: F 502 LYS cc_start: 0.4156 (tttp) cc_final: 0.3793 (tttp) REVERT: F 545 HIS cc_start: 0.7266 (t-170) cc_final: 0.6994 (t-170) REVERT: F 551 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4220 (tp) REVERT: F 561 MET cc_start: 0.5913 (mmm) cc_final: 0.5485 (mpp) outliers start: 89 outliers final: 36 residues processed: 319 average time/residue: 0.7184 time to fit residues: 268.1284 Evaluate side-chains 299 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 119 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 235 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN D 45 ASN E 43 ASN E 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.185839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111572 restraints weight = 38739.588| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.27 r_work: 0.3206 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30282 Z= 0.130 Angle : 0.570 14.626 41039 Z= 0.296 Chirality : 0.042 0.154 4674 Planarity : 0.004 0.072 5242 Dihedral : 10.907 89.709 4552 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.83 % Allowed : 14.85 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.09 (0.14), residues: 3661 helix: 1.90 (0.14), residues: 1484 sheet: 0.06 (0.26), residues: 415 loop : -1.65 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.014 0.001 TYR C1281 PHE 0.017 0.001 PHE C 514 TRP 0.008 0.001 TRP F 315 HIS 0.005 0.001 HIS F 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (30274) covalent geometry : angle 0.56677 / 0.30 (41027) hydrogen bonds : bond 0.04470 / 3.16 ( 1298) hydrogen bonds : angle 4.32895 / 3.06 ( 3708) metal coordination : bond 0.00459 / 0.24 ( 8) metal coordination : angle 3.32188 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (ttm-80) REVERT: B 95 LYS cc_start: 0.8245 (mppt) cc_final: 0.8013 (mtmt) REVERT: C 44 GLU cc_start: 0.8302 (mp0) cc_final: 0.8012 (mp0) REVERT: C 47 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7748 (p90) REVERT: C 214 ASN cc_start: 0.7999 (t0) cc_final: 0.7598 (t0) REVERT: C 370 MET cc_start: 0.6920 (tpt) cc_final: 0.6579 (mmp) REVERT: C 623 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8074 (mt) REVERT: C 624 ASP cc_start: 0.8317 (p0) cc_final: 0.8091 (p0) REVERT: C 626 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: C 1265 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: C 1297 ASP cc_start: 0.6966 (t0) cc_final: 0.6401 (p0) REVERT: D 75 TYR cc_start: 0.7390 (m-10) cc_final: 0.7139 (m-80) REVERT: D 83 VAL cc_start: 0.8213 (p) cc_final: 0.7975 (m) REVERT: D 545 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.6222 (p90) REVERT: D 724 MET cc_start: 0.8970 (mtp) cc_final: 0.8365 (mtp) REVERT: D 873 GLU cc_start: 0.7878 (tp30) cc_final: 0.6786 (mt-10) REVERT: D 1015 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7087 (pp20) REVERT: D 1020 TRP cc_start: 0.5699 (p-90) cc_final: 0.5394 (p-90) REVERT: D 1195 GLN cc_start: 0.7181 (pm20) cc_final: 0.6926 (pp30) REVERT: D 1215 GLU cc_start: 0.7011 (pm20) cc_final: 0.6717 (pt0) REVERT: D 1243 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7966 (tt) REVERT: D 1325 PHE cc_start: 0.7134 (p90) cc_final: 0.6749 (p90) REVERT: D 1371 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6207 (ptm160) REVERT: D 1372 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5801 (tpp-160) REVERT: E 55 GLU cc_start: 0.7345 (tt0) cc_final: 0.6750 (pt0) REVERT: E 62 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7285 (tt0) REVERT: F 100 MET cc_start: 0.5138 (mtt) cc_final: 0.4887 (mpp) REVERT: F 276 MET cc_start: 0.2366 (OUTLIER) cc_final: 0.2093 (tpt) REVERT: F 430 TYR cc_start: 0.4161 (OUTLIER) cc_final: 0.3836 (t80) REVERT: F 476 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7382 (ptt180) REVERT: F 502 LYS cc_start: 0.4088 (tttp) cc_final: 0.3750 (tttp) REVERT: F 545 HIS cc_start: 0.7234 (t-170) cc_final: 0.6997 (t-170) REVERT: F 551 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.4337 (tp) REVERT: F 561 MET cc_start: 0.6032 (mmm) cc_final: 0.5547 (mpp) outliers start: 89 outliers final: 45 residues processed: 318 average time/residue: 0.7112 time to fit residues: 264.3105 Evaluate side-chains 306 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 73 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 357 optimal weight: 0.3980 chunk 173 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C1257 GLN D 45 ASN D1044 GLN E 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110870 restraints weight = 38656.953| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.26 r_work: 0.3193 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30282 Z= 0.145 Angle : 0.582 12.061 41039 Z= 0.303 Chirality : 0.042 0.151 4674 Planarity : 0.004 0.074 5242 Dihedral : 10.917 89.684 4552 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.67 % Allowed : 15.29 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.05 (0.14), residues: 3661 helix: 1.88 (0.14), residues: 1481 sheet: 0.04 (0.27), residues: 403 loop : -1.67 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.015 0.001 TYR C1281 PHE 0.019 0.001 PHE C 514 TRP 0.008 0.001 TRP F 315 HIS 0.013 0.001 HIS F 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30274) covalent geometry : angle 0.57917 / 0.30 (41027) hydrogen bonds : bond 0.04678 / 3.30 ( 1298) hydrogen bonds : angle 4.31166 / 3.04 ( 3708) metal coordination : bond 0.00490 / 0.25 ( 8) metal coordination : angle 3.32954 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 251 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8283 (ttm-80) REVERT: B 95 LYS cc_start: 0.8265 (mppt) cc_final: 0.8024 (mtmt) REVERT: C 44 GLU cc_start: 0.8269 (mp0) cc_final: 0.7971 (mp0) REVERT: C 47 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7764 (p90) REVERT: C 214 ASN cc_start: 0.7994 (t0) cc_final: 0.7588 (t0) REVERT: C 370 MET cc_start: 0.6855 (tpt) cc_final: 0.6539 (mmp) REVERT: C 623 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (mt) REVERT: C 624 ASP cc_start: 0.8330 (p0) cc_final: 0.8101 (p0) REVERT: C 626 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6408 (mt-10) REVERT: C 1265 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: C 1297 ASP cc_start: 0.7011 (t0) cc_final: 0.6473 (p0) REVERT: D 75 TYR cc_start: 0.7399 (m-10) cc_final: 0.7148 (m-80) REVERT: D 83 VAL cc_start: 0.8253 (p) cc_final: 0.8001 (m) REVERT: D 156 ARG cc_start: 0.6169 (tmm-80) cc_final: 0.5596 (tmt170) REVERT: D 545 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.6234 (p90) REVERT: D 663 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6631 (pt0) REVERT: D 724 MET cc_start: 0.9004 (mtp) cc_final: 0.8413 (mtp) REVERT: D 873 GLU cc_start: 0.7856 (tp30) cc_final: 0.6737 (mt-10) REVERT: D 1015 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: D 1020 TRP cc_start: 0.5710 (p-90) cc_final: 0.5379 (p-90) REVERT: D 1195 GLN cc_start: 0.7190 (pm20) cc_final: 0.6919 (pp30) REVERT: D 1215 GLU cc_start: 0.6992 (pm20) cc_final: 0.6688 (pt0) REVERT: D 1243 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 1325 PHE cc_start: 0.7143 (p90) cc_final: 0.6742 (p90) REVERT: D 1327 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: D 1371 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6115 (ptm160) REVERT: D 1372 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5833 (tpp-160) REVERT: E 55 GLU cc_start: 0.7351 (tt0) cc_final: 0.6740 (pt0) REVERT: F 100 MET cc_start: 0.5094 (mtt) cc_final: 0.4882 (mpp) REVERT: F 276 MET cc_start: 0.2366 (OUTLIER) cc_final: 0.2098 (tpt) REVERT: F 430 TYR cc_start: 0.4174 (OUTLIER) cc_final: 0.3847 (t80) REVERT: F 502 LYS cc_start: 0.4176 (tttp) cc_final: 0.3726 (tttm) REVERT: F 545 HIS cc_start: 0.7222 (t-170) cc_final: 0.6980 (t-170) REVERT: F 551 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4238 (tp) REVERT: F 561 MET cc_start: 0.6074 (mmm) cc_final: 0.5539 (mpp) outliers start: 84 outliers final: 44 residues processed: 314 average time/residue: 0.7277 time to fit residues: 266.6881 Evaluate side-chains 301 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 282 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 260 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C 327 GLN C 677 ASN E 43 ASN E 62 GLN E 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.185445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111091 restraints weight = 38610.053| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.25 r_work: 0.3197 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30282 Z= 0.144 Angle : 0.588 12.137 41039 Z= 0.306 Chirality : 0.042 0.151 4674 Planarity : 0.004 0.075 5242 Dihedral : 10.909 89.492 4552 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.19 % Allowed : 16.03 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.06 (0.14), residues: 3661 helix: 1.87 (0.14), residues: 1481 sheet: 0.08 (0.27), residues: 405 loop : -1.66 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1034 TYR 0.014 0.001 TYR C1281 PHE 0.018 0.001 PHE C 514 TRP 0.008 0.001 TRP F 315 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (30274) covalent geometry : angle 0.58543 / 0.31 (41027) hydrogen bonds : bond 0.04649 / 3.29 ( 1298) hydrogen bonds : angle 4.31378 / 3.05 ( 3708) metal coordination : bond 0.00478 / 0.25 ( 8) metal coordination : angle 3.27926 / 1.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8277 (ttm-80) REVERT: B 95 LYS cc_start: 0.8253 (mppt) cc_final: 0.8006 (mtmt) REVERT: C 44 GLU cc_start: 0.8380 (mp0) cc_final: 0.8090 (mp0) REVERT: C 47 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7735 (p90) REVERT: C 623 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8145 (mt) REVERT: C 624 ASP cc_start: 0.8298 (p0) cc_final: 0.8072 (p0) REVERT: C 626 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: C 1265 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6726 (m-10) REVERT: C 1297 ASP cc_start: 0.6942 (t0) cc_final: 0.6487 (p0) REVERT: D 75 TYR cc_start: 0.7410 (m-10) cc_final: 0.7160 (m-80) REVERT: D 83 VAL cc_start: 0.8281 (p) cc_final: 0.8023 (m) REVERT: D 156 ARG cc_start: 0.6289 (tmm-80) cc_final: 0.5573 (tmt170) REVERT: D 545 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.6246 (p90) REVERT: D 663 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6574 (pt0) REVERT: D 724 MET cc_start: 0.9007 (mtp) cc_final: 0.8415 (mtp) REVERT: D 873 GLU cc_start: 0.7843 (tp30) cc_final: 0.6740 (mt-10) REVERT: D 1015 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: D 1020 TRP cc_start: 0.5717 (p-90) cc_final: 0.5387 (p-90) REVERT: D 1195 GLN cc_start: 0.7220 (pm20) cc_final: 0.6893 (pp30) REVERT: D 1215 GLU cc_start: 0.6907 (pm20) cc_final: 0.6655 (pt0) REVERT: D 1325 PHE cc_start: 0.7194 (p90) cc_final: 0.6759 (p90) REVERT: D 1327 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: D 1371 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6088 (ptm160) REVERT: D 1372 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5809 (tpp-160) REVERT: E 55 GLU cc_start: 0.7344 (tt0) cc_final: 0.6732 (pt0) REVERT: F 276 MET cc_start: 0.2157 (OUTLIER) cc_final: 0.1923 (tpt) REVERT: F 430 TYR cc_start: 0.4125 (OUTLIER) cc_final: 0.3880 (t80) REVERT: F 474 MET cc_start: 0.5972 (mtp) cc_final: 0.5580 (ttp) REVERT: F 502 LYS cc_start: 0.4182 (tttp) cc_final: 0.3739 (tttm) REVERT: F 545 HIS cc_start: 0.7203 (t-170) cc_final: 0.6963 (t-170) REVERT: F 551 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.4272 (tp) REVERT: F 561 MET cc_start: 0.5993 (mmm) cc_final: 0.5476 (mpp) outliers start: 69 outliers final: 46 residues processed: 300 average time/residue: 0.7296 time to fit residues: 255.8027 Evaluate side-chains 303 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 170 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 316 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.184396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111429 restraints weight = 38485.041| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.60 r_work: 0.3157 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30282 Z= 0.180 Angle : 0.626 11.849 41039 Z= 0.325 Chirality : 0.044 0.166 4674 Planarity : 0.005 0.076 5242 Dihedral : 10.966 89.477 4552 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.23 % Allowed : 16.28 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: -0.04 (0.14), residues: 3661 helix: 1.79 (0.14), residues: 1477 sheet: 0.04 (0.26), residues: 412 loop : -1.73 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.016 0.002 TYR C1149 PHE 0.023 0.001 PHE C 514 TRP 0.009 0.001 TRP C 997 HIS 0.005 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (30274) covalent geometry : angle 0.62270 / 0.32 (41027) hydrogen bonds : bond 0.05157 / 3.64 ( 1298) hydrogen bonds : angle 4.38375 / 3.10 ( 3708) metal coordination : bond 0.00565 / 0.30 ( 8) metal coordination : angle 3.53649 / 1.72 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8314 (ttm-80) REVERT: B 95 LYS cc_start: 0.8315 (mppt) cc_final: 0.8049 (mtmt) REVERT: C 44 GLU cc_start: 0.8432 (mp0) cc_final: 0.8147 (mp0) REVERT: C 47 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7791 (p90) REVERT: C 214 ASN cc_start: 0.7999 (t0) cc_final: 0.7592 (t0) REVERT: C 624 ASP cc_start: 0.8285 (p0) cc_final: 0.8065 (p0) REVERT: C 626 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: C 1265 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6869 (m-10) REVERT: D 75 TYR cc_start: 0.7441 (m-10) cc_final: 0.7183 (m-80) REVERT: D 83 VAL cc_start: 0.8293 (p) cc_final: 0.8036 (m) REVERT: D 545 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.6333 (p90) REVERT: D 724 MET cc_start: 0.9050 (mtp) cc_final: 0.8439 (mtp) REVERT: D 873 GLU cc_start: 0.7853 (tp30) cc_final: 0.6751 (mt-10) REVERT: D 1015 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: D 1020 TRP cc_start: 0.5652 (p-90) cc_final: 0.5315 (p-90) REVERT: D 1195 GLN cc_start: 0.7125 (pm20) cc_final: 0.6862 (pp30) REVERT: D 1215 GLU cc_start: 0.6925 (pm20) cc_final: 0.6684 (pt0) REVERT: D 1325 PHE cc_start: 0.7231 (p90) cc_final: 0.6846 (p90) REVERT: D 1327 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: D 1371 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6081 (ptm160) REVERT: D 1372 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5789 (tpp-160) REVERT: E 55 GLU cc_start: 0.7358 (tt0) cc_final: 0.6806 (pt0) REVERT: F 276 MET cc_start: 0.2381 (ptm) cc_final: 0.2098 (tpt) REVERT: F 430 TYR cc_start: 0.4190 (OUTLIER) cc_final: 0.3918 (t80) REVERT: F 474 MET cc_start: 0.5919 (mtp) cc_final: 0.5554 (ttp) REVERT: F 502 LYS cc_start: 0.4197 (tttp) cc_final: 0.3752 (tttm) REVERT: F 545 HIS cc_start: 0.7241 (t-170) cc_final: 0.6992 (t-170) REVERT: F 551 LEU cc_start: 0.4494 (OUTLIER) cc_final: 0.4271 (tp) REVERT: F 561 MET cc_start: 0.5987 (mmm) cc_final: 0.5501 (mpp) outliers start: 70 outliers final: 47 residues processed: 300 average time/residue: 0.7371 time to fit residues: 259.0843 Evaluate side-chains 302 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1371 ARG Chi-restraints excluded: chain D residue 1372 ARG Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 394 TYR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 430 TYR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 261 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 chunk 312 optimal weight: 0.0070 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN E 43 ASN E 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.185074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110528 restraints weight = 38738.166| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.26 r_work: 0.3190 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30282 Z= 0.146 Angle : 0.598 11.660 41039 Z= 0.311 Chirality : 0.043 0.176 4674 Planarity : 0.004 0.076 5242 Dihedral : 10.920 89.978 4552 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.10 % Allowed : 16.60 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.01 (0.14), residues: 3661 helix: 1.83 (0.14), residues: 1481 sheet: 0.08 (0.27), residues: 400 loop : -1.70 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1034 TYR 0.014 0.001 TYR C1281 PHE 0.019 0.001 PHE C 514 TRP 0.008 0.001 TRP C 807 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (30274) covalent geometry : angle 0.59556 / 0.31 (41027) hydrogen bonds : bond 0.04750 / 3.36 ( 1298) hydrogen bonds : angle 4.34662 / 3.07 ( 3708) metal coordination : bond 0.00509 / 0.27 ( 8) metal coordination : angle 3.33827 / 1.63 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15741.84 seconds wall clock time: 267 minutes 21.23 seconds (16041.23 seconds total)