Starting phenix.real_space_refine on Mon Sep 14 15:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570.map" model { file = "/net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szj_25570/09_2026/7szj_25570_trim.cif" } resolution = 3.11 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= 0.114 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 106 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19211 2.51 5 N 5523 2.21 5 O 6202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s 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: 31173 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: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1162 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "Y" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'RFP': 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 64.628 116.508 81.516 1.00 34.65 S ATOM 14629 SG CYS D 72 64.329 116.955 85.439 1.00 36.54 S ATOM 14737 SG CYS D 85 63.760 119.837 83.215 1.00 39.22 S ATOM 14761 SG CYS D 88 67.167 118.538 83.641 1.00 40.02 S ATOM 20449 SG CYS D 814 101.537 96.654 28.039 1.00 28.16 S ATOM 21014 SG CYS D 888 102.173 96.436 31.666 1.00 23.24 S ATOM 21065 SG CYS D 895 100.123 93.940 30.058 1.00 14.89 S ATOM 21086 SG CYS D 898 103.580 94.008 29.413 1.00 15.21 S Time building chain proxies: 6.31, per 1000 atoms: 0.20 Number of scatterers: 31173 At special positions: 0 Unit cell: (192.64, 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 106 15.00 Mg 1 11.99 O 6202 8.00 N 5523 7.00 C 19211 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 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 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " 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: 133 helices and 48 sheets defined 44.4% alpha, 14.0% beta 23 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.892A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.773A 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: 3.603A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.749A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.731A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.554A 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: 3.978A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.436A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.715A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.959A 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: 4.079A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.936A 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 242 through 247 removed outlier: 3.511A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.827A 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: 3.576A 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: 4.070A 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 437 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 removed outlier: 3.558A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 removed outlier: 4.325A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.817A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 4.033A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 removed outlier: 3.778A 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 removed outlier: 3.578A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) 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 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.244A 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 995 through 1000 removed outlier: 3.762A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.840A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.649A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.415A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.570A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.659A 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: 3.509A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.670A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.952A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.617A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.589A 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 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.501A 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 285 removed outlier: 4.035A 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: 3.760A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 332' 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 483 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 597 through 612 removed outlier: 3.740A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.898A 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: 3.567A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.089A 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: 3.961A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.504A 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 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.868A 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 1146 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.656A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.438A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 removed outlier: 3.695A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.871A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.562A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.870A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.757A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.517A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.937A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 removed outlier: 3.659A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 152 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: 4.672A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.578A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.728A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.308A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.180A 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: 3.621A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.743A 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 553 through 563 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 585 through 600 Processing helix chain 'F' and resid 604 through 611 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.581A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.820A 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: 7.508A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.562A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 17 removed outlier: 4.351A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 7.917A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.632A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.905A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.878A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.878A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.555A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.331A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.555A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.412A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.801A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.295A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.422A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.746A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.751A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.710A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD9, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AE1, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 3.675A pdb=" N VAL D 858 " --> pdb=" O VAL D 848 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 952 removed outlier: 7.188A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.552A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.636A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1187 through 1188 Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AF3, first strand: chain 'F' and resid 162 through 165 removed outlier: 5.696A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 7.45 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: 1.17 - 1.30: 5190 1.30 - 1.43: 7911 1.43 - 1.56: 18315 1.56 - 1.69: 217 1.69 - 1.81: 225 Bond restraints: 31858 Sorted by residual: bond pdb=" C6 RFP C3001 " pdb=" O3 RFP C3001 " ideal model delta sigma weight residual 1.339 1.531 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" C6 RFP C3001 " pdb=" C7 RFP C3001 " ideal model delta sigma weight residual 1.387 1.570 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C10 RFP C3001 " pdb=" C4 RFP C3001 " ideal model delta sigma weight residual 1.411 1.572 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C1 RFP C3001 " pdb=" C9 RFP C3001 " ideal model delta sigma weight residual 1.411 1.570 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C10 RFP C3001 " pdb=" C5 RFP C3001 " ideal model delta sigma weight residual 1.431 1.590 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 31853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 42825 2.02 - 4.05: 592 4.05 - 6.07: 42 6.07 - 8.10: 4 8.10 - 10.12: 7 Bond angle restraints: 43470 Sorted by residual: angle pdb=" N3 DT Y 44 " pdb=" C4 DT Y 44 " pdb=" O4 DT Y 44 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N PHE D1274 " pdb=" CA PHE D1274 " pdb=" CB PHE D1274 " ideal model delta sigma weight residual 114.17 109.49 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" N3 DT X 52 " pdb=" C4 DT X 52 " pdb=" O4 DT X 52 " 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 Y 51 " pdb=" C4 DT Y 51 " pdb=" O4 DT Y 51 " 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 39 " pdb=" C4 DT X 39 " pdb=" O4 DT X 39 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 43465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 18628 35.37 - 70.74: 709 70.74 - 106.11: 30 106.11 - 141.48: 7 141.48 - 176.85: 2 Dihedral angle restraints: 19376 sinusoidal: 8772 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 180.00 140.07 39.93 0 5.00e+00 4.00e-02 6.38e+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 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 19373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4373 0.067 - 0.133: 569 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C22 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C32 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C24 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C25 RFP C3001 " pdb=" C33 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C20 RFP C3001 " pdb=" C19 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C31 RFP C3001 " both_signs ideal model delta sigma weight residual False -2.56 -2.77 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4949 not shown) Planarity restraints: 5309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 697 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO C 698 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 178 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 179 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 104 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU F 104 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU F 104 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 5306 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 241 2.56 - 3.15: 26149 3.15 - 3.73: 46058 3.73 - 4.32: 64050 4.32 - 4.90: 108682 Nonbonded interactions: 245180 Sorted by model distance: nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 1.979 3.040 nonbonded pdb=" OE1 GLU D1030 " pdb=" OH TYR D1099 " model vdw 1.996 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" O ILE C 138 " model vdw 2.015 3.040 nonbonded pdb=" OG1 THR C 843 " pdb=" O GLY C 846 " model vdw 2.024 3.040 nonbonded pdb=" O LEU C 397 " pdb=" OG SER C 398 " model vdw 2.060 3.040 ... (remaining 245175 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: 3.410 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: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 31866 Z= 0.300 Angle : 0.562 10.124 43482 Z= 0.348 Chirality : 0.042 0.333 4952 Planarity : 0.004 0.061 5309 Dihedral : 17.127 176.854 12540 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.24 (0.14), residues: 3661 helix: 2.13 (0.14), residues: 1461 sheet: -0.30 (0.27), residues: 390 loop : -1.48 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 476 TYR 0.013 0.001 TYR D 631 PHE 0.019 0.001 PHE C 514 TRP 0.008 0.001 TRP F 326 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.29 (31858) covalent geometry : angle 0.56142 / 0.35 (43470) hydrogen bonds : bond 0.17940 / 12.53 ( 1358) hydrogen bonds : angle 6.66424 / 4.66 ( 3828) metal coordination : bond 0.10899 / 5.36 ( 8) metal coordination : angle 0.98185 / 0.55 ( 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 289 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.9007 (mmp) cc_final: 0.8481 (mmp) REVERT: C 1315 MET cc_start: 0.8477 (ptt) cc_final: 0.8249 (ptt) REVERT: D 697 MET cc_start: 0.8668 (ttp) cc_final: 0.8446 (ttp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2175 time to fit residues: 99.2394 Evaluate side-chains 251 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 0.0060 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.2980 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 23 HIS B 127 GLN C 69 GLN C 330 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D1197 ASN F 227 GLN F 294 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141861 restraints weight = 36458.288| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.54 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31866 Z= 0.148 Angle : 0.651 11.071 43482 Z= 0.342 Chirality : 0.045 0.259 4952 Planarity : 0.005 0.061 5309 Dihedral : 16.375 178.821 5261 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.60 % Allowed : 7.82 % Favored : 91.57 % 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: 0.27 (0.14), residues: 3661 helix: 1.94 (0.14), residues: 1479 sheet: -0.23 (0.26), residues: 426 loop : -1.31 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 245 TYR 0.027 0.001 TYR D 46 PHE 0.019 0.002 PHE C 337 TRP 0.027 0.002 TRP F 433 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (31858) covalent geometry : angle 0.64870 / 0.34 (43470) hydrogen bonds : bond 0.05430 / 3.84 ( 1358) hydrogen bonds : angle 4.81548 / 3.35 ( 3828) metal coordination : bond 0.01356 / 0.78 ( 8) metal coordination : angle 3.28854 / 1.79 ( 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 299 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 1.237 Fit side-chains REVERT: A 51 MET cc_start: 0.8797 (mmp) cc_final: 0.8159 (mmp) REVERT: B 16 ILE cc_start: 0.8280 (mp) cc_final: 0.8021 (mt) REVERT: C 1315 MET cc_start: 0.8421 (ptt) cc_final: 0.8161 (ptt) REVERT: D 697 MET cc_start: 0.8674 (ttp) cc_final: 0.8208 (ttp) REVERT: F 294 GLN cc_start: 0.1637 (OUTLIER) cc_final: 0.1352 (mp10) outliers start: 19 outliers final: 14 residues processed: 290 average time/residue: 0.2077 time to fit residues: 97.0261 Evaluate side-chains 264 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 294 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 331 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 370 optimal weight: 30.0000 chunk 354 optimal weight: 5.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 294 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131766 restraints weight = 36381.486| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.95 r_work: 0.2854 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31866 Z= 0.207 Angle : 0.651 9.709 43482 Z= 0.340 Chirality : 0.045 0.217 4952 Planarity : 0.005 0.060 5309 Dihedral : 16.443 179.427 5261 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 0.95 % Allowed : 11.00 % Favored : 88.04 % 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: 1.75 (0.14), residues: 1479 sheet: -0.09 (0.26), residues: 417 loop : -1.50 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 542 TYR 0.020 0.002 TYR D 46 PHE 0.019 0.002 PHE C 514 TRP 0.020 0.001 TRP F 433 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (31858) covalent geometry : angle 0.64835 / 0.34 (43470) hydrogen bonds : bond 0.06070 / 4.28 ( 1358) hydrogen bonds : angle 4.64690 / 3.22 ( 3828) metal coordination : bond 0.00977 / 0.48 ( 8) metal coordination : angle 3.84533 / 2.19 ( 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 284 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 1.099 Fit side-chains REVERT: A 51 MET cc_start: 0.9121 (mmp) cc_final: 0.8569 (mmp) REVERT: C 1315 MET cc_start: 0.8835 (ptt) cc_final: 0.8442 (ptt) REVERT: D 697 MET cc_start: 0.8973 (ttp) cc_final: 0.8571 (ttp) REVERT: D 992 LYS cc_start: 0.6751 (mptt) cc_final: 0.6489 (mmtt) REVERT: E 12 LYS cc_start: 0.7210 (tppt) cc_final: 0.7006 (tppt) REVERT: F 342 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6148 (mm-40) outliers start: 30 outliers final: 17 residues processed: 277 average time/residue: 0.2027 time to fit residues: 89.4786 Evaluate side-chains 261 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 342 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 13 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 354 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 375 optimal weight: 40.0000 chunk 219 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 526 HIS C 952 GLN D1098 GLN D1197 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN F 294 GLN F 331 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136398 restraints weight = 36247.721| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.76 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31866 Z= 0.168 Angle : 0.611 10.284 43482 Z= 0.321 Chirality : 0.044 0.230 4952 Planarity : 0.005 0.060 5309 Dihedral : 16.442 178.330 5261 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.75 % Allowed : 12.69 % Favored : 85.56 % 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: 1.77 (0.14), residues: 1473 sheet: -0.15 (0.25), residues: 418 loop : -1.50 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.019 0.001 TYR D 46 PHE 0.017 0.002 PHE C 337 TRP 0.012 0.001 TRP F 326 HIS 0.005 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (31858) covalent geometry : angle 0.60884 / 0.32 (43470) hydrogen bonds : bond 0.05475 / 3.86 ( 1358) hydrogen bonds : angle 4.48216 / 3.10 ( 3828) metal coordination : bond 0.00697 / 0.35 ( 8) metal coordination : angle 3.42309 / 1.93 ( 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 315 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 260 time to evaluate : 1.662 Fit side-chains REVERT: A 51 MET cc_start: 0.8819 (mmp) cc_final: 0.8251 (mmp) REVERT: C 1315 MET cc_start: 0.8550 (ptt) cc_final: 0.8110 (ptt) REVERT: D 81 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6838 (mtm-85) REVERT: D 129 ASP cc_start: 0.6879 (t0) cc_final: 0.6644 (t0) REVERT: D 697 MET cc_start: 0.8745 (ttp) cc_final: 0.8382 (ttp) REVERT: D 1286 LYS cc_start: 0.6949 (ptmt) cc_final: 0.6669 (pttt) REVERT: F 294 GLN cc_start: 0.1660 (OUTLIER) cc_final: 0.1390 (mt0) outliers start: 55 outliers final: 31 residues processed: 303 average time/residue: 0.1987 time to fit residues: 96.7678 Evaluate side-chains 280 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 494 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 149 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 310 optimal weight: 2.9990 chunk 370 optimal weight: 30.0000 chunk 328 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1367 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.180431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128730 restraints weight = 36196.918| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.72 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31866 Z= 0.211 Angle : 0.641 9.452 43482 Z= 0.335 Chirality : 0.045 0.238 4952 Planarity : 0.005 0.060 5309 Dihedral : 16.411 178.463 5261 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 1.91 % Allowed : 14.24 % Favored : 83.85 % 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: -0.07 (0.14), residues: 3661 helix: 1.67 (0.14), residues: 1472 sheet: -0.22 (0.25), residues: 418 loop : -1.57 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.016 0.002 TYR D 46 PHE 0.016 0.002 PHE C 514 TRP 0.021 0.002 TRP F 433 HIS 0.008 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (31858) covalent geometry : angle 0.63792 / 0.33 (43470) hydrogen bonds : bond 0.05906 / 4.16 ( 1358) hydrogen bonds : angle 4.50045 / 3.12 ( 3828) metal coordination : bond 0.00794 / 0.39 ( 8) metal coordination : angle 3.69131 / 2.13 ( 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 312 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 1.083 Fit side-chains REVERT: A 51 MET cc_start: 0.9050 (mmp) cc_final: 0.8595 (mmp) REVERT: A 186 ASN cc_start: 0.8613 (t0) cc_final: 0.8337 (t0) REVERT: C 800 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: C 955 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8089 (tp-100) REVERT: C 1315 MET cc_start: 0.8864 (ptt) cc_final: 0.8402 (ptt) REVERT: D 81 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7367 (mtm-85) REVERT: D 129 ASP cc_start: 0.7824 (t0) cc_final: 0.7528 (t0) REVERT: D 151 MET cc_start: 0.7703 (pmm) cc_final: 0.7230 (pmm) REVERT: D 664 ILE cc_start: 0.6773 (mm) cc_final: 0.6425 (tt) REVERT: D 697 MET cc_start: 0.9000 (ttp) cc_final: 0.8668 (ttp) REVERT: D 717 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9186 (t) REVERT: F 608 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7854 (mtp-110) outliers start: 60 outliers final: 40 residues processed: 293 average time/residue: 0.2102 time to fit residues: 99.1390 Evaluate side-chains 290 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 55 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 368 optimal weight: 50.0000 chunk 326 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 271 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133650 restraints weight = 35942.332| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.89 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31866 Z= 0.135 Angle : 0.572 8.579 43482 Z= 0.302 Chirality : 0.042 0.245 4952 Planarity : 0.004 0.061 5309 Dihedral : 16.326 178.595 5261 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.62 % Allowed : 15.26 % Favored : 83.12 % 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: 0.08 (0.14), residues: 3661 helix: 1.81 (0.14), residues: 1474 sheet: -0.15 (0.25), residues: 418 loop : -1.49 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1033 TYR 0.016 0.001 TYR D 46 PHE 0.010 0.001 PHE C 514 TRP 0.017 0.001 TRP F 433 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (31858) covalent geometry : angle 0.56933 / 0.30 (43470) hydrogen bonds : bond 0.05000 / 3.52 ( 1358) hydrogen bonds : angle 4.36501 / 3.03 ( 3828) metal coordination : bond 0.00542 / 0.27 ( 8) metal coordination : angle 3.13100 / 1.77 ( 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 306 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.154 Fit side-chains REVERT: C 145 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8632 (mm) REVERT: C 1315 MET cc_start: 0.8567 (ptt) cc_final: 0.8040 (ptt) REVERT: D 81 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6997 (mtm-85) REVERT: D 129 ASP cc_start: 0.7091 (t0) cc_final: 0.6796 (t0) REVERT: D 485 MET cc_start: 0.8885 (tpp) cc_final: 0.8668 (tpt) REVERT: D 664 ILE cc_start: 0.7471 (mm) cc_final: 0.7237 (tt) REVERT: D 697 MET cc_start: 0.8729 (ttp) cc_final: 0.8406 (ttp) REVERT: D 1286 LYS cc_start: 0.6906 (ptmt) cc_final: 0.6656 (pttt) REVERT: F 583 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.6880 (t) outliers start: 51 outliers final: 36 residues processed: 292 average time/residue: 0.2090 time to fit residues: 98.3252 Evaluate side-chains 284 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 283 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 362 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 187 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130724 restraints weight = 36228.885| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.99 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31866 Z= 0.215 Angle : 0.643 9.380 43482 Z= 0.335 Chirality : 0.045 0.253 4952 Planarity : 0.005 0.059 5309 Dihedral : 16.350 178.522 5261 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 2.42 % Allowed : 15.29 % Favored : 82.29 % 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: 1.67 (0.14), residues: 1472 sheet: -0.18 (0.25), residues: 416 loop : -1.61 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.015 0.002 TYR D 631 PHE 0.018 0.002 PHE A 35 TRP 0.021 0.002 TRP F 433 HIS 0.010 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.21 (31858) covalent geometry : angle 0.63982 / 0.33 (43470) hydrogen bonds : bond 0.05930 / 4.18 ( 1358) hydrogen bonds : angle 4.42175 / 3.07 ( 3828) metal coordination : bond 0.00797 / 0.39 ( 8) metal coordination : angle 3.61923 / 2.10 ( 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 328 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 1.307 Fit side-chains REVERT: C 145 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8562 (mm) REVERT: C 800 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: C 1315 MET cc_start: 0.8608 (ptt) cc_final: 0.8109 (ptt) REVERT: C 1340 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7442 (mm-30) REVERT: D 81 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7000 (mtm-85) REVERT: D 129 ASP cc_start: 0.7074 (t0) cc_final: 0.6736 (t0) REVERT: D 227 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7654 (t80) REVERT: D 664 ILE cc_start: 0.7649 (mm) cc_final: 0.7410 (tt) REVERT: D 697 MET cc_start: 0.8767 (ttp) cc_final: 0.8455 (ttp) REVERT: F 583 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6926 (t) outliers start: 76 outliers final: 55 residues processed: 307 average time/residue: 0.2049 time to fit residues: 101.5927 Evaluate side-chains 304 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 583 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 242 optimal weight: 2.9990 chunk 250 optimal weight: 0.3980 chunk 350 optimal weight: 0.7980 chunk 353 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 371 optimal weight: 30.0000 chunk 315 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 274 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130477 restraints weight = 36210.120| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.46 r_work: 0.2885 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31866 Z= 0.130 Angle : 0.559 7.884 43482 Z= 0.296 Chirality : 0.042 0.245 4952 Planarity : 0.004 0.061 5309 Dihedral : 16.195 178.673 5261 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.81 % Allowed : 16.18 % Favored : 82.00 % 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: 0.08 (0.14), residues: 3661 helix: 1.80 (0.14), residues: 1479 sheet: -0.13 (0.25), residues: 415 loop : -1.50 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1033 TYR 0.015 0.001 TYR D 46 PHE 0.009 0.001 PHE C1144 TRP 0.016 0.001 TRP F 433 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (31858) covalent geometry : angle 0.55735 / 0.30 (43470) hydrogen bonds : bond 0.04765 / 3.35 ( 1358) hydrogen bonds : angle 4.27392 / 2.97 ( 3828) metal coordination : bond 0.00520 / 0.26 ( 8) metal coordination : angle 2.95139 / 1.67 ( 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 313 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 1.354 Fit side-chains REVERT: B 170 ARG cc_start: 0.6814 (ttm110) cc_final: 0.6197 (ttm-80) REVERT: C 145 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8742 (mm) REVERT: C 631 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: C 1315 MET cc_start: 0.8859 (ptt) cc_final: 0.8351 (ptt) REVERT: D 129 ASP cc_start: 0.8001 (t0) cc_final: 0.7596 (t0) REVERT: D 213 LYS cc_start: 0.7364 (ttpp) cc_final: 0.7004 (mtmt) REVERT: D 227 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7396 (t80) REVERT: D 485 MET cc_start: 0.9058 (tpp) cc_final: 0.8843 (tpt) REVERT: D 697 MET cc_start: 0.8934 (ttp) cc_final: 0.8607 (ttp) REVERT: F 124 GLU cc_start: 0.7786 (tp30) cc_final: 0.7471 (mt-10) outliers start: 57 outliers final: 37 residues processed: 300 average time/residue: 0.2097 time to fit residues: 101.8424 Evaluate side-chains 285 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 262 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 360 optimal weight: 0.7980 chunk 241 optimal weight: 0.6980 chunk 99 optimal weight: 0.0270 chunk 347 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134326 restraints weight = 36119.518| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.03 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31866 Z= 0.120 Angle : 0.550 8.015 43482 Z= 0.291 Chirality : 0.042 0.204 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.127 178.155 5261 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.62 % Allowed : 16.34 % 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: 0.17 (0.14), residues: 3661 helix: 1.89 (0.14), residues: 1481 sheet: -0.20 (0.25), residues: 430 loop : -1.44 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.014 0.001 TYR D 46 PHE 0.015 0.001 PHE F 221 TRP 0.013 0.001 TRP F 433 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31858) covalent geometry : angle 0.54801 / 0.29 (43470) hydrogen bonds : bond 0.04514 / 3.18 ( 1358) hydrogen bonds : angle 4.20013 / 2.92 ( 3828) metal coordination : bond 0.00483 / 0.25 ( 8) metal coordination : angle 2.76882 / 1.57 ( 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 298 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 1.503 Fit side-chains REVERT: B 170 ARG cc_start: 0.6461 (ttm110) cc_final: 0.6221 (ttm-80) REVERT: C 145 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 542 ARG cc_start: 0.6682 (mtt-85) cc_final: 0.6464 (mtt-85) REVERT: C 1315 MET cc_start: 0.8568 (ptt) cc_final: 0.7995 (ptt) REVERT: D 129 ASP cc_start: 0.7064 (t0) cc_final: 0.6683 (t0) REVERT: D 227 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7545 (t80) REVERT: D 697 MET cc_start: 0.8674 (ttp) cc_final: 0.8287 (ttp) outliers start: 51 outliers final: 41 residues processed: 287 average time/residue: 0.2078 time to fit residues: 96.5313 Evaluate side-chains 286 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 147 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 280 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 299 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132666 restraints weight = 36050.114| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.97 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31866 Z= 0.151 Angle : 0.575 9.595 43482 Z= 0.302 Chirality : 0.043 0.216 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.144 177.546 5261 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.62 % Allowed : 16.41 % Favored : 81.97 % 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: 1.84 (0.14), residues: 1479 sheet: -0.23 (0.25), residues: 435 loop : -1.48 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 542 TYR 0.014 0.001 TYR D 631 PHE 0.013 0.001 PHE F 221 TRP 0.009 0.001 TRP F 326 HIS 0.006 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (31858) covalent geometry : angle 0.57310 / 0.30 (43470) hydrogen bonds : bond 0.04909 / 3.47 ( 1358) hydrogen bonds : angle 4.21896 / 2.93 ( 3828) metal coordination : bond 0.00586 / 0.29 ( 8) metal coordination : angle 2.99760 / 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 297 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 1.120 Fit side-chains REVERT: B 170 ARG cc_start: 0.6527 (ttm110) cc_final: 0.6261 (ttm-80) REVERT: C 145 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8651 (mm) REVERT: C 542 ARG cc_start: 0.6646 (mtt-85) cc_final: 0.6391 (mtt-85) REVERT: C 1315 MET cc_start: 0.8602 (ptt) cc_final: 0.8068 (ptt) REVERT: D 81 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6965 (mtm-85) REVERT: D 129 ASP cc_start: 0.7096 (t0) cc_final: 0.6713 (t0) REVERT: D 227 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7577 (t80) REVERT: D 697 MET cc_start: 0.8715 (ttp) cc_final: 0.8352 (ttp) outliers start: 51 outliers final: 44 residues processed: 287 average time/residue: 0.2096 time to fit residues: 96.7459 Evaluate side-chains 291 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 364 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 367 optimal weight: 50.0000 chunk 156 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130238 restraints weight = 36267.007| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.08 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31866 Z= 0.231 Angle : 0.658 9.431 43482 Z= 0.342 Chirality : 0.046 0.206 4952 Planarity : 0.005 0.060 5309 Dihedral : 16.257 177.552 5261 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 1.69 % Allowed : 16.53 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.12 (0.14), residues: 3661 helix: 1.64 (0.13), residues: 1475 sheet: -0.31 (0.25), residues: 440 loop : -1.60 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 45 TYR 0.016 0.002 TYR D 631 PHE 0.020 0.002 PHE A 35 TRP 0.011 0.002 TRP F 433 HIS 0.010 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.23 (31858) covalent geometry : angle 0.65570 / 0.34 (43470) hydrogen bonds : bond 0.06024 / 4.25 ( 1358) hydrogen bonds : angle 4.36140 / 3.03 ( 3828) metal coordination : bond 0.00819 / 0.40 ( 8) metal coordination : angle 3.61389 / 2.12 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7456.84 seconds wall clock time: 128 minutes 21.67 seconds (7701.67 seconds total)