Starting phenix.real_space_refine on Fri Mar 6 17:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkq_23903/03_2026/7mkq_23903.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 133 5.16 5 C 20562 2.51 5 N 5816 2.21 5 O 6308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32822 Number of models: 1 Model: "" Number of chains: 7 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: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10368 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1282} 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: "L" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7696 Classifications: {'peptide': 967} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 931} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 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 55.495 105.983 75.387 1.00133.55 S ATOM 14629 SG CYS D 72 55.698 108.938 73.205 1.00147.04 S ATOM 14737 SG CYS D 85 53.216 106.612 72.497 1.00124.31 S ATOM 14761 SG CYS D 88 56.783 105.846 71.863 1.00128.42 S ATOM 20449 SG CYS D 814 74.737 38.808 78.742 1.00 91.90 S ATOM 21014 SG CYS D 888 76.589 41.984 78.242 1.00 86.28 S ATOM 21065 SG CYS D 895 75.374 40.834 81.327 1.00 88.80 S ATOM 21086 SG CYS D 898 77.975 39.223 80.142 1.00 95.20 S Time building chain proxies: 7.50, per 1000 atoms: 0.23 Number of scatterers: 32822 At special positions: 0 Unit cell: (163.08, 167.4, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 133 16.00 Mg 1 11.99 O 6308 8.00 N 5816 7.00 C 20562 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " 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 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7760 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 51 sheets defined 42.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.247A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.944A 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 159 removed outlier: 3.548A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.075A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.775A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.527A 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: 3.988A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.816A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.556A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.595A 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 206 through 213 removed outlier: 3.889A 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: 3.651A 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: 3.815A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.710A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.593A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.538A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.677A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.952A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 removed outlier: 3.724A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.722A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.669A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.665A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.108A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.642A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.670A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.588A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 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 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.575A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.745A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.651A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.510A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.978A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.788A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) 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 417 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 485 through 489 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 581 Processing helix chain 'D' and resid 588 through 594 removed outlier: 4.327A pdb=" N GLN D 594 " --> pdb=" O ILE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.508A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.815A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.159A 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 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.644A 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 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.655A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.952A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.629A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.505A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.878A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.824A 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: 3.596A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.631A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 18 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'L' and resid 110 through 117 removed outlier: 4.672A pdb=" N LEU L 115 " --> pdb=" O GLN L 112 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE L 116 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 141 removed outlier: 3.748A pdb=" N ARG L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 167 removed outlier: 3.805A pdb=" N ARG L 167 " --> pdb=" O HIS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 Processing helix chain 'L' and resid 208 through 224 removed outlier: 4.523A pdb=" N HIS L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN L 214 " --> pdb=" O THR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 242 removed outlier: 3.523A pdb=" N ASP L 241 " --> pdb=" O GLU L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.557A pdb=" N THR L 248 " --> pdb=" O PRO L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 260 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 281 through 285 Processing helix chain 'L' and resid 293 through 303 removed outlier: 3.826A pdb=" N ALA L 298 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 323 Processing helix chain 'L' and resid 324 through 332 removed outlier: 4.138A pdb=" N LEU L 330 " --> pdb=" O ALA L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 362 removed outlier: 3.528A pdb=" N PHE L 342 " --> pdb=" O ASP L 338 " (cutoff:3.500A) Proline residue: L 351 - end of helix Processing helix chain 'L' and resid 366 through 377 removed outlier: 4.134A pdb=" N MET L 372 " --> pdb=" O ASP L 368 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU L 375 " --> pdb=" O ASN L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 392 removed outlier: 3.527A pdb=" N ALA L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 411 Processing helix chain 'L' and resid 441 through 455 Processing helix chain 'L' and resid 459 through 469 removed outlier: 4.286A pdb=" N TYR L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 472 No H-bonds generated for 'chain 'L' and resid 470 through 472' Processing helix chain 'L' and resid 473 through 478 removed outlier: 3.655A pdb=" N PHE L 477 " --> pdb=" O ILE L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 487 removed outlier: 3.684A pdb=" N PHE L 487 " --> pdb=" O TRP L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 501 removed outlier: 3.850A pdb=" N GLU L 492 " --> pdb=" O ASP L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 512 through 528 Processing helix chain 'L' and resid 539 through 552 Processing helix chain 'L' and resid 586 through 598 removed outlier: 3.517A pdb=" N LEU L 590 " --> pdb=" O ASN L 586 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU L 597 " --> pdb=" O ARG L 593 " (cutoff:3.500A) Processing helix chain 'L' and resid 616 through 628 Processing helix chain 'L' and resid 638 through 656 removed outlier: 5.490A pdb=" N ASN L 648 " --> pdb=" O ASP L 644 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP L 649 " --> pdb=" O SER L 645 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN L 652 " --> pdb=" O ASN L 648 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR L 653 " --> pdb=" O ASP L 649 " (cutoff:3.500A) Processing helix chain 'L' and resid 662 through 683 Processing helix chain 'L' and resid 686 through 694 Processing helix chain 'L' and resid 695 through 710 removed outlier: 3.745A pdb=" N ALA L 699 " --> pdb=" O GLY L 695 " (cutoff:3.500A) Processing helix chain 'L' and resid 712 through 727 removed outlier: 4.135A pdb=" N ILE L 716 " --> pdb=" O ASP L 712 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 721 " --> pdb=" O ALA L 717 " (cutoff:3.500A) Processing helix chain 'L' and resid 764 through 771 Processing helix chain 'L' and resid 781 through 794 Processing helix chain 'L' and resid 827 through 835 removed outlier: 6.215A pdb=" N LEU L 832 " --> pdb=" O GLN L 829 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN L 833 " --> pdb=" O LEU L 830 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 834 " --> pdb=" O GLN L 831 " (cutoff:3.500A) Processing helix chain 'L' and resid 857 through 864 removed outlier: 3.857A pdb=" N GLN L 864 " --> pdb=" O THR L 860 " (cutoff:3.500A) Processing helix chain 'L' and resid 869 through 879 removed outlier: 3.731A pdb=" N LYS L 875 " --> pdb=" O HIS L 871 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN L 878 " --> pdb=" O SER L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 880 through 926 removed outlier: 3.769A pdb=" N HIS L 885 " --> pdb=" O GLN L 881 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA L 886 " --> pdb=" O GLN L 882 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN L 889 " --> pdb=" O HIS L 885 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU L 890 " --> pdb=" O ALA L 886 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY L 891 " --> pdb=" O ILE L 887 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 893 " --> pdb=" O GLN L 889 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN L 894 " --> pdb=" O LEU L 890 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU L 896 " --> pdb=" O GLU L 892 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS L 897 " --> pdb=" O ALA L 893 " (cutoff:3.500A) Processing helix chain 'L' and resid 932 through 951 removed outlier: 3.609A pdb=" N LEU L 936 " --> pdb=" O ARG L 932 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.672A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.892A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.215A 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 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.690A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.784A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 6.067A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (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 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.573A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.144A 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: 5.129A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.129A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (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 451 through 454 removed outlier: 6.503A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.514A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.173A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.593A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.020A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.854A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.828A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.812A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.823A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 888 removed outlier: 4.163A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.734A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.386A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 147 removed outlier: 4.215A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.210A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.700A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.325A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 4.136A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1186 through 1190 removed outlier: 4.359A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AE9, first strand: chain 'L' and resid 40 through 44 removed outlier: 6.818A pdb=" N THR L 29 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL L 25 " --> pdb=" O THR L 29 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR L 31 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 60 through 62 removed outlier: 7.296A pdb=" N ILE L 84 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL L 74 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR L 82 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU L 76 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU L 81 " --> pdb=" O ARG L 98 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG L 98 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR L 83 " --> pdb=" O ALA L 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 96 " --> pdb=" O TYR L 83 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY L 85 " --> pdb=" O GLY L 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 228 through 229 removed outlier: 3.584A pdb=" N ILE L 253 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL L 203 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N CYS L 254 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE L 205 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU L 277 " --> pdb=" O LEU L 310 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU L 312 " --> pdb=" O LEU L 277 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL L 279 " --> pdb=" O LEU L 312 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N PHE L 418 " --> pdb=" O ARG L 172 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU L 174 " --> pdb=" O PHE L 418 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 431 through 438 removed outlier: 6.796A pdb=" N GLU L 432 " --> pdb=" O ILE L 608 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL L 610 " --> pdb=" O GLU L 432 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS L 434 " --> pdb=" O VAL L 610 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR L 612 " --> pdb=" O HIS L 434 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE L 436 " --> pdb=" O TYR L 612 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 531 through 532 removed outlier: 3.635A pdb=" N ALA L 532 " --> pdb=" O VAL L 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 729 through 732 removed outlier: 7.093A pdb=" N THR L 760 " --> pdb=" O GLN L 775 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 799 through 804 removed outlier: 3.523A pdb=" N THR L 800 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE L 819 " --> pdb=" O ASP L 958 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU L 960 " --> pdb=" O GLU L 817 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 817 " --> pdb=" O LEU L 960 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU L 962 " --> pdb=" O LEU L 815 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU L 815 " --> pdb=" O LEU L 962 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7000 1.33 - 1.45: 6896 1.45 - 1.57: 19205 1.57 - 1.69: 1 1.69 - 1.81: 233 Bond restraints: 33335 Sorted by residual: bond pdb=" N GLU B 29 " pdb=" CA GLU B 29 " ideal model delta sigma weight residual 1.461 1.494 -0.032 9.20e-03 1.18e+04 1.25e+01 bond pdb=" N VAL C1159 " pdb=" CA VAL C1159 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N THR B 27 " pdb=" CA THR B 27 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.88e+00 bond pdb=" N VAL C 939 " pdb=" CA VAL C 939 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.06e+00 ... (remaining 33330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 44697 3.79 - 7.58: 324 7.58 - 11.37: 31 11.37 - 15.16: 3 15.16 - 18.96: 2 Bond angle restraints: 45057 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 101.22 10.78 1.40e+00 5.10e-01 5.93e+01 angle pdb=" CA GLN C 46 " pdb=" CB GLN C 46 " pdb=" CG GLN C 46 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" N GLU L 912 " pdb=" CA GLU L 912 " pdb=" CB GLU L 912 " ideal model delta sigma weight residual 109.98 118.07 -8.09 1.45e+00 4.76e-01 3.11e+01 angle pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " pdb=" CD ARG D 77 " ideal model delta sigma weight residual 111.30 98.84 12.46 2.30e+00 1.89e-01 2.93e+01 angle pdb=" CA VAL C1159 " pdb=" C VAL C1159 " pdb=" O VAL C1159 " ideal model delta sigma weight residual 121.63 116.73 4.90 9.90e-01 1.02e+00 2.45e+01 ... (remaining 45052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18381 17.98 - 35.95: 1655 35.95 - 53.93: 329 53.93 - 71.91: 82 71.91 - 89.89: 46 Dihedral angle restraints: 20493 sinusoidal: 8455 harmonic: 12038 Sorted by residual: dihedral pdb=" CA LEU L 560 " pdb=" C LEU L 560 " pdb=" N LEU L 561 " pdb=" CA LEU L 561 " ideal model delta harmonic sigma weight residual 180.00 124.47 55.53 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLU L 564 " pdb=" C GLU L 564 " pdb=" N ILE L 565 " pdb=" CA ILE L 565 " ideal model delta harmonic sigma weight residual -180.00 -126.08 -53.92 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 ... (remaining 20490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4318 0.069 - 0.138: 732 0.138 - 0.207: 52 0.207 - 0.275: 6 0.275 - 0.344: 1 Chirality restraints: 5109 Sorted by residual: chirality pdb=" CA GLU L 912 " pdb=" N GLU L 912 " pdb=" C GLU L 912 " pdb=" CB GLU L 912 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE C1076 " pdb=" CA ILE C1076 " pdb=" CG1 ILE C1076 " pdb=" CG2 ILE C1076 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ASP C1160 " pdb=" N ASP C1160 " pdb=" C ASP C1160 " pdb=" CB ASP C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 5106 not shown) Planarity restraints: 5943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.06e-01 6.77e+01 pdb=" N PRO D 758 " 0.355 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.095 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 938 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLY C 938 " -0.074 2.00e-02 2.50e+03 pdb=" O GLY C 938 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL C 939 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 908 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ASN L 908 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN L 908 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU L 909 " -0.025 2.00e-02 2.50e+03 ... (remaining 5940 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 373 2.59 - 3.17: 29183 3.17 - 3.74: 49979 3.74 - 4.32: 67311 4.32 - 4.90: 109909 Nonbonded interactions: 256755 Sorted by model distance: nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.010 3.040 nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D2001 " model vdw 2.029 2.170 nonbonded pdb=" O LEU D1344 " pdb=" N GLY D1346 " model vdw 2.082 3.120 nonbonded pdb=" O PHE D 773 " pdb=" OG1 THR D 776 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR C 301 " pdb=" OE1 GLU C 334 " model vdw 2.106 3.040 ... (remaining 256750 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.110 Find NCS groups from input model: 0.270 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.368 33343 Z= 0.219 Angle : 0.908 18.956 45069 Z= 0.493 Chirality : 0.050 0.344 5109 Planarity : 0.006 0.206 5943 Dihedral : 15.073 89.886 12733 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.99 % Favored : 92.58 % Rotamer: Outliers : 1.16 % Allowed : 1.44 % Favored : 97.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.11), residues: 4166 helix: -0.92 (0.11), residues: 1544 sheet: -0.79 (0.21), residues: 507 loop : -2.38 (0.11), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 905 TYR 0.026 0.002 TYR D 46 PHE 0.041 0.002 PHE C 225 TRP 0.058 0.002 TRP L 624 HIS 0.026 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00388 (33335) covalent geometry : angle 0.90810 (45057) hydrogen bonds : bond 0.15407 ( 1457) hydrogen bonds : angle 7.13575 ( 4122) metal coordination : bond 0.18095 ( 8) metal coordination : angle 1.76192 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 746 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9682 (mp) cc_final: 0.8868 (tt) REVERT: A 83 LEU cc_start: 0.9606 (mt) cc_final: 0.9233 (mm) REVERT: A 86 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8786 (tppt) REVERT: A 177 TYR cc_start: 0.8863 (m-10) cc_final: 0.8447 (m-10) REVERT: B 27 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7638 (p) REVERT: B 85 LEU cc_start: 0.9317 (mt) cc_final: 0.9037 (tt) REVERT: B 177 TYR cc_start: 0.7962 (m-80) cc_final: 0.7581 (m-10) REVERT: C 27 LEU cc_start: 0.9071 (mt) cc_final: 0.8549 (mt) REVERT: C 146 VAL cc_start: 0.8656 (m) cc_final: 0.8438 (p) REVERT: C 171 LEU cc_start: 0.7365 (mp) cc_final: 0.6927 (mm) REVERT: C 290 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7617 (pp20) REVERT: C 357 ASN cc_start: 0.8636 (m-40) cc_final: 0.8390 (p0) REVERT: C 369 MET cc_start: 0.5935 (ttt) cc_final: 0.5616 (mmp) REVERT: C 439 LYS cc_start: 0.8120 (mppt) cc_final: 0.7532 (tptp) REVERT: C 459 MET cc_start: 0.9170 (mtp) cc_final: 0.8745 (mmm) REVERT: C 488 MET cc_start: 0.7977 (tpt) cc_final: 0.7775 (mmp) REVERT: C 659 GLN cc_start: 0.8650 (pt0) cc_final: 0.8412 (tm-30) REVERT: C 763 THR cc_start: 0.9198 (p) cc_final: 0.8915 (t) REVERT: C 781 ASP cc_start: 0.7675 (m-30) cc_final: 0.6878 (m-30) REVERT: C 820 GLU cc_start: 0.8680 (tt0) cc_final: 0.7824 (tp30) REVERT: C 882 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 884 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8657 (m) REVERT: C 909 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7078 (tppt) REVERT: C 916 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7510 (t) REVERT: C 1019 ASP cc_start: 0.9111 (t0) cc_final: 0.8821 (m-30) REVERT: C 1054 LEU cc_start: 0.8948 (mp) cc_final: 0.8706 (tt) REVERT: C 1131 MET cc_start: 0.8228 (ptm) cc_final: 0.7681 (ptm) REVERT: C 1151 LEU cc_start: 0.6947 (tp) cc_final: 0.6613 (mt) REVERT: C 1232 MET cc_start: 0.8213 (mtp) cc_final: 0.6369 (mtp) REVERT: C 1233 LEU cc_start: 0.9443 (mp) cc_final: 0.8992 (mp) REVERT: C 1235 LEU cc_start: 0.9276 (mt) cc_final: 0.9070 (mm) REVERT: C 1243 MET cc_start: 0.8018 (tmm) cc_final: 0.7410 (tmm) REVERT: C 1287 LEU cc_start: 0.9292 (tp) cc_final: 0.9040 (tp) REVERT: C 1289 GLU cc_start: 0.9306 (pt0) cc_final: 0.9033 (pp20) REVERT: C 1290 MET cc_start: 0.9032 (tpp) cc_final: 0.8818 (mmm) REVERT: C 1293 VAL cc_start: 0.9604 (t) cc_final: 0.9404 (p) REVERT: D 56 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (tp) REVERT: D 347 VAL cc_start: 0.9435 (m) cc_final: 0.8964 (p) REVERT: D 348 ASP cc_start: 0.8777 (m-30) cc_final: 0.8281 (m-30) REVERT: D 349 TYR cc_start: 0.8688 (m-80) cc_final: 0.8429 (m-10) REVERT: D 363 LEU cc_start: 0.9040 (tp) cc_final: 0.8710 (tp) REVERT: D 425 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8751 (tmm-80) REVERT: D 434 ILE cc_start: 0.9094 (mt) cc_final: 0.8873 (tp) REVERT: D 500 ILE cc_start: 0.9430 (pt) cc_final: 0.8991 (mp) REVERT: D 534 GLU cc_start: 0.8910 (tt0) cc_final: 0.8694 (tm-30) REVERT: D 579 LEU cc_start: 0.9641 (tp) cc_final: 0.9427 (tp) REVERT: D 582 ILE cc_start: 0.9298 (pt) cc_final: 0.9084 (mt) REVERT: D 596 LEU cc_start: 0.9397 (mt) cc_final: 0.9174 (tp) REVERT: D 622 ASP cc_start: 0.9188 (m-30) cc_final: 0.8940 (t0) REVERT: D 725 MET cc_start: 0.8590 (mtm) cc_final: 0.8360 (mtm) REVERT: D 768 ASN cc_start: 0.9045 (p0) cc_final: 0.8651 (m-40) REVERT: D 822 MET cc_start: 0.8781 (ttt) cc_final: 0.8516 (tpp) REVERT: D 1063 ASP cc_start: 0.6327 (t0) cc_final: 0.6045 (p0) REVERT: D 1090 ILE cc_start: 0.6277 (mm) cc_final: 0.6017 (mm) REVERT: D 1257 VAL cc_start: 0.9639 (t) cc_final: 0.9247 (m) REVERT: D 1282 TYR cc_start: 0.8098 (m-80) cc_final: 0.7893 (m-80) REVERT: E 3 ARG cc_start: 0.8595 (tpm170) cc_final: 0.7976 (tpp80) REVERT: E 5 THR cc_start: 0.8681 (m) cc_final: 0.8097 (m) REVERT: E 6 VAL cc_start: 0.8521 (m) cc_final: 0.8237 (m) REVERT: E 15 ASN cc_start: 0.6120 (t0) cc_final: 0.5916 (t0) REVERT: E 18 ASP cc_start: 0.8896 (p0) cc_final: 0.8671 (p0) REVERT: E 31 GLN cc_start: 0.8517 (tt0) cc_final: 0.8254 (tm-30) REVERT: E 45 LYS cc_start: 0.7022 (mtmt) cc_final: 0.6433 (mmtp) REVERT: E 48 VAL cc_start: 0.8799 (t) cc_final: 0.8031 (m) REVERT: L 77 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7847 (pm20) REVERT: L 185 ILE cc_start: 0.9636 (mt) cc_final: 0.9406 (mm) REVERT: L 358 MET cc_start: 0.8812 (mmt) cc_final: 0.8536 (mmp) REVERT: L 376 MET cc_start: 0.6737 (mmp) cc_final: 0.6519 (mmm) REVERT: L 509 ILE cc_start: 0.9090 (mt) cc_final: 0.8560 (tt) REVERT: L 594 ILE cc_start: 0.9354 (mt) cc_final: 0.8991 (tp) REVERT: L 732 ASP cc_start: 0.8745 (t0) cc_final: 0.7994 (p0) REVERT: L 942 ASN cc_start: 0.9286 (t0) cc_final: 0.9032 (t0) outliers start: 41 outliers final: 9 residues processed: 782 average time/residue: 0.2493 time to fit residues: 298.7763 Evaluate side-chains 388 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 462 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN D 667 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1227 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 397 GLN L 401 GLN L 786 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.061503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045365 restraints weight = 215993.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046621 restraints weight = 131700.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047446 restraints weight = 91645.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048042 restraints weight = 70989.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048429 restraints weight = 59370.319| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33343 Z= 0.222 Angle : 0.791 12.540 45069 Z= 0.405 Chirality : 0.046 0.378 5109 Planarity : 0.006 0.095 5943 Dihedral : 5.483 42.480 4581 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 0.14 % Allowed : 6.03 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4166 helix: 0.35 (0.13), residues: 1623 sheet: -0.37 (0.21), residues: 550 loop : -1.84 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C 359 TYR 0.018 0.002 TYR B 152 PHE 0.021 0.002 PHE L 572 TRP 0.025 0.002 TRP L 624 HIS 0.011 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00474 (33335) covalent geometry : angle 0.78912 (45057) hydrogen bonds : bond 0.04792 ( 1457) hydrogen bonds : angle 5.68473 ( 4122) metal coordination : bond 0.01449 ( 8) metal coordination : angle 3.76603 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 404 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9776 (mp) cc_final: 0.9205 (tt) REVERT: A 95 LYS cc_start: 0.8903 (mppt) cc_final: 0.8532 (mppt) REVERT: A 177 TYR cc_start: 0.9111 (m-10) cc_final: 0.8364 (m-10) REVERT: B 51 MET cc_start: 0.8593 (mmm) cc_final: 0.8347 (tpt) REVERT: B 137 ASN cc_start: 0.8352 (p0) cc_final: 0.8036 (p0) REVERT: B 177 TYR cc_start: 0.8455 (m-80) cc_final: 0.7980 (m-80) REVERT: B 227 GLN cc_start: 0.8932 (mp10) cc_final: 0.8627 (mp10) REVERT: C 40 GLU cc_start: 0.7382 (tp30) cc_final: 0.7137 (tm-30) REVERT: C 47 TYR cc_start: 0.8127 (m-10) cc_final: 0.7875 (m-80) REVERT: C 290 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7532 (pp20) REVERT: C 439 LYS cc_start: 0.8136 (mppt) cc_final: 0.7663 (tptp) REVERT: C 459 MET cc_start: 0.9441 (mtp) cc_final: 0.8857 (mmm) REVERT: C 587 LEU cc_start: 0.9483 (tp) cc_final: 0.9278 (tp) REVERT: C 681 MET cc_start: 0.8724 (mtp) cc_final: 0.8426 (ttm) REVERT: C 800 MET cc_start: 0.7924 (mpp) cc_final: 0.7617 (mpp) REVERT: C 820 GLU cc_start: 0.9505 (tt0) cc_final: 0.8726 (tm-30) REVERT: C 883 LEU cc_start: 0.8883 (mt) cc_final: 0.8318 (mt) REVERT: C 951 MET cc_start: 0.9343 (tpp) cc_final: 0.8669 (tmm) REVERT: C 1019 ASP cc_start: 0.9100 (t0) cc_final: 0.8443 (t0) REVERT: C 1101 LEU cc_start: 0.9175 (mt) cc_final: 0.8936 (mt) REVERT: C 1151 LEU cc_start: 0.6696 (tp) cc_final: 0.6164 (mt) REVERT: C 1232 MET cc_start: 0.7940 (mtp) cc_final: 0.7277 (mtp) REVERT: C 1243 MET cc_start: 0.8692 (tmm) cc_final: 0.8454 (tmm) REVERT: C 1279 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9057 (mt-10) REVERT: C 1289 GLU cc_start: 0.9485 (pt0) cc_final: 0.9075 (pp20) REVERT: C 1306 LYS cc_start: 0.9551 (mmtt) cc_final: 0.9325 (pptt) REVERT: D 29 MET cc_start: 0.9405 (mtp) cc_final: 0.9174 (mtp) REVERT: D 116 PHE cc_start: 0.8594 (m-80) cc_final: 0.8321 (m-80) REVERT: D 348 ASP cc_start: 0.8832 (m-30) cc_final: 0.8102 (m-30) REVERT: D 349 TYR cc_start: 0.9144 (m-80) cc_final: 0.8745 (m-10) REVERT: D 363 LEU cc_start: 0.9215 (tp) cc_final: 0.8938 (tp) REVERT: D 466 MET cc_start: 0.9282 (tpt) cc_final: 0.9038 (mmm) REVERT: D 500 ILE cc_start: 0.9708 (pt) cc_final: 0.9420 (mp) REVERT: D 534 GLU cc_start: 0.9506 (tt0) cc_final: 0.8968 (tm-30) REVERT: D 622 ASP cc_start: 0.9329 (m-30) cc_final: 0.9017 (t0) REVERT: D 725 MET cc_start: 0.8919 (mtm) cc_final: 0.8416 (mtt) REVERT: D 822 MET cc_start: 0.9223 (ttt) cc_final: 0.8761 (tpp) REVERT: D 913 GLU cc_start: 0.8262 (tp30) cc_final: 0.7894 (tm-30) REVERT: D 1063 ASP cc_start: 0.7025 (t0) cc_final: 0.6416 (p0) REVERT: D 1100 PHE cc_start: 0.7373 (t80) cc_final: 0.6220 (t80) REVERT: D 1260 MET cc_start: 0.8694 (tpp) cc_final: 0.8358 (tpt) REVERT: D 1282 TYR cc_start: 0.8245 (m-80) cc_final: 0.7979 (m-80) REVERT: E 3 ARG cc_start: 0.8627 (tpm170) cc_final: 0.8141 (tpt170) REVERT: E 5 THR cc_start: 0.8808 (m) cc_final: 0.6764 (m) REVERT: E 15 ASN cc_start: 0.6710 (t0) cc_final: 0.6506 (t0) REVERT: E 31 GLN cc_start: 0.8680 (tt0) cc_final: 0.8185 (tm-30) REVERT: E 45 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7058 (mmtp) REVERT: E 53 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7925 (mt-10) REVERT: L 68 GLN cc_start: 0.8789 (mt0) cc_final: 0.8426 (mp10) REVERT: L 185 ILE cc_start: 0.9685 (mt) cc_final: 0.9468 (mm) REVERT: L 195 LEU cc_start: 0.8892 (mm) cc_final: 0.8648 (mm) REVERT: L 218 GLU cc_start: 0.7579 (pp20) cc_final: 0.6439 (pp20) REVERT: L 358 MET cc_start: 0.9106 (mmt) cc_final: 0.8873 (mmp) REVERT: L 376 MET cc_start: 0.6879 (mmp) cc_final: 0.6212 (mtt) REVERT: L 406 MET cc_start: 0.9306 (mtm) cc_final: 0.9082 (mtp) REVERT: L 467 MET cc_start: 0.8464 (tmm) cc_final: 0.7925 (tmm) REVERT: L 486 ASN cc_start: 0.8336 (m110) cc_final: 0.8035 (m-40) REVERT: L 578 MET cc_start: 0.8629 (tmm) cc_final: 0.8340 (tmm) REVERT: L 720 MET cc_start: 0.9450 (ppp) cc_final: 0.9118 (ppp) REVERT: L 732 ASP cc_start: 0.9028 (t0) cc_final: 0.8070 (p0) REVERT: L 912 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: L 942 ASN cc_start: 0.9386 (t0) cc_final: 0.9119 (t0) outliers start: 5 outliers final: 0 residues processed: 409 average time/residue: 0.2385 time to fit residues: 154.4343 Evaluate side-chains 268 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 68 optimal weight: 0.9980 chunk 328 optimal weight: 30.0000 chunk 234 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 228 optimal weight: 0.0980 chunk 366 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 377 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 932 GLN C1288 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 786 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045202 restraints weight = 213950.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046424 restraints weight = 131229.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047275 restraints weight = 92256.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047788 restraints weight = 71340.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048176 restraints weight = 60165.651| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33343 Z= 0.174 Angle : 0.692 11.908 45069 Z= 0.358 Chirality : 0.044 0.287 5109 Planarity : 0.005 0.059 5943 Dihedral : 5.216 36.665 4581 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.72 (0.13), residues: 4166 helix: 0.67 (0.13), residues: 1620 sheet: -0.06 (0.21), residues: 542 loop : -1.60 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 260 TYR 0.016 0.002 TYR D 46 PHE 0.018 0.002 PHE A 231 TRP 0.017 0.001 TRP C1276 HIS 0.015 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00373 (33335) covalent geometry : angle 0.69020 (45057) hydrogen bonds : bond 0.04325 ( 1457) hydrogen bonds : angle 5.35297 ( 4122) metal coordination : bond 0.01083 ( 8) metal coordination : angle 3.13559 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9715 (mp) cc_final: 0.9230 (tt) REVERT: A 102 LEU cc_start: 0.8817 (tp) cc_final: 0.8298 (pp) REVERT: A 177 TYR cc_start: 0.9235 (m-10) cc_final: 0.8354 (m-10) REVERT: B 51 MET cc_start: 0.8634 (mmm) cc_final: 0.8363 (tpt) REVERT: B 177 TYR cc_start: 0.8221 (m-80) cc_final: 0.7793 (m-10) REVERT: C 47 TYR cc_start: 0.8116 (m-10) cc_final: 0.7864 (m-80) REVERT: C 459 MET cc_start: 0.9456 (mtp) cc_final: 0.8948 (mmm) REVERT: C 490 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8634 (pm20) REVERT: C 681 MET cc_start: 0.8877 (mtp) cc_final: 0.8627 (ttm) REVERT: C 800 MET cc_start: 0.7987 (mpp) cc_final: 0.7675 (mpp) REVERT: C 883 LEU cc_start: 0.9031 (mt) cc_final: 0.8546 (mt) REVERT: C 892 GLU cc_start: 0.7872 (pt0) cc_final: 0.7424 (pp20) REVERT: C 1019 ASP cc_start: 0.9211 (t0) cc_final: 0.8404 (t0) REVERT: C 1066 MET cc_start: 0.8515 (tpt) cc_final: 0.7555 (tpp) REVERT: C 1101 LEU cc_start: 0.9182 (mt) cc_final: 0.8940 (mt) REVERT: C 1131 MET cc_start: 0.8631 (ptp) cc_final: 0.8323 (ptp) REVERT: C 1151 LEU cc_start: 0.6793 (tp) cc_final: 0.6491 (mt) REVERT: C 1232 MET cc_start: 0.8443 (mtp) cc_final: 0.8003 (mtp) REVERT: C 1233 LEU cc_start: 0.9638 (mp) cc_final: 0.9081 (mm) REVERT: C 1279 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8976 (mt-10) REVERT: C 1285 TYR cc_start: 0.9020 (m-80) cc_final: 0.8472 (m-10) REVERT: C 1287 LEU cc_start: 0.9320 (tp) cc_final: 0.9101 (tp) REVERT: C 1289 GLU cc_start: 0.9529 (pt0) cc_final: 0.9249 (pt0) REVERT: C 1304 MET cc_start: 0.8466 (tpp) cc_final: 0.8139 (mmm) REVERT: D 29 MET cc_start: 0.9418 (mtp) cc_final: 0.9206 (mtp) REVERT: D 349 TYR cc_start: 0.9188 (m-80) cc_final: 0.8897 (m-10) REVERT: D 363 LEU cc_start: 0.9201 (tp) cc_final: 0.8968 (tp) REVERT: D 372 MET cc_start: 0.8435 (mmm) cc_final: 0.8158 (mmp) REVERT: D 485 MET cc_start: 0.9040 (mmm) cc_final: 0.8777 (mmm) REVERT: D 622 ASP cc_start: 0.9423 (m-30) cc_final: 0.9026 (t0) REVERT: D 698 MET cc_start: 0.9420 (tpt) cc_final: 0.9152 (tpp) REVERT: D 725 MET cc_start: 0.8933 (mtm) cc_final: 0.8434 (mtt) REVERT: D 864 LEU cc_start: 0.9438 (mm) cc_final: 0.9135 (tp) REVERT: D 869 CYS cc_start: 0.8844 (m) cc_final: 0.8564 (m) REVERT: D 915 ILE cc_start: 0.9674 (pt) cc_final: 0.9197 (mt) REVERT: D 917 VAL cc_start: 0.9583 (m) cc_final: 0.9246 (p) REVERT: D 1063 ASP cc_start: 0.7128 (t0) cc_final: 0.6434 (p0) REVERT: D 1260 MET cc_start: 0.8994 (tpp) cc_final: 0.8641 (tpt) REVERT: D 1282 TYR cc_start: 0.8453 (m-80) cc_final: 0.8116 (m-80) REVERT: D 1370 MET cc_start: 0.9499 (mtm) cc_final: 0.8994 (mtt) REVERT: E 3 ARG cc_start: 0.8636 (tpm170) cc_final: 0.8205 (tpt170) REVERT: E 5 THR cc_start: 0.8863 (m) cc_final: 0.6904 (m) REVERT: E 31 GLN cc_start: 0.8621 (tt0) cc_final: 0.7861 (tm-30) REVERT: E 35 LYS cc_start: 0.5973 (mmtt) cc_final: 0.5683 (mmtm) REVERT: E 53 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7623 (mt-10) REVERT: L 34 PHE cc_start: 0.8961 (m-80) cc_final: 0.8647 (m-10) REVERT: L 68 GLN cc_start: 0.8809 (mt0) cc_final: 0.8445 (mp10) REVERT: L 189 MET cc_start: 0.9240 (mtm) cc_final: 0.9037 (mtm) REVERT: L 195 LEU cc_start: 0.8900 (mm) cc_final: 0.8550 (mm) REVERT: L 214 GLN cc_start: 0.9204 (mp10) cc_final: 0.8957 (mp10) REVERT: L 225 LEU cc_start: 0.9374 (mt) cc_final: 0.8859 (mt) REVERT: L 376 MET cc_start: 0.6840 (mmp) cc_final: 0.6116 (mtt) REVERT: L 395 ASP cc_start: 0.8768 (t0) cc_final: 0.7474 (p0) REVERT: L 406 MET cc_start: 0.9353 (mtm) cc_final: 0.9062 (mtp) REVERT: L 538 MET cc_start: 0.8697 (mtp) cc_final: 0.8455 (mtp) REVERT: L 720 MET cc_start: 0.9484 (ppp) cc_final: 0.9074 (ppp) REVERT: L 732 ASP cc_start: 0.9102 (t0) cc_final: 0.8007 (p0) REVERT: L 746 MET cc_start: 0.6586 (mtm) cc_final: 0.6259 (mtt) REVERT: L 942 ASN cc_start: 0.9431 (t0) cc_final: 0.9159 (t0) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.2205 time to fit residues: 128.0821 Evaluate side-chains 252 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 95 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 521 GLN L 558 GLN L 602 GLN L 786 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.043801 restraints weight = 218634.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045033 restraints weight = 130333.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045908 restraints weight = 89919.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046438 restraints weight = 68908.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046856 restraints weight = 57602.608| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 33343 Z= 0.201 Angle : 0.700 11.825 45069 Z= 0.359 Chirality : 0.044 0.320 5109 Planarity : 0.005 0.061 5943 Dihedral : 5.242 32.236 4581 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.69 (0.13), residues: 4166 helix: 0.65 (0.13), residues: 1628 sheet: 0.07 (0.22), residues: 536 loop : -1.56 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 69 TYR 0.016 0.002 TYR B 152 PHE 0.017 0.002 PHE A 231 TRP 0.011 0.001 TRP L 215 HIS 0.015 0.002 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00427 (33335) covalent geometry : angle 0.69797 (45057) hydrogen bonds : bond 0.04246 ( 1457) hydrogen bonds : angle 5.37100 ( 4122) metal coordination : bond 0.01268 ( 8) metal coordination : angle 3.68664 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9741 (mp) cc_final: 0.9300 (tt) REVERT: A 95 LYS cc_start: 0.8914 (mppt) cc_final: 0.8526 (mppt) REVERT: B 51 MET cc_start: 0.8686 (mmm) cc_final: 0.8406 (mmm) REVERT: B 177 TYR cc_start: 0.8135 (m-80) cc_final: 0.7867 (m-10) REVERT: C 47 TYR cc_start: 0.8000 (m-10) cc_final: 0.7774 (m-80) REVERT: C 459 MET cc_start: 0.9488 (mtp) cc_final: 0.8808 (mmp) REVERT: C 490 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8754 (pm20) REVERT: C 492 MET cc_start: 0.7100 (ptp) cc_final: 0.6877 (ptt) REVERT: C 515 MET cc_start: 0.8983 (tmm) cc_final: 0.7167 (tmm) REVERT: C 523 GLU cc_start: 0.9270 (pt0) cc_final: 0.8845 (mm-30) REVERT: C 883 LEU cc_start: 0.9180 (mt) cc_final: 0.8694 (mt) REVERT: C 892 GLU cc_start: 0.7913 (pt0) cc_final: 0.7597 (pp20) REVERT: C 1066 MET cc_start: 0.8625 (tpt) cc_final: 0.7536 (tpp) REVERT: C 1101 LEU cc_start: 0.9182 (mt) cc_final: 0.8945 (mt) REVERT: C 1131 MET cc_start: 0.8661 (ptp) cc_final: 0.8317 (ptp) REVERT: C 1151 LEU cc_start: 0.7008 (tp) cc_final: 0.6522 (mt) REVERT: C 1232 MET cc_start: 0.8568 (mtp) cc_final: 0.8039 (mtp) REVERT: C 1233 LEU cc_start: 0.9670 (mp) cc_final: 0.9143 (mm) REVERT: C 1279 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8995 (mt-10) REVERT: C 1285 TYR cc_start: 0.8962 (m-80) cc_final: 0.8376 (m-10) REVERT: C 1287 LEU cc_start: 0.9362 (tp) cc_final: 0.9097 (tp) REVERT: C 1289 GLU cc_start: 0.9547 (pt0) cc_final: 0.9283 (pt0) REVERT: C 1304 MET cc_start: 0.8463 (tpp) cc_final: 0.8234 (mmm) REVERT: D 29 MET cc_start: 0.9388 (mtp) cc_final: 0.9157 (mtp) REVERT: D 349 TYR cc_start: 0.9090 (m-80) cc_final: 0.8847 (m-10) REVERT: D 363 LEU cc_start: 0.9145 (tp) cc_final: 0.8846 (tp) REVERT: D 372 MET cc_start: 0.8764 (mmm) cc_final: 0.8394 (mmp) REVERT: D 484 MET cc_start: 0.9286 (mmm) cc_final: 0.8866 (mmm) REVERT: D 622 ASP cc_start: 0.9414 (m-30) cc_final: 0.9032 (t0) REVERT: D 725 MET cc_start: 0.8958 (mtm) cc_final: 0.8487 (mtt) REVERT: D 917 VAL cc_start: 0.9604 (m) cc_final: 0.9304 (p) REVERT: D 1063 ASP cc_start: 0.7126 (t0) cc_final: 0.6376 (p0) REVERT: D 1188 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8181 (mm-30) REVERT: D 1189 MET cc_start: 0.8179 (ttt) cc_final: 0.7763 (ttt) REVERT: D 1260 MET cc_start: 0.8915 (tpp) cc_final: 0.8454 (tpt) REVERT: D 1282 TYR cc_start: 0.8455 (m-80) cc_final: 0.8203 (m-80) REVERT: D 1370 MET cc_start: 0.9505 (mtm) cc_final: 0.8972 (mtt) REVERT: E 3 ARG cc_start: 0.8690 (tpm170) cc_final: 0.8264 (tpt170) REVERT: E 5 THR cc_start: 0.8906 (m) cc_final: 0.7068 (m) REVERT: E 31 GLN cc_start: 0.8489 (tt0) cc_final: 0.8159 (tm-30) REVERT: E 53 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7663 (mt-10) REVERT: L 68 GLN cc_start: 0.8781 (mt0) cc_final: 0.8381 (mp10) REVERT: L 195 LEU cc_start: 0.8949 (mm) cc_final: 0.8632 (mm) REVERT: L 214 GLN cc_start: 0.9152 (mp10) cc_final: 0.8944 (mp10) REVERT: L 358 MET cc_start: 0.9136 (mmt) cc_final: 0.8894 (mmp) REVERT: L 376 MET cc_start: 0.7149 (mmp) cc_final: 0.6482 (mtt) REVERT: L 395 ASP cc_start: 0.8794 (t0) cc_final: 0.7556 (p0) REVERT: L 406 MET cc_start: 0.9357 (mtm) cc_final: 0.9073 (mtp) REVERT: L 467 MET cc_start: 0.8538 (tmm) cc_final: 0.7921 (tmm) REVERT: L 579 VAL cc_start: 0.9539 (p) cc_final: 0.9338 (p) REVERT: L 720 MET cc_start: 0.9454 (ppp) cc_final: 0.8964 (ppp) REVERT: L 732 ASP cc_start: 0.9074 (t0) cc_final: 0.7990 (p0) REVERT: L 942 ASN cc_start: 0.9460 (t0) cc_final: 0.9173 (t0) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2191 time to fit residues: 114.6500 Evaluate side-chains 223 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 394 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 379 optimal weight: 0.9980 chunk 410 optimal weight: 10.0000 chunk 405 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 103 ASN C 46 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C 932 GLN C 952 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN E 29 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 786 ASN L 889 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043772 restraints weight = 221812.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.044964 restraints weight = 134962.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045764 restraints weight = 94198.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046231 restraints weight = 73066.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046629 restraints weight = 62142.784| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 33343 Z= 0.190 Angle : 0.679 13.853 45069 Z= 0.350 Chirality : 0.044 0.293 5109 Planarity : 0.005 0.061 5943 Dihedral : 5.216 29.873 4581 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4166 helix: 0.67 (0.13), residues: 1632 sheet: 0.09 (0.22), residues: 539 loop : -1.52 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 222 TYR 0.017 0.002 TYR D 899 PHE 0.019 0.002 PHE L 572 TRP 0.023 0.002 TRP C1276 HIS 0.013 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00410 (33335) covalent geometry : angle 0.67714 (45057) hydrogen bonds : bond 0.04130 ( 1457) hydrogen bonds : angle 5.35467 ( 4122) metal coordination : bond 0.01778 ( 8) metal coordination : angle 3.03787 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8942 (mppt) cc_final: 0.8539 (mppt) REVERT: B 177 TYR cc_start: 0.8070 (m-80) cc_final: 0.7670 (m-80) REVERT: B 188 GLU cc_start: 0.8130 (mp0) cc_final: 0.7888 (mp0) REVERT: C 47 TYR cc_start: 0.8001 (m-10) cc_final: 0.7759 (m-80) REVERT: C 459 MET cc_start: 0.9510 (mtp) cc_final: 0.8843 (mmp) REVERT: C 653 MET cc_start: 0.9354 (ptt) cc_final: 0.8850 (ppp) REVERT: C 800 MET cc_start: 0.7913 (mpp) cc_final: 0.7567 (mpp) REVERT: C 892 GLU cc_start: 0.7861 (pt0) cc_final: 0.7546 (pp20) REVERT: C 951 MET cc_start: 0.9356 (tpp) cc_final: 0.8806 (tmm) REVERT: C 1023 HIS cc_start: 0.8681 (m-70) cc_final: 0.8441 (m-70) REVERT: C 1066 MET cc_start: 0.8552 (tpt) cc_final: 0.7579 (tpp) REVERT: C 1101 LEU cc_start: 0.9137 (mt) cc_final: 0.8917 (mt) REVERT: C 1108 ASN cc_start: 0.8485 (p0) cc_final: 0.8224 (p0) REVERT: C 1131 MET cc_start: 0.8579 (ptp) cc_final: 0.8317 (ptp) REVERT: C 1151 LEU cc_start: 0.7181 (tp) cc_final: 0.6723 (mt) REVERT: C 1232 MET cc_start: 0.8449 (mtp) cc_final: 0.7848 (mtp) REVERT: C 1233 LEU cc_start: 0.9676 (mp) cc_final: 0.9098 (mm) REVERT: C 1279 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8879 (mt-10) REVERT: C 1285 TYR cc_start: 0.8934 (m-80) cc_final: 0.8372 (m-10) REVERT: C 1287 LEU cc_start: 0.9321 (tp) cc_final: 0.9065 (tp) REVERT: C 1306 LYS cc_start: 0.9508 (mmtt) cc_final: 0.9179 (pptt) REVERT: D 29 MET cc_start: 0.9340 (mtp) cc_final: 0.9081 (mtp) REVERT: D 349 TYR cc_start: 0.9095 (m-80) cc_final: 0.8820 (m-10) REVERT: D 363 LEU cc_start: 0.9223 (tp) cc_final: 0.8926 (tp) REVERT: D 372 MET cc_start: 0.8952 (mmm) cc_final: 0.8617 (mmp) REVERT: D 466 MET cc_start: 0.9482 (tpt) cc_final: 0.9030 (tmm) REVERT: D 622 ASP cc_start: 0.9410 (m-30) cc_final: 0.9023 (t0) REVERT: D 698 MET cc_start: 0.9457 (tpt) cc_final: 0.9174 (tpp) REVERT: D 725 MET cc_start: 0.8966 (mtm) cc_final: 0.8502 (mtt) REVERT: D 795 TYR cc_start: 0.8818 (t80) cc_final: 0.8502 (t80) REVERT: D 864 LEU cc_start: 0.9392 (mm) cc_final: 0.9110 (tp) REVERT: D 869 CYS cc_start: 0.8845 (m) cc_final: 0.8566 (m) REVERT: D 917 VAL cc_start: 0.9646 (m) cc_final: 0.9388 (p) REVERT: D 1063 ASP cc_start: 0.7081 (t0) cc_final: 0.6369 (p0) REVERT: D 1188 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 1260 MET cc_start: 0.8916 (tpp) cc_final: 0.8468 (tpt) REVERT: D 1282 TYR cc_start: 0.8486 (m-80) cc_final: 0.8202 (m-80) REVERT: D 1370 MET cc_start: 0.9502 (mtm) cc_final: 0.8983 (mtt) REVERT: E 3 ARG cc_start: 0.8755 (tpm170) cc_final: 0.8339 (tpt170) REVERT: E 5 THR cc_start: 0.8809 (m) cc_final: 0.6964 (m) REVERT: E 30 MET cc_start: 0.8962 (tpt) cc_final: 0.8665 (tpp) REVERT: E 31 GLN cc_start: 0.8418 (tt0) cc_final: 0.8214 (tm-30) REVERT: E 53 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7682 (mt-10) REVERT: L 34 PHE cc_start: 0.8876 (m-10) cc_final: 0.8654 (m-80) REVERT: L 195 LEU cc_start: 0.8947 (mm) cc_final: 0.8602 (mm) REVERT: L 214 GLN cc_start: 0.9171 (mp10) cc_final: 0.8947 (mp10) REVERT: L 376 MET cc_start: 0.7164 (mmp) cc_final: 0.6420 (mtt) REVERT: L 406 MET cc_start: 0.9329 (mtm) cc_final: 0.9042 (mtp) REVERT: L 720 MET cc_start: 0.9491 (ppp) cc_final: 0.8994 (ppp) REVERT: L 732 ASP cc_start: 0.9052 (t0) cc_final: 0.8011 (p0) REVERT: L 942 ASN cc_start: 0.9476 (t0) cc_final: 0.9201 (t0) outliers start: 1 outliers final: 1 residues processed: 305 average time/residue: 0.2144 time to fit residues: 107.7427 Evaluate side-chains 227 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 52 optimal weight: 20.0000 chunk 273 optimal weight: 40.0000 chunk 387 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 193 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 331 optimal weight: 0.0010 chunk 411 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 359 optimal weight: 2.9990 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 83 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 486 ASN ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 736 ASN L 786 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.042179 restraints weight = 223552.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.043333 restraints weight = 133045.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.044147 restraints weight = 92370.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044698 restraints weight = 70940.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.045009 restraints weight = 59313.660| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 33343 Z= 0.224 Angle : 0.724 13.950 45069 Z= 0.373 Chirality : 0.045 0.304 5109 Planarity : 0.005 0.063 5943 Dihedral : 5.415 28.686 4581 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4166 helix: 0.54 (0.13), residues: 1632 sheet: 0.00 (0.22), residues: 538 loop : -1.53 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 28 TYR 0.017 0.002 TYR D 631 PHE 0.023 0.002 PHE C 35 TRP 0.019 0.002 TRP C1276 HIS 0.014 0.002 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00477 (33335) covalent geometry : angle 0.72233 (45057) hydrogen bonds : bond 0.04350 ( 1457) hydrogen bonds : angle 5.51877 ( 4122) metal coordination : bond 0.01670 ( 8) metal coordination : angle 3.36983 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8962 (mppt) cc_final: 0.8598 (mppt) REVERT: A 142 MET cc_start: 0.8502 (tmm) cc_final: 0.8300 (tmm) REVERT: B 177 TYR cc_start: 0.7960 (m-80) cc_final: 0.7660 (m-80) REVERT: B 188 GLU cc_start: 0.8031 (mp0) cc_final: 0.7803 (mp0) REVERT: C 171 LEU cc_start: 0.7940 (mp) cc_final: 0.7716 (mp) REVERT: C 459 MET cc_start: 0.9564 (mtp) cc_final: 0.9053 (mmm) REVERT: C 892 GLU cc_start: 0.7835 (pt0) cc_final: 0.7512 (pp20) REVERT: C 951 MET cc_start: 0.9215 (tpp) cc_final: 0.8835 (tmm) REVERT: C 1023 HIS cc_start: 0.8704 (m-70) cc_final: 0.8441 (m-70) REVERT: C 1066 MET cc_start: 0.8392 (tpt) cc_final: 0.7149 (tpt) REVERT: C 1101 LEU cc_start: 0.9144 (mt) cc_final: 0.8904 (mt) REVERT: C 1131 MET cc_start: 0.8544 (ptp) cc_final: 0.8308 (ptp) REVERT: C 1232 MET cc_start: 0.8520 (mtp) cc_final: 0.7474 (mtp) REVERT: C 1233 LEU cc_start: 0.9685 (mp) cc_final: 0.9004 (mt) REVERT: C 1279 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8924 (mt-10) REVERT: C 1306 LYS cc_start: 0.9509 (mmtt) cc_final: 0.9159 (pptt) REVERT: D 29 MET cc_start: 0.9343 (mtp) cc_final: 0.9049 (mtp) REVERT: D 349 TYR cc_start: 0.9063 (m-80) cc_final: 0.8844 (m-10) REVERT: D 363 LEU cc_start: 0.9266 (tp) cc_final: 0.8987 (tp) REVERT: D 372 MET cc_start: 0.8982 (mmm) cc_final: 0.8730 (mmp) REVERT: D 403 ARG cc_start: 0.9324 (mmp80) cc_final: 0.9086 (mmp80) REVERT: D 472 LEU cc_start: 0.9668 (mt) cc_final: 0.9439 (mt) REVERT: D 484 MET cc_start: 0.9081 (mmp) cc_final: 0.8670 (mmm) REVERT: D 544 LEU cc_start: 0.9165 (tp) cc_final: 0.8760 (tp) REVERT: D 622 ASP cc_start: 0.9401 (m-30) cc_final: 0.9035 (t0) REVERT: D 698 MET cc_start: 0.9527 (tpt) cc_final: 0.9230 (tpp) REVERT: D 725 MET cc_start: 0.8958 (mtm) cc_final: 0.8559 (mtt) REVERT: D 864 LEU cc_start: 0.9339 (mm) cc_final: 0.9110 (tp) REVERT: D 869 CYS cc_start: 0.8885 (m) cc_final: 0.8619 (m) REVERT: D 917 VAL cc_start: 0.9651 (m) cc_final: 0.9419 (p) REVERT: D 1063 ASP cc_start: 0.7260 (t0) cc_final: 0.6483 (p0) REVERT: D 1260 MET cc_start: 0.8876 (tpp) cc_final: 0.8566 (tpt) REVERT: D 1282 TYR cc_start: 0.8467 (m-80) cc_final: 0.8225 (m-80) REVERT: D 1370 MET cc_start: 0.9462 (mtm) cc_final: 0.9034 (mtp) REVERT: E 3 ARG cc_start: 0.8726 (tpm170) cc_final: 0.8363 (tpt170) REVERT: E 5 THR cc_start: 0.8829 (m) cc_final: 0.6966 (m) REVERT: E 30 MET cc_start: 0.8980 (tpt) cc_final: 0.8649 (tpp) REVERT: E 31 GLN cc_start: 0.8538 (tt0) cc_final: 0.8273 (tm-30) REVERT: E 53 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7695 (mt-10) REVERT: L 34 PHE cc_start: 0.8878 (m-10) cc_final: 0.8620 (m-80) REVERT: L 189 MET cc_start: 0.9175 (mtm) cc_final: 0.8927 (mtp) REVERT: L 214 GLN cc_start: 0.9186 (mp10) cc_final: 0.8929 (mp10) REVERT: L 376 MET cc_start: 0.7242 (mmp) cc_final: 0.6454 (mtt) REVERT: L 509 ILE cc_start: 0.9084 (mt) cc_final: 0.8851 (mt) REVERT: L 538 MET cc_start: 0.8835 (mtp) cc_final: 0.8508 (mtp) REVERT: L 720 MET cc_start: 0.9530 (ppp) cc_final: 0.9020 (ppp) REVERT: L 732 ASP cc_start: 0.8972 (t0) cc_final: 0.8066 (p0) REVERT: L 942 ASN cc_start: 0.9475 (t0) cc_final: 0.9181 (t0) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2013 time to fit residues: 95.7628 Evaluate side-chains 219 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 386 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 207 optimal weight: 0.0370 chunk 5 optimal weight: 5.9990 chunk 341 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 410 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 513 GLN ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043394 restraints weight = 221223.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044646 restraints weight = 131962.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045466 restraints weight = 90804.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046038 restraints weight = 69768.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046408 restraints weight = 58255.691| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33343 Z= 0.148 Angle : 0.662 11.764 45069 Z= 0.341 Chirality : 0.044 0.282 5109 Planarity : 0.004 0.060 5943 Dihedral : 5.142 28.174 4581 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4166 helix: 0.71 (0.13), residues: 1623 sheet: 0.06 (0.22), residues: 545 loop : -1.47 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 28 TYR 0.016 0.001 TYR C1285 PHE 0.019 0.001 PHE A 231 TRP 0.021 0.001 TRP C1276 HIS 0.010 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00322 (33335) covalent geometry : angle 0.66095 (45057) hydrogen bonds : bond 0.04012 ( 1457) hydrogen bonds : angle 5.30973 ( 4122) metal coordination : bond 0.00931 ( 8) metal coordination : angle 2.22057 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9007 (mppt) cc_final: 0.8577 (mppt) REVERT: A 142 MET cc_start: 0.8426 (tmm) cc_final: 0.8219 (tmm) REVERT: B 177 TYR cc_start: 0.7829 (m-80) cc_final: 0.7539 (m-80) REVERT: B 188 GLU cc_start: 0.8046 (mp0) cc_final: 0.7824 (mp0) REVERT: C 47 TYR cc_start: 0.8410 (m-80) cc_final: 0.8081 (m-80) REVERT: C 459 MET cc_start: 0.9525 (mtp) cc_final: 0.8880 (mmp) REVERT: C 883 LEU cc_start: 0.9408 (mt) cc_final: 0.9173 (mm) REVERT: C 892 GLU cc_start: 0.7896 (pt0) cc_final: 0.7560 (pp20) REVERT: C 951 MET cc_start: 0.9263 (tpp) cc_final: 0.8818 (tmm) REVERT: C 1023 HIS cc_start: 0.8772 (m-70) cc_final: 0.8522 (m-70) REVERT: C 1066 MET cc_start: 0.8255 (tpt) cc_final: 0.7245 (tpt) REVERT: C 1101 LEU cc_start: 0.9138 (mt) cc_final: 0.8899 (mt) REVERT: C 1108 ASN cc_start: 0.8611 (p0) cc_final: 0.8334 (p0) REVERT: C 1131 MET cc_start: 0.8505 (ptp) cc_final: 0.8269 (ptp) REVERT: C 1151 LEU cc_start: 0.7264 (tp) cc_final: 0.6710 (mt) REVERT: C 1230 MET cc_start: 0.8820 (tmm) cc_final: 0.8499 (tmm) REVERT: C 1232 MET cc_start: 0.8496 (mtp) cc_final: 0.7138 (mtp) REVERT: C 1233 LEU cc_start: 0.9670 (mp) cc_final: 0.8975 (mt) REVERT: C 1279 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8904 (mt-10) REVERT: C 1306 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9120 (pptt) REVERT: D 29 MET cc_start: 0.9347 (mtp) cc_final: 0.9115 (mtp) REVERT: D 349 TYR cc_start: 0.9064 (m-80) cc_final: 0.8846 (m-10) REVERT: D 363 LEU cc_start: 0.9256 (tp) cc_final: 0.8967 (tp) REVERT: D 431 ARG cc_start: 0.9120 (ptt180) cc_final: 0.8742 (ptm160) REVERT: D 472 LEU cc_start: 0.9629 (mt) cc_final: 0.9424 (mt) REVERT: D 484 MET cc_start: 0.9094 (mmp) cc_final: 0.8670 (mmm) REVERT: D 485 MET cc_start: 0.9180 (mmm) cc_final: 0.8918 (mmm) REVERT: D 622 ASP cc_start: 0.9384 (m-30) cc_final: 0.9030 (t0) REVERT: D 698 MET cc_start: 0.9500 (tpt) cc_final: 0.9147 (tpp) REVERT: D 725 MET cc_start: 0.8987 (mtm) cc_final: 0.8655 (mtm) REVERT: D 795 TYR cc_start: 0.8790 (t80) cc_final: 0.8477 (t80) REVERT: D 917 VAL cc_start: 0.9628 (m) cc_final: 0.9363 (p) REVERT: D 1063 ASP cc_start: 0.7252 (t0) cc_final: 0.6480 (p0) REVERT: D 1260 MET cc_start: 0.8841 (tpp) cc_final: 0.8487 (tpt) REVERT: D 1282 TYR cc_start: 0.8458 (m-80) cc_final: 0.8207 (m-80) REVERT: D 1370 MET cc_start: 0.9453 (mtm) cc_final: 0.9033 (mtp) REVERT: E 5 THR cc_start: 0.8819 (m) cc_final: 0.8601 (m) REVERT: E 30 MET cc_start: 0.8907 (tpt) cc_final: 0.8700 (tpp) REVERT: E 31 GLN cc_start: 0.8576 (tt0) cc_final: 0.8280 (tm-30) REVERT: E 53 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7673 (mt-10) REVERT: L 214 GLN cc_start: 0.9156 (mp10) cc_final: 0.8851 (tm-30) REVERT: L 376 MET cc_start: 0.7197 (mmp) cc_final: 0.6391 (mtt) REVERT: L 395 ASP cc_start: 0.8860 (t0) cc_final: 0.7598 (p0) REVERT: L 720 MET cc_start: 0.9506 (ppp) cc_final: 0.9015 (ppp) REVERT: L 732 ASP cc_start: 0.8863 (t0) cc_final: 0.7898 (p0) REVERT: L 942 ASN cc_start: 0.9470 (t0) cc_final: 0.9169 (t0) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1929 time to fit residues: 98.8041 Evaluate side-chains 229 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 198 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 415 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 786 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041296 restraints weight = 225468.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.042438 restraints weight = 135179.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043226 restraints weight = 94111.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043765 restraints weight = 72653.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044082 restraints weight = 60822.162| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 33343 Z= 0.250 Angle : 0.768 13.837 45069 Z= 0.395 Chirality : 0.046 0.312 5109 Planarity : 0.005 0.060 5943 Dihedral : 5.598 30.044 4581 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4166 helix: 0.36 (0.13), residues: 1635 sheet: -0.02 (0.22), residues: 518 loop : -1.59 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 28 TYR 0.023 0.002 TYR C1285 PHE 0.023 0.002 PHE L 572 TRP 0.019 0.002 TRP C 183 HIS 0.014 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00530 (33335) covalent geometry : angle 0.76554 (45057) hydrogen bonds : bond 0.04525 ( 1457) hydrogen bonds : angle 5.62933 ( 4122) metal coordination : bond 0.01812 ( 8) metal coordination : angle 3.89755 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9035 (mppt) cc_final: 0.8633 (mppt) REVERT: B 51 MET cc_start: 0.8407 (mmp) cc_final: 0.8110 (mmm) REVERT: B 188 GLU cc_start: 0.7955 (mp0) cc_final: 0.7612 (mp0) REVERT: C 47 TYR cc_start: 0.8598 (m-80) cc_final: 0.8214 (m-80) REVERT: C 459 MET cc_start: 0.9577 (mtp) cc_final: 0.8963 (mmp) REVERT: C 515 MET cc_start: 0.8778 (tmm) cc_final: 0.7727 (tmm) REVERT: C 523 GLU cc_start: 0.9256 (pt0) cc_final: 0.8816 (mt-10) REVERT: C 800 MET cc_start: 0.8022 (mpp) cc_final: 0.7748 (mpp) REVERT: C 805 MET cc_start: 0.8779 (ppp) cc_final: 0.8548 (ppp) REVERT: C 883 LEU cc_start: 0.9473 (mt) cc_final: 0.9215 (mm) REVERT: C 892 GLU cc_start: 0.8086 (pt0) cc_final: 0.7810 (pp20) REVERT: C 1023 HIS cc_start: 0.8710 (m-70) cc_final: 0.8415 (m-70) REVERT: C 1101 LEU cc_start: 0.9169 (mt) cc_final: 0.8885 (mt) REVERT: C 1279 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8892 (mt-10) REVERT: C 1306 LYS cc_start: 0.9510 (mmtt) cc_final: 0.9118 (pptt) REVERT: D 349 TYR cc_start: 0.9136 (m-80) cc_final: 0.8922 (m-10) REVERT: D 363 LEU cc_start: 0.9274 (tp) cc_final: 0.8985 (tp) REVERT: D 484 MET cc_start: 0.9092 (mmp) cc_final: 0.8857 (mmm) REVERT: D 485 MET cc_start: 0.9185 (mmm) cc_final: 0.8964 (mmm) REVERT: D 544 LEU cc_start: 0.9209 (tp) cc_final: 0.8864 (tp) REVERT: D 622 ASP cc_start: 0.9345 (m-30) cc_final: 0.9020 (t0) REVERT: D 644 MET cc_start: 0.8974 (pmm) cc_final: 0.8678 (pmm) REVERT: D 698 MET cc_start: 0.9502 (tpt) cc_final: 0.9223 (tpp) REVERT: D 724 MET cc_start: 0.9597 (mtp) cc_final: 0.9331 (mtp) REVERT: D 725 MET cc_start: 0.8969 (mtm) cc_final: 0.8704 (mtm) REVERT: D 743 MET cc_start: 0.8376 (ppp) cc_final: 0.8151 (ppp) REVERT: D 917 VAL cc_start: 0.9665 (m) cc_final: 0.9416 (p) REVERT: D 1063 ASP cc_start: 0.7174 (t0) cc_final: 0.6346 (p0) REVERT: D 1260 MET cc_start: 0.8820 (tpp) cc_final: 0.8515 (tpt) REVERT: D 1282 TYR cc_start: 0.8498 (m-80) cc_final: 0.8220 (m-80) REVERT: D 1370 MET cc_start: 0.9461 (mtm) cc_final: 0.9074 (mtp) REVERT: E 5 THR cc_start: 0.8770 (m) cc_final: 0.8236 (m) REVERT: E 29 GLN cc_start: 0.9276 (mp10) cc_final: 0.8887 (mp10) REVERT: E 31 GLN cc_start: 0.8588 (tt0) cc_final: 0.8260 (tm-30) REVERT: L 34 PHE cc_start: 0.8969 (m-10) cc_final: 0.8655 (m-10) REVERT: L 214 GLN cc_start: 0.9167 (mp10) cc_final: 0.8909 (tm-30) REVERT: L 376 MET cc_start: 0.7438 (mmp) cc_final: 0.6567 (mtt) REVERT: L 509 ILE cc_start: 0.9038 (mt) cc_final: 0.8724 (mt) REVERT: L 581 PHE cc_start: 0.7539 (t80) cc_final: 0.7271 (t80) REVERT: L 720 MET cc_start: 0.9539 (ppp) cc_final: 0.9056 (ppp) REVERT: L 732 ASP cc_start: 0.8795 (t0) cc_final: 0.8217 (p0) REVERT: L 942 ASN cc_start: 0.9463 (t0) cc_final: 0.9185 (t0) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1948 time to fit residues: 90.0855 Evaluate side-chains 207 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 204 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 299 optimal weight: 8.9990 chunk 174 optimal weight: 0.1980 chunk 399 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN C 235 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1049 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 786 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.041230 restraints weight = 226322.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.042420 restraints weight = 134483.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043208 restraints weight = 92969.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043744 restraints weight = 71912.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044059 restraints weight = 60339.070| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 33343 Z= 0.234 Angle : 0.748 13.739 45069 Z= 0.386 Chirality : 0.046 0.296 5109 Planarity : 0.005 0.058 5943 Dihedral : 5.623 28.915 4581 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.96 % Favored : 93.01 % Rotamer: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4166 helix: 0.29 (0.13), residues: 1634 sheet: -0.26 (0.22), residues: 531 loop : -1.66 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 28 TYR 0.020 0.002 TYR C1285 PHE 0.016 0.002 PHE C 35 TRP 0.015 0.002 TRP C1276 HIS 0.012 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00499 (33335) covalent geometry : angle 0.74608 (45057) hydrogen bonds : bond 0.04468 ( 1457) hydrogen bonds : angle 5.67257 ( 4122) metal coordination : bond 0.01549 ( 8) metal coordination : angle 3.29942 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9131 (mppt) cc_final: 0.8728 (mppt) REVERT: A 142 MET cc_start: 0.8573 (tmm) cc_final: 0.8291 (tmm) REVERT: B 188 GLU cc_start: 0.7955 (mp0) cc_final: 0.7635 (mp0) REVERT: C 47 TYR cc_start: 0.8555 (m-80) cc_final: 0.8147 (m-80) REVERT: C 459 MET cc_start: 0.9571 (mtp) cc_final: 0.8971 (mmp) REVERT: C 653 MET cc_start: 0.8732 (ppp) cc_final: 0.8377 (ppp) REVERT: C 741 MET cc_start: 0.7991 (mmp) cc_final: 0.7751 (mmm) REVERT: C 800 MET cc_start: 0.8077 (mpp) cc_final: 0.7806 (mpp) REVERT: C 805 MET cc_start: 0.8780 (ppp) cc_final: 0.8544 (ppp) REVERT: C 883 LEU cc_start: 0.9473 (mt) cc_final: 0.9261 (mm) REVERT: C 892 GLU cc_start: 0.8269 (pt0) cc_final: 0.8016 (pp20) REVERT: C 1023 HIS cc_start: 0.8736 (m-70) cc_final: 0.8426 (m-70) REVERT: C 1066 MET cc_start: 0.8410 (tpt) cc_final: 0.7284 (tpt) REVERT: C 1085 MET cc_start: 0.9305 (mmm) cc_final: 0.8845 (mpp) REVERT: C 1131 MET cc_start: 0.8558 (ptp) cc_final: 0.8160 (ptp) REVERT: C 1233 LEU cc_start: 0.9628 (mm) cc_final: 0.8904 (mt) REVERT: C 1279 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8790 (mt-10) REVERT: C 1306 LYS cc_start: 0.9517 (mmtt) cc_final: 0.9089 (pptt) REVERT: D 349 TYR cc_start: 0.9164 (m-80) cc_final: 0.8957 (m-10) REVERT: D 363 LEU cc_start: 0.9308 (tp) cc_final: 0.9052 (tp) REVERT: D 485 MET cc_start: 0.9164 (mmm) cc_final: 0.8936 (mmm) REVERT: D 513 MET cc_start: 0.8561 (tpp) cc_final: 0.8342 (tpp) REVERT: D 544 LEU cc_start: 0.9036 (tp) cc_final: 0.8637 (tp) REVERT: D 622 ASP cc_start: 0.9350 (m-30) cc_final: 0.9025 (t0) REVERT: D 644 MET cc_start: 0.8909 (pmm) cc_final: 0.8512 (pmm) REVERT: D 698 MET cc_start: 0.9513 (tpt) cc_final: 0.9257 (tpp) REVERT: D 724 MET cc_start: 0.9579 (mtp) cc_final: 0.9299 (mtp) REVERT: D 725 MET cc_start: 0.8953 (mtm) cc_final: 0.8557 (mtt) REVERT: D 743 MET cc_start: 0.8367 (ppp) cc_final: 0.8149 (ppp) REVERT: D 795 TYR cc_start: 0.8858 (t80) cc_final: 0.8525 (t80) REVERT: D 837 ASP cc_start: 0.9261 (p0) cc_final: 0.8994 (m-30) REVERT: D 863 LEU cc_start: 0.9491 (tp) cc_final: 0.9133 (tt) REVERT: D 1025 MET cc_start: 0.8632 (tpt) cc_final: 0.8308 (mtt) REVERT: D 1063 ASP cc_start: 0.7333 (t0) cc_final: 0.6558 (p0) REVERT: D 1260 MET cc_start: 0.8842 (tpp) cc_final: 0.8580 (tpt) REVERT: D 1282 TYR cc_start: 0.8566 (m-80) cc_final: 0.8276 (m-80) REVERT: D 1370 MET cc_start: 0.9469 (mtm) cc_final: 0.8948 (mtt) REVERT: E 5 THR cc_start: 0.8802 (m) cc_final: 0.8176 (m) REVERT: E 29 GLN cc_start: 0.9244 (mp10) cc_final: 0.9029 (mp-120) REVERT: E 31 GLN cc_start: 0.8567 (tt0) cc_final: 0.8297 (tm-30) REVERT: L 34 PHE cc_start: 0.8911 (m-10) cc_final: 0.8652 (m-10) REVERT: L 189 MET cc_start: 0.9373 (mtp) cc_final: 0.9029 (mtp) REVERT: L 214 GLN cc_start: 0.9189 (mp10) cc_final: 0.8923 (tm-30) REVERT: L 376 MET cc_start: 0.7417 (mmp) cc_final: 0.6548 (mtt) REVERT: L 509 ILE cc_start: 0.9066 (mt) cc_final: 0.8766 (mt) REVERT: L 581 PHE cc_start: 0.7559 (t80) cc_final: 0.7245 (t80) REVERT: L 720 MET cc_start: 0.9547 (ppp) cc_final: 0.9080 (ppp) REVERT: L 732 ASP cc_start: 0.8744 (t0) cc_final: 0.8195 (p0) REVERT: L 942 ASN cc_start: 0.9474 (t0) cc_final: 0.9206 (t0) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1866 time to fit residues: 88.4707 Evaluate side-chains 217 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 122 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 0.0010 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS C 513 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1336 ASN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 786 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041935 restraints weight = 227190.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043109 restraints weight = 134657.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.043899 restraints weight = 92659.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044464 restraints weight = 71491.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.044804 restraints weight = 59765.378| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33343 Z= 0.185 Angle : 0.713 13.023 45069 Z= 0.367 Chirality : 0.045 0.282 5109 Planarity : 0.005 0.059 5943 Dihedral : 5.437 27.806 4581 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 4166 helix: 0.40 (0.13), residues: 1630 sheet: -0.15 (0.22), residues: 513 loop : -1.62 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 122 TYR 0.025 0.002 TYR C1149 PHE 0.017 0.002 PHE A 231 TRP 0.014 0.002 TRP C1276 HIS 0.012 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00402 (33335) covalent geometry : angle 0.71166 (45057) hydrogen bonds : bond 0.04264 ( 1457) hydrogen bonds : angle 5.51218 ( 4122) metal coordination : bond 0.01149 ( 8) metal coordination : angle 2.83621 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9220 (mppt) cc_final: 0.8771 (mppt) REVERT: A 142 MET cc_start: 0.8512 (tmm) cc_final: 0.8240 (tmm) REVERT: B 188 GLU cc_start: 0.7985 (mp0) cc_final: 0.7705 (mp0) REVERT: B 224 LEU cc_start: 0.9335 (tp) cc_final: 0.9124 (tp) REVERT: C 47 TYR cc_start: 0.8485 (m-80) cc_final: 0.8087 (m-80) REVERT: C 459 MET cc_start: 0.9550 (mtp) cc_final: 0.8952 (mmp) REVERT: C 488 MET cc_start: 0.8204 (mmp) cc_final: 0.7693 (mmp) REVERT: C 515 MET cc_start: 0.8712 (tmm) cc_final: 0.7670 (tmm) REVERT: C 523 GLU cc_start: 0.9209 (pt0) cc_final: 0.8756 (mt-10) REVERT: C 653 MET cc_start: 0.8662 (ppp) cc_final: 0.8298 (ppp) REVERT: C 741 MET cc_start: 0.8306 (mmp) cc_final: 0.8015 (mmm) REVERT: C 800 MET cc_start: 0.7933 (mpp) cc_final: 0.7625 (mpp) REVERT: C 883 LEU cc_start: 0.9512 (mt) cc_final: 0.9293 (mm) REVERT: C 892 GLU cc_start: 0.8322 (pt0) cc_final: 0.8078 (pp20) REVERT: C 1023 HIS cc_start: 0.8769 (m-70) cc_final: 0.8455 (m-70) REVERT: C 1066 MET cc_start: 0.8393 (tpt) cc_final: 0.7388 (tpt) REVERT: C 1085 MET cc_start: 0.9273 (mmm) cc_final: 0.8917 (mpp) REVERT: C 1101 LEU cc_start: 0.9290 (mt) cc_final: 0.9031 (mt) REVERT: C 1108 ASN cc_start: 0.8805 (p0) cc_final: 0.8524 (p0) REVERT: C 1131 MET cc_start: 0.8503 (ptp) cc_final: 0.8159 (ptp) REVERT: C 1233 LEU cc_start: 0.9664 (mm) cc_final: 0.8940 (mt) REVERT: C 1235 LEU cc_start: 0.9732 (mm) cc_final: 0.9521 (mm) REVERT: C 1279 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8864 (mt-10) REVERT: C 1306 LYS cc_start: 0.9498 (mmtt) cc_final: 0.9108 (pptt) REVERT: D 349 TYR cc_start: 0.9114 (m-80) cc_final: 0.8899 (m-10) REVERT: D 363 LEU cc_start: 0.9360 (tp) cc_final: 0.9088 (tp) REVERT: D 431 ARG cc_start: 0.9165 (ptt180) cc_final: 0.8652 (ptm160) REVERT: D 466 MET cc_start: 0.9431 (tpt) cc_final: 0.8887 (tpp) REVERT: D 485 MET cc_start: 0.9129 (mmm) cc_final: 0.8880 (mmm) REVERT: D 622 ASP cc_start: 0.9396 (m-30) cc_final: 0.9069 (t0) REVERT: D 644 MET cc_start: 0.8861 (pmm) cc_final: 0.8502 (pmm) REVERT: D 698 MET cc_start: 0.9507 (tpt) cc_final: 0.9298 (tpp) REVERT: D 724 MET cc_start: 0.9557 (mtp) cc_final: 0.9346 (mtp) REVERT: D 725 MET cc_start: 0.8955 (mtm) cc_final: 0.8672 (mtm) REVERT: D 795 TYR cc_start: 0.8822 (t80) cc_final: 0.8506 (t80) REVERT: D 837 ASP cc_start: 0.9218 (p0) cc_final: 0.8936 (m-30) REVERT: D 863 LEU cc_start: 0.9501 (tp) cc_final: 0.9171 (tt) REVERT: D 1025 MET cc_start: 0.8659 (tpt) cc_final: 0.8360 (mmp) REVERT: D 1063 ASP cc_start: 0.7226 (t0) cc_final: 0.6422 (p0) REVERT: D 1260 MET cc_start: 0.8856 (tpp) cc_final: 0.8588 (tpt) REVERT: D 1282 TYR cc_start: 0.8565 (m-80) cc_final: 0.8250 (m-80) REVERT: D 1370 MET cc_start: 0.9456 (mtm) cc_final: 0.8910 (mtt) REVERT: E 5 THR cc_start: 0.8797 (m) cc_final: 0.8272 (m) REVERT: E 31 GLN cc_start: 0.8604 (tt0) cc_final: 0.8257 (tm-30) REVERT: L 34 PHE cc_start: 0.8880 (m-10) cc_final: 0.8636 (m-10) REVERT: L 189 MET cc_start: 0.9419 (mtp) cc_final: 0.9136 (mtp) REVERT: L 214 GLN cc_start: 0.9170 (mp10) cc_final: 0.8930 (tm-30) REVERT: L 376 MET cc_start: 0.7407 (mmp) cc_final: 0.6422 (mtt) REVERT: L 509 ILE cc_start: 0.9049 (mt) cc_final: 0.8813 (mt) REVERT: L 581 PHE cc_start: 0.7563 (t80) cc_final: 0.7270 (t80) REVERT: L 720 MET cc_start: 0.9531 (ppp) cc_final: 0.9026 (ppp) REVERT: L 732 ASP cc_start: 0.8709 (t0) cc_final: 0.8198 (p0) REVERT: L 942 ASN cc_start: 0.9461 (t0) cc_final: 0.9212 (t0) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1940 time to fit residues: 92.4269 Evaluate side-chains 210 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 246 optimal weight: 8.9990 chunk 302 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 406 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C 932 GLN C1244 HIS ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 921 GLN ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 GLN ** L 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.043881 restraints weight = 220135.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045188 restraints weight = 129234.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046053 restraints weight = 88006.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046639 restraints weight = 67221.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046968 restraints weight = 55726.986| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33343 Z= 0.119 Angle : 0.662 13.469 45069 Z= 0.339 Chirality : 0.045 0.258 5109 Planarity : 0.004 0.068 5943 Dihedral : 5.015 29.326 4581 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4166 helix: 0.72 (0.13), residues: 1617 sheet: -0.01 (0.22), residues: 537 loop : -1.49 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 125 TYR 0.012 0.001 TYR L 130 PHE 0.018 0.001 PHE A 231 TRP 0.019 0.001 TRP C1276 HIS 0.011 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00261 (33335) covalent geometry : angle 0.66086 (45057) hydrogen bonds : bond 0.03795 ( 1457) hydrogen bonds : angle 5.15789 ( 4122) metal coordination : bond 0.00319 ( 8) metal coordination : angle 2.02006 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5489.48 seconds wall clock time: 96 minutes 14.30 seconds (5774.30 seconds total)