Starting phenix.real_space_refine on Fri Mar 6 20:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.map" model { file = "/net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wmu_21853/03_2026/6wmu_21853.cif" } resolution = 3.18 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 145 5.16 5 C 21146 2.51 5 N 5997 2.21 5 O 6717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34094 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10556 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1363, 10504 Classifications: {'peptide': 1363} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 55, 'TRANS': 1307} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 660 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3836 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 14, 'TRANS': 456} Chain breaks: 2 Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 746 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "H" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "K" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1592 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 183} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1631 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 188} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 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 14630 SG CYS D 70 53.797 62.949 105.921 1.00 81.71 S ATOM 14644 SG CYS D 72 53.849 59.997 107.414 1.00 82.67 S ATOM 14752 SG CYS D 85 55.750 62.067 109.520 1.00 80.19 S ATOM 14776 SG CYS D 88 56.856 61.235 106.340 1.00 80.89 S ATOM 20461 SG CYS D 814 93.357 110.796 79.681 1.00 88.30 S ATOM 21026 SG CYS D 888 92.390 107.564 79.268 1.00 87.75 S ATOM 21077 SG CYS D 895 90.307 110.733 78.060 1.00 83.20 S ATOM 21098 SG CYS D 898 93.435 109.829 76.521 1.00 82.14 S Time building chain proxies: 7.35, per 1000 atoms: 0.22 Number of scatterers: 34094 At special positions: 0 Unit cell: (159, 164.3, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 86 15.00 Mg 1 11.99 O 6717 8.00 N 5997 7.00 C 21146 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " 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 " Number of angles added : 12 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 49 sheets defined 45.5% alpha, 12.7% beta 36 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.718A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.733A 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 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: 3.668A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 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: 4.176A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 4.318A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.589A 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 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 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: 3.818A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.590A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 527 removed outlier: 3.898A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.817A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 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 896 through 907 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.374A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.885A 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: 3.746A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.810A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.586A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.267A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 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: 4.107A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.886A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) 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 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 574 through 581 removed outlier: 3.856A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.521A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.996A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.557A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.922A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.864A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.691A 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 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.020A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.448A 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 1324 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.679A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.502A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.218A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.738A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 88 removed outlier: 3.655A pdb=" N GLU E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.944A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 removed outlier: 3.624A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 4.259A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 233 removed outlier: 3.776A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 257 Processing helix chain 'F' and resid 262 through 294 Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.572A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 323 removed outlier: 3.718A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 394 removed outlier: 5.552A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.927A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.695A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 492 through 501 removed outlier: 3.718A pdb=" N ALA F 501 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.796A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.913A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU F 551 " --> pdb=" O VAL F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 585 through 600 Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 47 through 54 Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 92 through 120 removed outlier: 3.570A pdb=" N GLU K 107 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR K 112 " --> pdb=" O LYS K 108 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU K 113 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 144 Proline residue: K 141 - end of helix Processing helix chain 'K' and resid 155 through 167 Proline residue: K 163 - end of helix Processing helix chain 'K' and resid 177 through 193 removed outlier: 3.770A pdb=" N LYS K 181 " --> pdb=" O GLY K 177 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU K 182 " --> pdb=" O PRO K 178 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG K 193 " --> pdb=" O ARG K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 200 Processing helix chain 'K' and resid 201 through 206 removed outlier: 3.742A pdb=" N GLU K 206 " --> pdb=" O GLU K 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 71 through 83 removed outlier: 3.639A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 120 removed outlier: 5.265A pdb=" N THR L 112 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU L 113 " --> pdb=" O ASP L 109 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE L 118 " --> pdb=" O MET L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 144 Proline residue: L 141 - end of helix removed outlier: 4.018A pdb=" N GLY L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 166 Proline residue: L 163 - end of helix Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.552A pdb=" N GLN L 170 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 192 Processing helix chain 'L' and resid 193 through 200 Processing helix chain 'L' and resid 201 through 207 removed outlier: 3.660A pdb=" N MET L 207 " --> pdb=" O ALA L 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.184A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.640A 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: 7.156A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.450A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 6.385A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.319A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.497A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.626A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.408A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.550A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.468A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 262 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 257 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.779A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.853A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.557A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (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 716 through 717 removed outlier: 6.271A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.637A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.388A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 5.938A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.656A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.544A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.541A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.507A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.587A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 7.070A pdb=" N VAL D 894 " --> pdb=" O THR D 810 " (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 825 through 827 removed outlier: 6.642A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 827 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 951 through 952 removed outlier: 3.843A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 981 through 984 removed outlier: 3.661A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE6, first strand: chain 'D' and resid 1027 through 1028 Processing sheet with id=AE7, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.620A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1161 through 1163 Processing sheet with id=AE9, first strand: chain 'D' and resid 1172 through 1176 Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 3.949A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 37 through 40 removed outlier: 5.997A pdb=" N LEU K 13 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 12 through 15 removed outlier: 5.786A pdb=" N LEU L 13 " --> pdb=" O GLU L 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 62 through 63 1484 hydrogen bonds defined for protein. 4233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 11.47 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8367 1.32 - 1.44: 6695 1.44 - 1.57: 19316 1.57 - 1.69: 169 1.69 - 1.81: 257 Bond restraints: 34804 Sorted by residual: bond pdb=" C GLN L 145 " pdb=" N LYS L 146 " ideal model delta sigma weight residual 1.333 1.228 0.105 2.74e-02 1.33e+03 1.46e+01 bond pdb=" C ASN C 519 " pdb=" N PRO C 520 " ideal model delta sigma weight residual 1.334 1.253 0.081 2.34e-02 1.83e+03 1.19e+01 bond pdb=" N VAL C1155 " pdb=" CA VAL C1155 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C GLU D 418 " pdb=" N HIS D 419 " ideal model delta sigma weight residual 1.333 1.285 0.049 1.50e-02 4.44e+03 1.06e+01 bond pdb=" N VAL C1159 " pdb=" CA VAL C1159 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.69e+00 ... (remaining 34799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 45776 2.46 - 4.91: 1458 4.91 - 7.37: 129 7.37 - 9.82: 15 9.82 - 12.28: 9 Bond angle restraints: 47387 Sorted by residual: angle pdb=" N PRO C1317 " pdb=" CA PRO C1317 " pdb=" C PRO C1317 " ideal model delta sigma weight residual 113.53 120.84 -7.31 1.39e+00 5.18e-01 2.76e+01 angle pdb=" O3' DG J 12 " pdb=" C3' DG J 12 " pdb=" C2' DG J 12 " ideal model delta sigma weight residual 111.50 103.85 7.65 1.50e+00 4.44e-01 2.60e+01 angle pdb=" C SER L 9 " pdb=" N VAL L 10 " pdb=" CA VAL L 10 " ideal model delta sigma weight residual 121.97 128.87 -6.90 1.80e+00 3.09e-01 1.47e+01 angle pdb=" C ARG D 311 " pdb=" N ARG D 312 " pdb=" CA ARG D 312 " ideal model delta sigma weight residual 120.81 126.99 -6.18 1.63e+00 3.76e-01 1.44e+01 angle pdb=" C GLY C 373 " pdb=" N GLU C 374 " pdb=" CA GLU C 374 " ideal model delta sigma weight residual 120.97 110.29 10.68 2.84e+00 1.24e-01 1.42e+01 ... (remaining 47382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 19931 33.17 - 66.33: 1199 66.33 - 99.50: 62 99.50 - 132.67: 0 132.67 - 165.83: 1 Dihedral angle restraints: 21193 sinusoidal: 9301 harmonic: 11892 Sorted by residual: dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA ARG L 8 " pdb=" C ARG L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta harmonic sigma weight residual -180.00 -136.29 -43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 136.80 43.20 0 5.00e+00 4.00e-02 7.46e+01 ... (remaining 21190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4123 0.066 - 0.133: 1146 0.133 - 0.199: 105 0.199 - 0.265: 13 0.265 - 0.331: 2 Chirality restraints: 5389 Sorted by residual: chirality pdb=" CA VAL D1027 " pdb=" N VAL D1027 " pdb=" C VAL D1027 " pdb=" CB VAL D1027 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL D1255 " pdb=" CA VAL D1255 " pdb=" CG1 VAL D1255 " pdb=" CG2 VAL D1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA GLU C1316 " pdb=" N GLU C1316 " pdb=" C GLU C1316 " pdb=" CB GLU C1316 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5386 not shown) Planarity restraints: 5902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C1223 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO C1224 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C1224 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C1224 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " -0.040 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO C 520 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 337 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ARG D 337 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG D 337 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE D 338 " 0.014 2.00e-02 2.50e+03 ... (remaining 5899 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 997 2.63 - 3.20: 34823 3.20 - 3.77: 55736 3.77 - 4.33: 75184 4.33 - 4.90: 120978 Nonbonded interactions: 287718 Sorted by model distance: nonbonded pdb=" O SER F 604 " pdb=" N LEU F 607 " model vdw 2.066 3.120 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D2001 " model vdw 2.077 2.170 nonbonded pdb=" OG1 THR F 572 " pdb=" OE1 GLU F 575 " model vdw 2.077 3.040 nonbonded pdb=" O2 DC I 20 " pdb=" N2 DG J 8 " model vdw 2.078 2.496 nonbonded pdb=" O GLU F 605 " pdb=" OG SER F 609 " model vdw 2.082 3.040 ... (remaining 287713 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 233) selection = (chain 'B' and resid 7 through 233) } ncs_group { reference = (chain 'K' and (resid 10 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 125 or (resid 126 through 128 and \ (name N or name CA or name C or name O or name CB )) or resid 129 through 151 or \ (resid 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 169 or (resid 170 and (name N or name CA or name C or name O or name C \ B )) or resid 171 through 208)) selection = (chain 'L' and (resid 10 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 144 or (resid 145 through 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 207 or \ (resid 208 and (name N or name CA or name C or name O or name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.110 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.016 0.171 34812 Z= 0.705 Angle : 1.036 35.573 47399 Z= 0.555 Chirality : 0.057 0.331 5389 Planarity : 0.005 0.077 5902 Dihedral : 18.816 165.832 13523 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.69 % Favored : 88.02 % Rotamer: Outliers : 9.93 % Allowed : 19.63 % Favored : 70.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.11), residues: 4099 helix: -1.77 (0.10), residues: 1739 sheet: -2.42 (0.22), residues: 386 loop : -3.20 (0.11), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 385 TYR 0.026 0.002 TYR D 631 PHE 0.022 0.003 PHE D 461 TRP 0.011 0.003 TRP D 409 HIS 0.013 0.002 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.01587 (34804) covalent geometry : angle 1.00880 (47387) hydrogen bonds : bond 0.13429 ( 1569) hydrogen bonds : angle 6.81366 ( 4403) metal coordination : bond 0.10915 ( 8) metal coordination : angle 14.91498 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 347 poor density : 578 time to evaluate : 1.225 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 58 GLU cc_start: 0.8391 (pt0) cc_final: 0.7849 (mt-10) REVERT: A 231 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 25 LYS cc_start: 0.7916 (tttt) cc_final: 0.7388 (ttmt) REVERT: B 95 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7013 (mtmt) REVERT: B 148 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7827 (mtp85) REVERT: B 150 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (ttp80) REVERT: B 181 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 200 LYS cc_start: 0.8656 (tttt) cc_final: 0.8401 (tttt) REVERT: B 233 ASP cc_start: 0.6059 (OUTLIER) cc_final: 0.5808 (m-30) REVERT: C 14 ASP cc_start: 0.7718 (t70) cc_final: 0.7319 (t0) REVERT: C 37 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7837 (mtmt) REVERT: C 118 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7765 (tmtt) REVERT: C 122 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 161 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6895 (ptpt) REVERT: C 476 LYS cc_start: 0.7845 (mttt) cc_final: 0.7629 (tppt) REVERT: C 488 MET cc_start: 0.7851 (mtm) cc_final: 0.7617 (mtt) REVERT: C 681 MET cc_start: 0.8031 (mtp) cc_final: 0.7803 (mtt) REVERT: C 685 MET cc_start: 0.8211 (mtm) cc_final: 0.7924 (mtp) REVERT: C 765 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8303 (pt) REVERT: C 849 GLU cc_start: 0.6935 (tt0) cc_final: 0.6539 (tt0) REVERT: C 957 LYS cc_start: 0.8256 (tttt) cc_final: 0.7800 (tptt) REVERT: C 1072 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.7729 (p0) REVERT: C 1073 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8437 (mtmm) REVERT: C 1107 MET cc_start: 0.8543 (mtm) cc_final: 0.8245 (mpp) REVERT: C 1119 MET cc_start: 0.7532 (tpt) cc_final: 0.7276 (ttt) REVERT: C 1143 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7455 (pt0) REVERT: C 1211 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7541 (ttp80) REVERT: D 29 MET cc_start: 0.7441 (ttp) cc_final: 0.7226 (ttm) REVERT: D 46 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8493 (p90) REVERT: D 50 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7906 (mttt) REVERT: D 133 ARG cc_start: 0.6855 (mpp-170) cc_final: 0.6465 (mtm110) REVERT: D 201 LEU cc_start: 0.8148 (mt) cc_final: 0.7940 (mm) REVERT: D 219 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7358 (mmtt) REVERT: D 314 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5878 (mtt90) REVERT: D 322 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7681 (mtp85) REVERT: D 332 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7277 (pttp) REVERT: D 504 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: D 582 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8057 (mp) REVERT: D 712 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6131 (pp30) REVERT: D 715 LYS cc_start: 0.7719 (ptpt) cc_final: 0.7345 (mtpt) REVERT: D 811 GLU cc_start: 0.7682 (tt0) cc_final: 0.7431 (mt-10) REVERT: D 901 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6943 (ptt180) REVERT: D 932 MET cc_start: 0.5101 (ttp) cc_final: 0.4866 (ttm) REVERT: D 1072 LYS cc_start: 0.3327 (OUTLIER) cc_final: 0.1982 (mttt) REVERT: D 1170 LYS cc_start: 0.2794 (OUTLIER) cc_final: 0.2434 (tptt) REVERT: D 1189 MET cc_start: 0.7065 (mmt) cc_final: 0.5981 (mmp) REVERT: D 1193 TRP cc_start: 0.6152 (m-90) cc_final: 0.5603 (m-10) REVERT: D 1199 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.3826 (m-80) REVERT: D 1316 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8041 (p) REVERT: E 3 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7448 (tpt90) REVERT: E 42 GLU cc_start: 0.9063 (mm-30) cc_final: 0.7667 (mp0) REVERT: E 67 ARG cc_start: 0.6721 (tpt90) cc_final: 0.6023 (mtp85) REVERT: E 72 GLN cc_start: 0.7442 (mt0) cc_final: 0.6992 (tt0) REVERT: F 114 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: F 259 PHE cc_start: 0.4356 (m-80) cc_final: 0.3764 (m-80) REVERT: F 266 PHE cc_start: 0.7169 (t80) cc_final: 0.6969 (t80) REVERT: F 305 LEU cc_start: 0.2906 (OUTLIER) cc_final: 0.2394 (pp) REVERT: F 362 ASN cc_start: 0.4089 (p0) cc_final: 0.3805 (p0) REVERT: F 456 MET cc_start: 0.7971 (tpp) cc_final: 0.7663 (tpt) REVERT: F 469 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: F 509 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8248 (p) REVERT: F 566 ASP cc_start: 0.8303 (p0) cc_final: 0.8057 (p0) REVERT: F 581 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5124 (m-30) REVERT: K 12 THR cc_start: 0.7953 (t) cc_final: 0.7583 (t) REVERT: K 14 PHE cc_start: 0.7500 (m-80) cc_final: 0.6792 (m-10) REVERT: K 31 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: K 78 TYR cc_start: 0.8417 (t80) cc_final: 0.8165 (t80) REVERT: K 124 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: K 166 TRP cc_start: 0.6920 (t-100) cc_final: 0.6554 (t-100) REVERT: L 37 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6142 (tm-30) REVERT: L 45 ASN cc_start: 0.1220 (OUTLIER) cc_final: -0.0403 (t0) REVERT: L 66 GLU cc_start: 0.6575 (pm20) cc_final: 0.6360 (pm20) REVERT: L 131 GLN cc_start: 0.8410 (tt0) cc_final: 0.8181 (mt0) REVERT: L 142 VAL cc_start: 0.7153 (OUTLIER) cc_final: 0.6753 (p) REVERT: L 192 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6377 (tm-30) REVERT: L 202 GLU cc_start: 0.7296 (pp20) cc_final: 0.7065 (pt0) REVERT: L 207 MET cc_start: 0.7116 (mmp) cc_final: 0.5437 (ptp) outliers start: 347 outliers final: 168 residues processed: 877 average time/residue: 0.2283 time to fit residues: 313.7804 Evaluate side-chains 602 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 403 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1004 ASP Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1302 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1015 GLU Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1087 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1106 ILE Chi-restraints excluded: chain D residue 1160 SER Chi-restraints excluded: chain D residue 1170 LYS Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 581 ASP Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 143 PHE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 45 ASN Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 188 THR Chi-restraints excluded: chain L residue 194 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 160 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 128 HIS C 139 ASN C 165 HIS C 330 HIS C 628 HIS C 760 ASN C1116 HIS C1237 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN C1288 GLN D 157 GLN D 232 ASN D 294 ASN D 320 ASN D 365 GLN D 419 HIS D 712 GLN D 720 ASN D 805 GLN D 861 ASN D 951 GLN D1108 GLN D1197 ASN D1235 ASN D1238 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 309 ASN F 323 ASN F 406 GLN F 446 GLN F 464 ASN K 24 GLN K 40 HIS K 85 HIS L 24 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.162829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120120 restraints weight = 49252.159| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.89 r_work: 0.3229 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34812 Z= 0.158 Angle : 0.663 11.669 47399 Z= 0.345 Chirality : 0.043 0.235 5389 Planarity : 0.005 0.049 5902 Dihedral : 16.647 170.500 5801 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 5.67 % Allowed : 21.72 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.98 (0.12), residues: 4099 helix: -0.06 (0.12), residues: 1784 sheet: -1.76 (0.24), residues: 360 loop : -2.49 (0.12), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 352 TYR 0.024 0.001 TYR D 631 PHE 0.025 0.002 PHE L 149 TRP 0.011 0.001 TRP K 166 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00352 (34804) covalent geometry : angle 0.66188 (47387) hydrogen bonds : bond 0.04794 ( 1569) hydrogen bonds : angle 4.95904 ( 4403) metal coordination : bond 0.00750 ( 8) metal coordination : angle 2.74197 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 515 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8746 (pt0) cc_final: 0.8204 (mt-10) REVERT: A 117 HIS cc_start: 0.8264 (m90) cc_final: 0.7884 (t-170) REVERT: A 219 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (ttm-80) REVERT: A 231 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7784 (t80) REVERT: B 25 LYS cc_start: 0.8419 (tttt) cc_final: 0.8122 (ttmt) REVERT: B 95 LYS cc_start: 0.7545 (mtpt) cc_final: 0.6983 (mtmt) REVERT: B 181 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 200 LYS cc_start: 0.9058 (tttt) cc_final: 0.8780 (tttp) REVERT: C 304 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4875 (mp0) REVERT: C 315 MET cc_start: 0.7296 (tpp) cc_final: 0.6674 (ttm) REVERT: C 316 GLU cc_start: 0.7554 (pm20) cc_final: 0.7282 (pt0) REVERT: C 337 PHE cc_start: 0.7816 (t80) cc_final: 0.7568 (t80) REVERT: C 379 GLU cc_start: 0.7677 (mp0) cc_final: 0.7101 (tp30) REVERT: C 392 GLU cc_start: 0.8254 (tp30) cc_final: 0.7874 (mp0) REVERT: C 441 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 546 GLU cc_start: 0.8504 (tp30) cc_final: 0.7970 (mp0) REVERT: C 637 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7991 (mtm-85) REVERT: C 685 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: C 765 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8770 (mt) REVERT: C 957 LYS cc_start: 0.8634 (tttt) cc_final: 0.8227 (tptt) REVERT: C 1119 MET cc_start: 0.8778 (tpt) cc_final: 0.8513 (ttt) REVERT: C 1274 GLU cc_start: 0.8772 (mp0) cc_final: 0.8365 (mp0) REVERT: D 50 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8368 (mttt) REVERT: D 80 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (m90) REVERT: D 133 ARG cc_start: 0.7862 (mpp-170) cc_final: 0.7216 (mtm110) REVERT: D 217 LEU cc_start: 0.8691 (mp) cc_final: 0.8217 (mp) REVERT: D 322 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8195 (mtp85) REVERT: D 332 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8256 (pttp) REVERT: D 582 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (mp) REVERT: D 712 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: D 789 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8751 (ttpp) REVERT: D 805 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: D 932 MET cc_start: 0.5333 (ttp) cc_final: 0.4664 (ptp) REVERT: D 983 LYS cc_start: 0.7804 (mttt) cc_final: 0.7493 (ttmt) REVERT: D 1062 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.4336 (tp) REVERT: D 1072 LYS cc_start: 0.3702 (OUTLIER) cc_final: 0.1886 (mttt) REVERT: D 1187 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: D 1193 TRP cc_start: 0.5863 (m-90) cc_final: 0.5427 (m-10) REVERT: D 1199 PHE cc_start: 0.4581 (OUTLIER) cc_final: 0.3697 (m-80) REVERT: D 1208 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: D 1349 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: D 1353 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9055 (t) REVERT: D 1369 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7367 (ttt-90) REVERT: E 3 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7447 (tpt90) REVERT: E 42 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8277 (mp0) REVERT: E 68 GLU cc_start: 0.8039 (tt0) cc_final: 0.7035 (mt-10) REVERT: F 104 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: F 114 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: F 266 PHE cc_start: 0.7690 (t80) cc_final: 0.7301 (t80) REVERT: F 305 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.3122 (tt) REVERT: F 309 ASN cc_start: 0.2971 (OUTLIER) cc_final: 0.2496 (m110) REVERT: F 470 MET cc_start: 0.8680 (mtp) cc_final: 0.8405 (mtp) REVERT: F 485 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7436 (tm-30) REVERT: F 532 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (tp) REVERT: F 538 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: F 588 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5206 (ptp-170) REVERT: K 17 PRO cc_start: 0.6768 (Cg_endo) cc_final: 0.6308 (Cg_exo) REVERT: K 36 PHE cc_start: 0.7452 (p90) cc_final: 0.7192 (p90) REVERT: K 104 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8527 (t70) REVERT: K 121 SER cc_start: 0.2371 (OUTLIER) cc_final: 0.2170 (t) REVERT: K 126 ASP cc_start: 0.6476 (m-30) cc_final: 0.5932 (t0) REVERT: K 133 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6423 (ttp80) REVERT: K 160 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7555 (t80) REVERT: K 167 ARG cc_start: 0.6220 (mtt90) cc_final: 0.5653 (mtt90) REVERT: K 170 GLN cc_start: 0.8564 (tp40) cc_final: 0.7580 (tm-30) REVERT: K 204 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6445 (mm-30) REVERT: K 207 MET cc_start: 0.6556 (mtt) cc_final: 0.6279 (mtt) REVERT: L 136 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8177 (pp) REVERT: L 142 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6596 (p) REVERT: L 166 TRP cc_start: 0.8461 (t-100) cc_final: 0.7720 (t-100) REVERT: L 192 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6374 (tm-30) outliers start: 198 outliers final: 107 residues processed: 682 average time/residue: 0.2157 time to fit residues: 236.2125 Evaluate side-chains 546 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 408 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1302 THR Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1208 ASP Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 278 optimal weight: 8.9990 chunk 384 optimal weight: 0.7980 chunk 400 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 380 optimal weight: 0.0670 chunk 145 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 308 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 489 ASN D 739 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 309 ASN K 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.161853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119034 restraints weight = 48843.457| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.92 r_work: 0.3224 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34812 Z= 0.164 Angle : 0.625 11.945 47399 Z= 0.324 Chirality : 0.043 0.180 5389 Planarity : 0.005 0.051 5902 Dihedral : 16.032 168.158 5594 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.49 % Rotamer: Outliers : 5.21 % Allowed : 22.35 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.33 (0.13), residues: 4099 helix: 0.55 (0.12), residues: 1784 sheet: -1.36 (0.24), residues: 385 loop : -2.23 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 599 TYR 0.018 0.001 TYR D 631 PHE 0.026 0.002 PHE K 191 TRP 0.015 0.001 TRP K 166 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00379 (34804) covalent geometry : angle 0.62325 (47387) hydrogen bonds : bond 0.04574 ( 1569) hydrogen bonds : angle 4.69548 ( 4403) metal coordination : bond 0.00560 ( 8) metal coordination : angle 2.73655 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 447 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.8231 (m90) cc_final: 0.7920 (t-170) REVERT: A 231 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 25 LYS cc_start: 0.8372 (tttt) cc_final: 0.8060 (ttmt) REVERT: B 95 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7006 (mtmt) REVERT: B 181 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8139 (mt-10) REVERT: C 304 GLU cc_start: 0.5113 (OUTLIER) cc_final: 0.4872 (mp0) REVERT: C 379 GLU cc_start: 0.7677 (mp0) cc_final: 0.7235 (tp30) REVERT: C 392 GLU cc_start: 0.8187 (tp30) cc_final: 0.7905 (mp0) REVERT: C 546 GLU cc_start: 0.8576 (tp30) cc_final: 0.8174 (mp0) REVERT: C 694 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8081 (ptt-90) REVERT: C 765 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8646 (mt) REVERT: C 781 ASP cc_start: 0.8530 (t0) cc_final: 0.8308 (m-30) REVERT: C 870 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9010 (mt) REVERT: C 951 MET cc_start: 0.8563 (ttm) cc_final: 0.8278 (ttp) REVERT: C 957 LYS cc_start: 0.8677 (tttt) cc_final: 0.8312 (tptt) REVERT: C 1119 MET cc_start: 0.8921 (tpt) cc_final: 0.8567 (ttt) REVERT: C 1236 ASN cc_start: 0.8649 (p0) cc_final: 0.8220 (t0) REVERT: D 133 ARG cc_start: 0.7950 (mpp-170) cc_final: 0.7370 (mtm110) REVERT: D 217 LEU cc_start: 0.8645 (mp) cc_final: 0.8230 (mp) REVERT: D 332 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8452 (pttp) REVERT: D 805 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: D 932 MET cc_start: 0.5280 (ttp) cc_final: 0.4653 (ptp) REVERT: D 983 LYS cc_start: 0.7891 (mttt) cc_final: 0.7587 (ttmt) REVERT: D 1072 LYS cc_start: 0.3918 (OUTLIER) cc_final: 0.2080 (mmtt) REVERT: D 1189 MET cc_start: 0.8190 (mmt) cc_final: 0.7830 (mmm) REVERT: D 1193 TRP cc_start: 0.5726 (m-90) cc_final: 0.5365 (m-10) REVERT: D 1199 PHE cc_start: 0.4264 (OUTLIER) cc_final: 0.3645 (m-80) REVERT: D 1282 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: D 1369 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7532 (ttt-90) REVERT: E 3 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7169 (tpt170) REVERT: E 18 ASP cc_start: 0.8530 (m-30) cc_final: 0.8328 (m-30) REVERT: E 42 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8210 (mp0) REVERT: E 67 ARG cc_start: 0.7924 (tpt90) cc_final: 0.7488 (mtp85) REVERT: E 68 GLU cc_start: 0.8074 (tt0) cc_final: 0.7043 (mt-10) REVERT: E 71 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7677 (mm-30) REVERT: F 114 GLU cc_start: 0.7481 (pp20) cc_final: 0.7124 (tp30) REVERT: F 266 PHE cc_start: 0.7596 (t80) cc_final: 0.7242 (t80) REVERT: F 273 MET cc_start: 0.7218 (tpt) cc_final: 0.6718 (tpt) REVERT: F 288 MET cc_start: 0.3627 (tpt) cc_final: 0.3328 (tpp) REVERT: F 305 LEU cc_start: 0.3693 (OUTLIER) cc_final: 0.3147 (tp) REVERT: F 309 ASN cc_start: 0.4178 (OUTLIER) cc_final: 0.2567 (m-40) REVERT: F 485 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7414 (tm-30) REVERT: F 508 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: F 509 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8865 (p) REVERT: F 532 LEU cc_start: 0.8526 (tp) cc_final: 0.8296 (tp) REVERT: F 538 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: F 581 ASP cc_start: 0.5882 (m-30) cc_final: 0.5534 (m-30) REVERT: K 17 PRO cc_start: 0.6898 (Cg_endo) cc_final: 0.6636 (Cg_exo) REVERT: K 36 PHE cc_start: 0.7624 (p90) cc_final: 0.7333 (p90) REVERT: K 68 THR cc_start: 0.8781 (p) cc_final: 0.8462 (m) REVERT: K 126 ASP cc_start: 0.6413 (m-30) cc_final: 0.5953 (p0) REVERT: K 133 ARG cc_start: 0.6566 (ttp80) cc_final: 0.6296 (ptm-80) REVERT: K 166 TRP cc_start: 0.7249 (t-100) cc_final: 0.6940 (t-100) REVERT: K 167 ARG cc_start: 0.6186 (mtt90) cc_final: 0.5769 (mtt90) REVERT: K 170 GLN cc_start: 0.8642 (tp40) cc_final: 0.7715 (tm-30) REVERT: K 204 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6166 (mm-30) REVERT: K 207 MET cc_start: 0.6725 (mtt) cc_final: 0.6479 (mtt) REVERT: L 136 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8186 (pp) REVERT: L 166 TRP cc_start: 0.8508 (t-100) cc_final: 0.8133 (t-100) REVERT: L 192 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6261 (tm-30) REVERT: L 196 PHE cc_start: 0.7934 (t80) cc_final: 0.7674 (t80) REVERT: L 207 MET cc_start: 0.7337 (mmp) cc_final: 0.6877 (mmm) outliers start: 182 outliers final: 121 residues processed: 602 average time/residue: 0.2028 time to fit residues: 199.9723 Evaluate side-chains 540 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 403 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 386 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 99 optimal weight: 0.0040 chunk 321 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 327 GLN C 510 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 424 ASN ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 309 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119169 restraints weight = 48732.917| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.00 r_work: 0.3211 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34812 Z= 0.130 Angle : 0.592 14.190 47399 Z= 0.307 Chirality : 0.042 0.176 5389 Planarity : 0.004 0.056 5902 Dihedral : 15.818 168.702 5561 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 5.04 % Allowed : 23.15 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.95 (0.13), residues: 4099 helix: 0.87 (0.12), residues: 1785 sheet: -1.06 (0.26), residues: 355 loop : -2.04 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1269 TYR 0.018 0.001 TYR D 631 PHE 0.020 0.001 PHE L 149 TRP 0.011 0.001 TRP F 433 HIS 0.014 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00293 (34804) covalent geometry : angle 0.59167 (47387) hydrogen bonds : bond 0.04171 ( 1569) hydrogen bonds : angle 4.47146 ( 4403) metal coordination : bond 0.00336 ( 8) metal coordination : angle 1.95118 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 426 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.8325 (m90) cc_final: 0.7896 (t-170) REVERT: A 231 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 15 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7521 (p0) REVERT: B 25 LYS cc_start: 0.8314 (tttt) cc_final: 0.7989 (ttmt) REVERT: B 95 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7011 (mtmt) REVERT: C 304 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4656 (mp0) REVERT: C 379 GLU cc_start: 0.7807 (mp0) cc_final: 0.7207 (tp30) REVERT: C 392 GLU cc_start: 0.8259 (tp30) cc_final: 0.7936 (mp0) REVERT: C 546 GLU cc_start: 0.8695 (tp30) cc_final: 0.8230 (mp0) REVERT: C 637 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8125 (mtm-85) REVERT: C 694 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8000 (ptt-90) REVERT: C 765 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 870 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.9002 (mt) REVERT: C 951 MET cc_start: 0.8492 (ttm) cc_final: 0.8207 (ttp) REVERT: C 957 LYS cc_start: 0.8619 (tttt) cc_final: 0.8257 (tptt) REVERT: C 963 GLU cc_start: 0.6154 (tm-30) cc_final: 0.4808 (mm-30) REVERT: C 1005 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4198 (tp30) REVERT: C 1119 MET cc_start: 0.8911 (tpt) cc_final: 0.8555 (ttt) REVERT: D 67 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8369 (t0) REVERT: D 133 ARG cc_start: 0.7992 (mpp-170) cc_final: 0.7371 (mtm110) REVERT: D 137 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7572 (mtm-85) REVERT: D 217 LEU cc_start: 0.8643 (mp) cc_final: 0.8278 (mp) REVERT: D 332 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8302 (pttp) REVERT: D 338 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8187 (t80) REVERT: D 582 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8671 (mp) REVERT: D 712 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: D 805 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 932 MET cc_start: 0.5297 (ttp) cc_final: 0.4650 (ptp) REVERT: D 983 LYS cc_start: 0.7832 (mttt) cc_final: 0.7397 (tppt) REVERT: D 993 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6743 (mp0) REVERT: D 1072 LYS cc_start: 0.3847 (OUTLIER) cc_final: 0.2170 (mmtt) REVERT: D 1189 MET cc_start: 0.8301 (mmt) cc_final: 0.7885 (mmm) REVERT: D 1193 TRP cc_start: 0.5767 (m-90) cc_final: 0.5414 (m-10) REVERT: D 1199 PHE cc_start: 0.4213 (OUTLIER) cc_final: 0.3870 (m-80) REVERT: D 1282 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: D 1353 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9060 (t) REVERT: D 1369 ARG cc_start: 0.7824 (ttt180) cc_final: 0.7409 (ttt-90) REVERT: E 3 ARG cc_start: 0.8237 (tpp-160) cc_final: 0.7162 (tpt170) REVERT: E 42 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8112 (mp0) REVERT: E 56 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7933 (tt0) REVERT: E 67 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7253 (mtp85) REVERT: E 68 GLU cc_start: 0.8046 (tt0) cc_final: 0.7004 (mt-10) REVERT: E 71 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7607 (mm-30) REVERT: F 114 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: F 266 PHE cc_start: 0.7560 (t80) cc_final: 0.7206 (t80) REVERT: F 273 MET cc_start: 0.7207 (tpt) cc_final: 0.6601 (tpt) REVERT: F 305 LEU cc_start: 0.3653 (OUTLIER) cc_final: 0.3182 (tp) REVERT: F 309 ASN cc_start: 0.3360 (OUTLIER) cc_final: 0.1357 (t0) REVERT: F 365 MET cc_start: 0.7642 (ttm) cc_final: 0.7430 (ttp) REVERT: F 485 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7438 (tm-30) REVERT: F 509 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8872 (p) REVERT: F 532 LEU cc_start: 0.8497 (tp) cc_final: 0.8242 (tp) REVERT: F 579 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.6117 (pp30) REVERT: K 24 GLN cc_start: 0.6693 (mt0) cc_final: 0.6302 (mt0) REVERT: K 36 PHE cc_start: 0.7487 (p90) cc_final: 0.7171 (p90) REVERT: K 68 THR cc_start: 0.8835 (p) cc_final: 0.8557 (m) REVERT: K 133 ARG cc_start: 0.6519 (ttp80) cc_final: 0.6119 (ptm-80) REVERT: K 166 TRP cc_start: 0.7119 (t-100) cc_final: 0.6905 (t-100) REVERT: K 167 ARG cc_start: 0.6638 (mtt90) cc_final: 0.6154 (mtt90) REVERT: K 170 GLN cc_start: 0.8622 (tp40) cc_final: 0.7939 (tm-30) REVERT: K 204 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6357 (mm-30) REVERT: K 207 MET cc_start: 0.6426 (mtt) cc_final: 0.6071 (mtt) REVERT: L 136 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8157 (pp) REVERT: L 166 TRP cc_start: 0.8423 (t-100) cc_final: 0.7460 (t-100) REVERT: L 186 TYR cc_start: 0.6268 (t80) cc_final: 0.5962 (t80) REVERT: L 207 MET cc_start: 0.7218 (mmp) cc_final: 0.6886 (mmm) outliers start: 176 outliers final: 119 residues processed: 573 average time/residue: 0.2089 time to fit residues: 195.5030 Evaluate side-chains 533 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 390 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 188 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 293 optimal weight: 20.0000 chunk 340 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 266 optimal weight: 0.6980 chunk 230 optimal weight: 8.9990 chunk 399 optimal weight: 0.0670 chunk 145 optimal weight: 6.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1146 GLN C1236 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 70 GLN E 72 GLN F 309 ASN F 383 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118323 restraints weight = 48783.271| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.98 r_work: 0.3194 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34812 Z= 0.153 Angle : 0.594 13.990 47399 Z= 0.309 Chirality : 0.042 0.166 5389 Planarity : 0.004 0.057 5902 Dihedral : 15.704 167.548 5552 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.17 % Favored : 92.78 % Rotamer: Outliers : 5.44 % Allowed : 23.61 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.75 (0.13), residues: 4099 helix: 1.01 (0.12), residues: 1782 sheet: -0.90 (0.26), residues: 358 loop : -1.92 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 322 TYR 0.039 0.001 TYR D 144 PHE 0.017 0.001 PHE K 191 TRP 0.008 0.001 TRP F 326 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00355 (34804) covalent geometry : angle 0.59310 (47387) hydrogen bonds : bond 0.04229 ( 1569) hydrogen bonds : angle 4.41050 ( 4403) metal coordination : bond 0.00438 ( 8) metal coordination : angle 2.14050 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 425 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: A 231 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7902 (t80) REVERT: B 15 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7488 (p0) REVERT: B 25 LYS cc_start: 0.8367 (tttt) cc_final: 0.8011 (ttmt) REVERT: B 95 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7027 (mtmt) REVERT: C 379 GLU cc_start: 0.7831 (mp0) cc_final: 0.7235 (tp30) REVERT: C 392 GLU cc_start: 0.8267 (tp30) cc_final: 0.7916 (mp0) REVERT: C 546 GLU cc_start: 0.8617 (tp30) cc_final: 0.8200 (mp0) REVERT: C 688 GLN cc_start: 0.9045 (mt0) cc_final: 0.8736 (tt0) REVERT: C 694 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7997 (ptt-90) REVERT: C 870 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9088 (mt) REVERT: C 951 MET cc_start: 0.8491 (ttm) cc_final: 0.8207 (ttp) REVERT: C 957 LYS cc_start: 0.8639 (tttt) cc_final: 0.8295 (tptt) REVERT: C 984 VAL cc_start: 0.4725 (OUTLIER) cc_final: 0.4383 (m) REVERT: C 1005 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4056 (tp30) REVERT: C 1119 MET cc_start: 0.8951 (tpt) cc_final: 0.8566 (ttt) REVERT: C 1303 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8762 (mmmt) REVERT: D 133 ARG cc_start: 0.8016 (mpp-170) cc_final: 0.7402 (mtm110) REVERT: D 137 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7666 (mtm-85) REVERT: D 217 LEU cc_start: 0.8636 (mp) cc_final: 0.8279 (mp) REVERT: D 332 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8308 (pttp) REVERT: D 582 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8692 (mp) REVERT: D 663 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: D 712 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: D 805 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: D 874 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5908 (tp30) REVERT: D 932 MET cc_start: 0.5371 (ttp) cc_final: 0.4740 (ptp) REVERT: D 955 LYS cc_start: 0.6912 (tmtt) cc_final: 0.6707 (mppt) REVERT: D 983 LYS cc_start: 0.7839 (mttt) cc_final: 0.7363 (tppt) REVERT: D 993 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6791 (mp0) REVERT: D 1062 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.4103 (tt) REVERT: D 1072 LYS cc_start: 0.3969 (OUTLIER) cc_final: 0.2319 (mmtt) REVERT: D 1189 MET cc_start: 0.8287 (mmt) cc_final: 0.8054 (mmm) REVERT: D 1193 TRP cc_start: 0.5596 (m-90) cc_final: 0.5266 (m-10) REVERT: D 1199 PHE cc_start: 0.4142 (OUTLIER) cc_final: 0.3798 (m-80) REVERT: D 1282 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: D 1353 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9046 (t) REVERT: D 1369 ARG cc_start: 0.7858 (ttt180) cc_final: 0.7404 (ttt-90) REVERT: E 3 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.7147 (tpt170) REVERT: E 42 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8825 (mp0) REVERT: E 56 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7889 (tt0) REVERT: E 67 ARG cc_start: 0.7769 (tpt90) cc_final: 0.7245 (mtp85) REVERT: E 68 GLU cc_start: 0.8014 (tt0) cc_final: 0.7038 (mt-10) REVERT: E 71 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7664 (mm-30) REVERT: F 114 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: F 266 PHE cc_start: 0.7569 (t80) cc_final: 0.7061 (t80) REVERT: F 273 MET cc_start: 0.7016 (tpt) cc_final: 0.6566 (tpt) REVERT: F 305 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3208 (tp) REVERT: F 309 ASN cc_start: 0.3495 (OUTLIER) cc_final: 0.1623 (t0) REVERT: F 509 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8877 (p) REVERT: F 538 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: K 36 PHE cc_start: 0.7408 (p90) cc_final: 0.7109 (p90) REVERT: K 52 ASP cc_start: 0.7506 (m-30) cc_final: 0.7216 (m-30) REVERT: K 68 THR cc_start: 0.8752 (p) cc_final: 0.8480 (m) REVERT: K 103 MET cc_start: 0.8806 (mtm) cc_final: 0.8453 (mtp) REVERT: K 126 ASP cc_start: 0.6623 (m-30) cc_final: 0.6235 (p0) REVERT: K 167 ARG cc_start: 0.6571 (mtt90) cc_final: 0.6038 (mtt90) REVERT: K 170 GLN cc_start: 0.8568 (tp40) cc_final: 0.8107 (tm-30) REVERT: K 193 ARG cc_start: 0.6560 (mtp-110) cc_final: 0.6267 (mtp-110) REVERT: K 204 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6531 (mm-30) REVERT: L 136 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8106 (pp) REVERT: L 166 TRP cc_start: 0.8537 (t-100) cc_final: 0.7827 (t-100) REVERT: L 186 TYR cc_start: 0.6427 (t80) cc_final: 0.6076 (t80) REVERT: L 207 MET cc_start: 0.7297 (mmp) cc_final: 0.7030 (mmm) outliers start: 190 outliers final: 127 residues processed: 586 average time/residue: 0.2097 time to fit residues: 199.0842 Evaluate side-chains 544 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 393 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 106 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 393 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 328 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 309 ASN F 446 GLN K 40 HIS L 24 GLN L 85 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118864 restraints weight = 47883.286| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.90 r_work: 0.3205 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34812 Z= 0.148 Angle : 0.594 14.857 47399 Z= 0.307 Chirality : 0.042 0.196 5389 Planarity : 0.004 0.059 5902 Dihedral : 15.582 167.346 5539 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.90 % Favored : 93.05 % Rotamer: Outliers : 5.92 % Allowed : 22.98 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.62 (0.13), residues: 4099 helix: 1.11 (0.13), residues: 1779 sheet: -0.86 (0.25), residues: 374 loop : -1.84 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1269 TYR 0.032 0.001 TYR D 144 PHE 0.020 0.001 PHE K 191 TRP 0.009 0.001 TRP K 166 HIS 0.006 0.001 HIS L 85 Details of bonding type rmsd covalent geometry : bond 0.00342 (34804) covalent geometry : angle 0.59273 (47387) hydrogen bonds : bond 0.04168 ( 1569) hydrogen bonds : angle 4.36422 ( 4403) metal coordination : bond 0.00378 ( 8) metal coordination : angle 2.23593 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 406 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7472 (p0) REVERT: B 25 LYS cc_start: 0.8375 (tttt) cc_final: 0.8012 (ttmt) REVERT: B 95 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7044 (mtmt) REVERT: C 379 GLU cc_start: 0.7692 (mp0) cc_final: 0.7208 (tp30) REVERT: C 392 GLU cc_start: 0.8278 (tp30) cc_final: 0.7933 (mp0) REVERT: C 546 GLU cc_start: 0.8560 (tp30) cc_final: 0.8186 (mp0) REVERT: C 688 GLN cc_start: 0.9065 (mt0) cc_final: 0.8858 (tt0) REVERT: C 694 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7973 (ptt-90) REVERT: C 870 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9089 (mt) REVERT: C 940 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: C 951 MET cc_start: 0.8467 (ttm) cc_final: 0.8183 (ttp) REVERT: C 957 LYS cc_start: 0.8662 (tttt) cc_final: 0.8349 (tptt) REVERT: C 984 VAL cc_start: 0.4701 (OUTLIER) cc_final: 0.4349 (m) REVERT: C 1005 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.3982 (tp30) REVERT: C 1119 MET cc_start: 0.8979 (tpt) cc_final: 0.8587 (ttt) REVERT: C 1303 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8747 (mmmt) REVERT: D 133 ARG cc_start: 0.8063 (mpp-170) cc_final: 0.7419 (mtm110) REVERT: D 137 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7676 (mtm-85) REVERT: D 217 LEU cc_start: 0.8619 (mp) cc_final: 0.8274 (mp) REVERT: D 332 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8542 (pttp) REVERT: D 582 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8744 (mp) REVERT: D 663 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: D 712 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: D 764 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7385 (tmt90) REVERT: D 805 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: D 874 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5911 (tp30) REVERT: D 932 MET cc_start: 0.5358 (ttp) cc_final: 0.4742 (ptp) REVERT: D 955 LYS cc_start: 0.6904 (tmtt) cc_final: 0.6701 (mppt) REVERT: D 983 LYS cc_start: 0.7811 (mttt) cc_final: 0.7368 (tppt) REVERT: D 1062 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4166 (tt) REVERT: D 1072 LYS cc_start: 0.3933 (OUTLIER) cc_final: 0.2329 (mmtt) REVERT: D 1189 MET cc_start: 0.8365 (mmt) cc_final: 0.8126 (mmm) REVERT: D 1193 TRP cc_start: 0.5617 (m-90) cc_final: 0.5395 (m-10) REVERT: D 1199 PHE cc_start: 0.4205 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: D 1282 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: D 1353 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9032 (t) REVERT: D 1369 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7526 (ttt-90) REVERT: E 3 ARG cc_start: 0.8197 (tpp-160) cc_final: 0.7230 (tpt170) REVERT: E 42 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8794 (mp0) REVERT: E 56 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8017 (tt0) REVERT: E 67 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7356 (mtp85) REVERT: E 68 GLU cc_start: 0.8030 (tt0) cc_final: 0.7108 (mt-10) REVERT: F 102 MET cc_start: 0.8968 (mmm) cc_final: 0.7424 (mmm) REVERT: F 266 PHE cc_start: 0.7484 (t80) cc_final: 0.7060 (t80) REVERT: F 273 MET cc_start: 0.6991 (tpt) cc_final: 0.6540 (tpt) REVERT: F 288 MET cc_start: 0.3779 (tpt) cc_final: 0.3387 (tpp) REVERT: F 305 LEU cc_start: 0.3726 (OUTLIER) cc_final: 0.3288 (tp) REVERT: F 309 ASN cc_start: 0.3028 (OUTLIER) cc_final: 0.1229 (t0) REVERT: F 509 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8872 (p) REVERT: F 532 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8328 (tp) REVERT: F 538 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: K 36 PHE cc_start: 0.7444 (p90) cc_final: 0.7155 (p90) REVERT: K 52 ASP cc_start: 0.7544 (m-30) cc_final: 0.7240 (m-30) REVERT: K 68 THR cc_start: 0.8732 (p) cc_final: 0.8489 (m) REVERT: K 126 ASP cc_start: 0.6685 (m-30) cc_final: 0.6325 (p0) REVERT: K 170 GLN cc_start: 0.8546 (tp40) cc_final: 0.8093 (tm-30) REVERT: K 193 ARG cc_start: 0.6494 (mtp-110) cc_final: 0.6229 (mtp-110) REVERT: K 204 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6605 (mm-30) REVERT: L 102 TYR cc_start: 0.8508 (m-10) cc_final: 0.8287 (m-10) REVERT: L 136 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8092 (pp) REVERT: L 186 TYR cc_start: 0.6695 (t80) cc_final: 0.6275 (t80) REVERT: L 196 PHE cc_start: 0.8133 (t80) cc_final: 0.7599 (t80) REVERT: L 207 MET cc_start: 0.7312 (mmp) cc_final: 0.7047 (mmm) outliers start: 207 outliers final: 142 residues processed: 581 average time/residue: 0.2059 time to fit residues: 196.5332 Evaluate side-chains 554 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 387 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 503 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 177 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 309 ASN F 446 GLN K 40 HIS L 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117719 restraints weight = 48784.525| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.90 r_work: 0.3184 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34812 Z= 0.190 Angle : 0.617 14.595 47399 Z= 0.319 Chirality : 0.043 0.182 5389 Planarity : 0.004 0.058 5902 Dihedral : 15.524 166.421 5530 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 5.55 % Allowed : 23.53 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.66 (0.13), residues: 4099 helix: 1.05 (0.12), residues: 1779 sheet: -0.85 (0.24), residues: 387 loop : -1.84 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1269 TYR 0.026 0.001 TYR D 144 PHE 0.029 0.002 PHE L 191 TRP 0.012 0.001 TRP L 166 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00452 (34804) covalent geometry : angle 0.61561 (47387) hydrogen bonds : bond 0.04349 ( 1569) hydrogen bonds : angle 4.39633 ( 4403) metal coordination : bond 0.00599 ( 8) metal coordination : angle 2.39281 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 393 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8693 (tp) REVERT: B 25 LYS cc_start: 0.8414 (tttt) cc_final: 0.8142 (tttt) REVERT: B 95 LYS cc_start: 0.7597 (mtpt) cc_final: 0.6999 (mtmt) REVERT: C 118 LYS cc_start: 0.8058 (mttp) cc_final: 0.7644 (pptt) REVERT: C 379 GLU cc_start: 0.7680 (mp0) cc_final: 0.7343 (tp30) REVERT: C 439 LYS cc_start: 0.8732 (ptmm) cc_final: 0.8526 (ptmt) REVERT: C 546 GLU cc_start: 0.8528 (tp30) cc_final: 0.8186 (mp0) REVERT: C 694 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: C 870 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mt) REVERT: C 940 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: C 951 MET cc_start: 0.8413 (ttm) cc_final: 0.8136 (ttp) REVERT: C 957 LYS cc_start: 0.8683 (tttt) cc_final: 0.8350 (tptt) REVERT: C 984 VAL cc_start: 0.4812 (OUTLIER) cc_final: 0.4461 (m) REVERT: C 1119 MET cc_start: 0.8937 (tpt) cc_final: 0.8531 (ttt) REVERT: C 1303 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8613 (mmmm) REVERT: D 60 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8707 (ttm-80) REVERT: D 133 ARG cc_start: 0.8097 (mpp-170) cc_final: 0.7853 (mpp80) REVERT: D 137 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7830 (mmm-85) REVERT: D 217 LEU cc_start: 0.8650 (mp) cc_final: 0.8285 (mp) REVERT: D 332 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8469 (pttp) REVERT: D 663 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: D 805 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: D 874 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5967 (tp30) REVERT: D 932 MET cc_start: 0.5217 (ttp) cc_final: 0.4769 (ptp) REVERT: D 983 LYS cc_start: 0.7837 (mttt) cc_final: 0.7506 (ttmt) REVERT: D 1062 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4195 (tt) REVERT: D 1072 LYS cc_start: 0.4301 (OUTLIER) cc_final: 0.2587 (mmtt) REVERT: D 1189 MET cc_start: 0.8344 (mmt) cc_final: 0.7915 (mtm) REVERT: D 1199 PHE cc_start: 0.4189 (OUTLIER) cc_final: 0.3831 (m-80) REVERT: D 1282 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: D 1286 LYS cc_start: 0.6664 (ttmt) cc_final: 0.6168 (ptmt) REVERT: D 1353 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9059 (t) REVERT: D 1369 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7607 (ttp80) REVERT: E 3 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7196 (tpt170) REVERT: E 42 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8785 (mp0) REVERT: E 56 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8040 (tt0) REVERT: E 67 ARG cc_start: 0.7796 (tpt90) cc_final: 0.7501 (mtp85) REVERT: E 68 GLU cc_start: 0.8022 (tt0) cc_final: 0.7169 (mt-10) REVERT: E 71 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7124 (mm-30) REVERT: F 102 MET cc_start: 0.9005 (mmm) cc_final: 0.7505 (mmm) REVERT: F 266 PHE cc_start: 0.7470 (t80) cc_final: 0.6904 (t80) REVERT: F 273 MET cc_start: 0.6996 (tpt) cc_final: 0.6618 (tpt) REVERT: F 288 MET cc_start: 0.3877 (tpt) cc_final: 0.3497 (tpp) REVERT: F 305 LEU cc_start: 0.3694 (OUTLIER) cc_final: 0.3265 (tp) REVERT: F 309 ASN cc_start: 0.2957 (OUTLIER) cc_final: 0.1192 (t0) REVERT: F 509 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8841 (p) REVERT: F 532 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8295 (tp) REVERT: F 538 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: F 587 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7198 (mp) REVERT: K 36 PHE cc_start: 0.7443 (p90) cc_final: 0.7124 (p90) REVERT: K 52 ASP cc_start: 0.7555 (m-30) cc_final: 0.7247 (m-30) REVERT: K 68 THR cc_start: 0.8759 (p) cc_final: 0.8502 (m) REVERT: K 103 MET cc_start: 0.8810 (mtm) cc_final: 0.8483 (mtp) REVERT: K 148 TYR cc_start: 0.8221 (m-80) cc_final: 0.7798 (m-80) REVERT: K 170 GLN cc_start: 0.8570 (tp40) cc_final: 0.8070 (tm-30) REVERT: K 193 ARG cc_start: 0.6538 (mtp-110) cc_final: 0.6188 (mtp-110) REVERT: L 136 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (pp) REVERT: L 148 TYR cc_start: 0.7474 (m-80) cc_final: 0.7046 (m-80) REVERT: L 166 TRP cc_start: 0.8506 (t-100) cc_final: 0.8008 (t-100) REVERT: L 207 MET cc_start: 0.7441 (mmp) cc_final: 0.7102 (mmm) outliers start: 194 outliers final: 151 residues processed: 559 average time/residue: 0.2021 time to fit residues: 185.7707 Evaluate side-chains 551 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 378 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 394 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 688 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 309 ASN K 40 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.161526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117778 restraints weight = 48129.572| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.91 r_work: 0.3186 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34812 Z= 0.164 Angle : 0.607 14.732 47399 Z= 0.313 Chirality : 0.042 0.195 5389 Planarity : 0.004 0.057 5902 Dihedral : 15.478 166.928 5528 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 5.47 % Allowed : 23.81 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.58 (0.13), residues: 4099 helix: 1.10 (0.12), residues: 1777 sheet: -0.76 (0.25), residues: 365 loop : -1.77 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 322 TYR 0.023 0.001 TYR D 144 PHE 0.030 0.002 PHE K 191 TRP 0.018 0.001 TRP F 433 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00384 (34804) covalent geometry : angle 0.60561 (47387) hydrogen bonds : bond 0.04225 ( 1569) hydrogen bonds : angle 4.37065 ( 4403) metal coordination : bond 0.00431 ( 8) metal coordination : angle 2.34870 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 389 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.8390 (tttt) cc_final: 0.8125 (tttt) REVERT: B 95 LYS cc_start: 0.7619 (mtpt) cc_final: 0.6987 (mtmt) REVERT: C 118 LYS cc_start: 0.8123 (mttp) cc_final: 0.7590 (pptt) REVERT: C 379 GLU cc_start: 0.7732 (mp0) cc_final: 0.7269 (tp30) REVERT: C 546 GLU cc_start: 0.8523 (tp30) cc_final: 0.8157 (mp0) REVERT: C 653 MET cc_start: 0.9169 (ttt) cc_final: 0.8915 (ttt) REVERT: C 694 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7964 (ptt-90) REVERT: C 870 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9127 (mt) REVERT: C 940 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: C 951 MET cc_start: 0.8411 (ttm) cc_final: 0.8135 (ttp) REVERT: C 957 LYS cc_start: 0.8709 (tttt) cc_final: 0.8369 (tptt) REVERT: C 984 VAL cc_start: 0.4817 (OUTLIER) cc_final: 0.4484 (m) REVERT: C 1005 GLU cc_start: 0.4872 (OUTLIER) cc_final: 0.4033 (tp30) REVERT: C 1085 MET cc_start: 0.9154 (mmm) cc_final: 0.8938 (mmm) REVERT: C 1119 MET cc_start: 0.8944 (tpt) cc_final: 0.8533 (ttt) REVERT: C 1303 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8618 (mmmm) REVERT: D 60 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8682 (ttm-80) REVERT: D 217 LEU cc_start: 0.8594 (mp) cc_final: 0.8235 (mp) REVERT: D 332 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8391 (pttp) REVERT: D 663 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: D 684 ASP cc_start: 0.8016 (m-30) cc_final: 0.7737 (m-30) REVERT: D 712 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: D 764 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.7542 (tmt90) REVERT: D 805 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: D 874 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5990 (tp30) REVERT: D 932 MET cc_start: 0.5258 (ttp) cc_final: 0.4795 (ptp) REVERT: D 983 LYS cc_start: 0.7817 (mttt) cc_final: 0.7499 (ttmt) REVERT: D 1062 LEU cc_start: 0.4224 (OUTLIER) cc_final: 0.3950 (tt) REVERT: D 1072 LYS cc_start: 0.4233 (OUTLIER) cc_final: 0.2566 (mmtt) REVERT: D 1199 PHE cc_start: 0.4232 (OUTLIER) cc_final: 0.3901 (m-80) REVERT: D 1282 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: D 1286 LYS cc_start: 0.6614 (ttmt) cc_final: 0.6122 (ptmt) REVERT: D 1353 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.9053 (t) REVERT: D 1369 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7641 (ttt-90) REVERT: E 3 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7688 (tpp-160) REVERT: E 42 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8792 (mp0) REVERT: E 56 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8060 (tt0) REVERT: E 67 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7461 (mtp85) REVERT: E 68 GLU cc_start: 0.7989 (tt0) cc_final: 0.7143 (mt-10) REVERT: E 71 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7429 (mm-30) REVERT: F 102 MET cc_start: 0.8970 (mmm) cc_final: 0.7471 (mmm) REVERT: F 266 PHE cc_start: 0.7470 (t80) cc_final: 0.6985 (t80) REVERT: F 273 MET cc_start: 0.7031 (tpt) cc_final: 0.6724 (tpt) REVERT: F 288 MET cc_start: 0.3892 (tpt) cc_final: 0.3529 (tpp) REVERT: F 305 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3158 (tt) REVERT: F 309 ASN cc_start: 0.2730 (OUTLIER) cc_final: 0.1067 (t0) REVERT: F 392 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7737 (ttmt) REVERT: F 509 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8847 (p) REVERT: F 532 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8291 (tp) REVERT: F 538 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: K 36 PHE cc_start: 0.7432 (p90) cc_final: 0.7117 (p90) REVERT: K 52 ASP cc_start: 0.7559 (m-30) cc_final: 0.7248 (m-30) REVERT: K 68 THR cc_start: 0.8756 (p) cc_final: 0.8526 (m) REVERT: K 103 MET cc_start: 0.8782 (mtm) cc_final: 0.8430 (mtp) REVERT: K 148 TYR cc_start: 0.8218 (m-80) cc_final: 0.7848 (m-80) REVERT: K 170 GLN cc_start: 0.8587 (tp40) cc_final: 0.7951 (tm-30) REVERT: K 184 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7413 (mmmt) REVERT: K 193 ARG cc_start: 0.6528 (mtp-110) cc_final: 0.6123 (mtp-110) REVERT: K 207 MET cc_start: 0.6849 (mtt) cc_final: 0.6440 (mtt) REVERT: L 98 GLU cc_start: 0.8681 (tt0) cc_final: 0.8479 (tt0) REVERT: L 136 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8075 (pp) REVERT: L 186 TYR cc_start: 0.7067 (t80) cc_final: 0.6626 (t80) REVERT: L 196 PHE cc_start: 0.8108 (t80) cc_final: 0.7713 (t80) outliers start: 191 outliers final: 151 residues processed: 551 average time/residue: 0.2064 time to fit residues: 185.9612 Evaluate side-chains 554 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 379 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 88 optimal weight: 0.0020 chunk 263 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 409 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 329 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 361 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118821 restraints weight = 48012.199| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.91 r_work: 0.3197 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34812 Z= 0.135 Angle : 0.590 15.360 47399 Z= 0.305 Chirality : 0.042 0.206 5389 Planarity : 0.004 0.056 5902 Dihedral : 15.398 167.615 5527 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.86 % Favored : 93.10 % Rotamer: Outliers : 5.09 % Allowed : 24.18 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.48 (0.13), residues: 4099 helix: 1.18 (0.13), residues: 1781 sheet: -0.75 (0.25), residues: 363 loop : -1.72 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 322 TYR 0.021 0.001 TYR D 144 PHE 0.030 0.001 PHE K 191 TRP 0.011 0.001 TRP L 166 HIS 0.011 0.001 HIS K 40 Details of bonding type rmsd covalent geometry : bond 0.00308 (34804) covalent geometry : angle 0.58931 (47387) hydrogen bonds : bond 0.04055 ( 1569) hydrogen bonds : angle 4.31796 ( 4403) metal coordination : bond 0.00297 ( 8) metal coordination : angle 2.12331 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 394 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 25 LYS cc_start: 0.8408 (tttt) cc_final: 0.8128 (tttt) REVERT: B 95 LYS cc_start: 0.7618 (mtpt) cc_final: 0.6988 (mtmt) REVERT: C 118 LYS cc_start: 0.8053 (mttp) cc_final: 0.7538 (pptt) REVERT: C 379 GLU cc_start: 0.7734 (mp0) cc_final: 0.7272 (tp30) REVERT: C 546 GLU cc_start: 0.8527 (tp30) cc_final: 0.8156 (mp0) REVERT: C 653 MET cc_start: 0.9141 (ttt) cc_final: 0.8883 (ttt) REVERT: C 694 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7967 (ptt-90) REVERT: C 870 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9122 (mt) REVERT: C 940 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: C 951 MET cc_start: 0.8423 (ttm) cc_final: 0.8137 (ttp) REVERT: C 957 LYS cc_start: 0.8680 (tttt) cc_final: 0.8362 (tptt) REVERT: C 984 VAL cc_start: 0.4826 (OUTLIER) cc_final: 0.4482 (m) REVERT: C 1005 GLU cc_start: 0.4871 (OUTLIER) cc_final: 0.4008 (tp30) REVERT: C 1085 MET cc_start: 0.9138 (mmm) cc_final: 0.8919 (mmm) REVERT: C 1119 MET cc_start: 0.8965 (tpt) cc_final: 0.8572 (ttt) REVERT: C 1303 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8634 (mmmm) REVERT: D 159 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 217 LEU cc_start: 0.8632 (mp) cc_final: 0.8288 (mp) REVERT: D 332 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (pttp) REVERT: D 582 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8704 (mp) REVERT: D 663 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: D 684 ASP cc_start: 0.7989 (m-30) cc_final: 0.7698 (m-30) REVERT: D 712 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: D 764 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.7517 (tmt90) REVERT: D 805 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: D 874 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5959 (tp30) REVERT: D 932 MET cc_start: 0.5111 (ttp) cc_final: 0.4716 (ptp) REVERT: D 983 LYS cc_start: 0.7820 (mttt) cc_final: 0.7325 (tppt) REVERT: D 1062 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.3821 (tt) REVERT: D 1072 LYS cc_start: 0.4238 (OUTLIER) cc_final: 0.2605 (mmtt) REVERT: D 1189 MET cc_start: 0.8105 (mmm) cc_final: 0.7851 (mmm) REVERT: D 1199 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3875 (m-80) REVERT: D 1282 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: D 1286 LYS cc_start: 0.6596 (ttmt) cc_final: 0.6119 (ptmt) REVERT: D 1353 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9032 (t) REVERT: D 1369 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7588 (ttp80) REVERT: E 3 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7656 (tpp-160) REVERT: E 42 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8744 (mp0) REVERT: E 56 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8054 (tt0) REVERT: E 67 ARG cc_start: 0.7863 (tpt90) cc_final: 0.7456 (mtp85) REVERT: E 68 GLU cc_start: 0.7991 (tt0) cc_final: 0.7086 (mt-10) REVERT: E 71 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7495 (mm-30) REVERT: F 266 PHE cc_start: 0.7465 (t80) cc_final: 0.6968 (t80) REVERT: F 273 MET cc_start: 0.6995 (tpt) cc_final: 0.6678 (tpt) REVERT: F 288 MET cc_start: 0.3858 (tpt) cc_final: 0.3492 (tpp) REVERT: F 305 LEU cc_start: 0.3611 (OUTLIER) cc_final: 0.3065 (tt) REVERT: F 509 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8881 (p) REVERT: F 538 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: K 36 PHE cc_start: 0.7412 (p90) cc_final: 0.7093 (p90) REVERT: K 52 ASP cc_start: 0.7784 (m-30) cc_final: 0.7439 (m-30) REVERT: K 68 THR cc_start: 0.8710 (p) cc_final: 0.8492 (m) REVERT: K 103 MET cc_start: 0.8741 (mtm) cc_final: 0.8372 (mtp) REVERT: K 148 TYR cc_start: 0.8190 (m-80) cc_final: 0.7799 (m-80) REVERT: K 184 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7428 (mmmt) REVERT: K 193 ARG cc_start: 0.6499 (mtp-110) cc_final: 0.6112 (mtp-110) REVERT: K 207 MET cc_start: 0.6853 (mtt) cc_final: 0.6465 (mtt) REVERT: L 98 GLU cc_start: 0.8674 (tt0) cc_final: 0.8367 (tt0) REVERT: L 136 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8079 (pp) REVERT: L 186 TYR cc_start: 0.7006 (t80) cc_final: 0.6686 (t80) REVERT: L 196 PHE cc_start: 0.8034 (t80) cc_final: 0.7671 (t80) outliers start: 178 outliers final: 144 residues processed: 546 average time/residue: 0.2065 time to fit residues: 184.8681 Evaluate side-chains 547 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 380 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 53 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 353 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN F 589 GLN K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118145 restraints weight = 48047.568| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.90 r_work: 0.3194 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34812 Z= 0.159 Angle : 0.608 15.354 47399 Z= 0.314 Chirality : 0.042 0.216 5389 Planarity : 0.004 0.056 5902 Dihedral : 15.336 165.975 5520 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 5.18 % Allowed : 23.96 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.48 (0.13), residues: 4099 helix: 1.16 (0.12), residues: 1780 sheet: -0.62 (0.26), residues: 358 loop : -1.72 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 322 TYR 0.020 0.001 TYR D 144 PHE 0.024 0.001 PHE K 191 TRP 0.020 0.001 TRP K 110 HIS 0.013 0.001 HIS K 104 Details of bonding type rmsd covalent geometry : bond 0.00373 (34804) covalent geometry : angle 0.60656 (47387) hydrogen bonds : bond 0.04137 ( 1569) hydrogen bonds : angle 4.33010 ( 4403) metal coordination : bond 0.00411 ( 8) metal coordination : angle 2.34016 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 383 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8664 (tp) REVERT: B 25 LYS cc_start: 0.8427 (tttt) cc_final: 0.8174 (tttt) REVERT: B 95 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7024 (mtmt) REVERT: C 118 LYS cc_start: 0.8060 (mttp) cc_final: 0.7566 (pptt) REVERT: C 379 GLU cc_start: 0.7735 (mp0) cc_final: 0.7261 (tp30) REVERT: C 546 GLU cc_start: 0.8515 (tp30) cc_final: 0.8160 (mp0) REVERT: C 653 MET cc_start: 0.9147 (ttt) cc_final: 0.8883 (ttt) REVERT: C 694 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8006 (ptt-90) REVERT: C 870 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9128 (mt) REVERT: C 940 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: C 951 MET cc_start: 0.8429 (ttm) cc_final: 0.8155 (ttp) REVERT: C 957 LYS cc_start: 0.8692 (tttt) cc_final: 0.8381 (tptt) REVERT: C 984 VAL cc_start: 0.4826 (OUTLIER) cc_final: 0.4478 (m) REVERT: C 1005 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.3910 (tp30) REVERT: C 1085 MET cc_start: 0.9132 (mmm) cc_final: 0.8912 (mmm) REVERT: C 1119 MET cc_start: 0.8939 (tpt) cc_final: 0.8543 (ttt) REVERT: C 1303 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8612 (mmmm) REVERT: D 159 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8887 (mt) REVERT: D 217 LEU cc_start: 0.8640 (mp) cc_final: 0.8297 (mp) REVERT: D 332 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (pttp) REVERT: D 513 MET cc_start: 0.9053 (ttp) cc_final: 0.8816 (ttm) REVERT: D 663 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: D 684 ASP cc_start: 0.7997 (m-30) cc_final: 0.7707 (m-30) REVERT: D 712 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: D 764 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7535 (tmt90) REVERT: D 805 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: D 874 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5962 (tp30) REVERT: D 932 MET cc_start: 0.5127 (ttp) cc_final: 0.4705 (ptp) REVERT: D 983 LYS cc_start: 0.7807 (mttt) cc_final: 0.7501 (ttmt) REVERT: D 1062 LEU cc_start: 0.4062 (OUTLIER) cc_final: 0.3765 (tt) REVERT: D 1072 LYS cc_start: 0.4219 (OUTLIER) cc_final: 0.2632 (mmtt) REVERT: D 1189 MET cc_start: 0.8124 (mmm) cc_final: 0.7857 (mmm) REVERT: D 1199 PHE cc_start: 0.4163 (OUTLIER) cc_final: 0.3873 (m-80) REVERT: D 1282 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: D 1286 LYS cc_start: 0.6621 (ttmt) cc_final: 0.6120 (ptmt) REVERT: D 1353 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9038 (t) REVERT: D 1369 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7570 (ttp80) REVERT: E 3 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7648 (tpp-160) REVERT: E 42 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8744 (mp0) REVERT: E 56 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8106 (tt0) REVERT: E 67 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7507 (mtp85) REVERT: E 68 GLU cc_start: 0.8030 (tt0) cc_final: 0.7202 (mt-10) REVERT: E 71 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7567 (mm-30) REVERT: F 266 PHE cc_start: 0.7476 (t80) cc_final: 0.6973 (t80) REVERT: F 273 MET cc_start: 0.6967 (tpt) cc_final: 0.6696 (tpt) REVERT: F 288 MET cc_start: 0.4023 (tpt) cc_final: 0.3661 (tpp) REVERT: F 305 LEU cc_start: 0.3226 (OUTLIER) cc_final: 0.2688 (tt) REVERT: F 509 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8865 (p) REVERT: F 532 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8275 (tp) REVERT: F 538 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: F 574 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6156 (mt-10) REVERT: K 36 PHE cc_start: 0.7427 (p90) cc_final: 0.7130 (p90) REVERT: K 52 ASP cc_start: 0.7803 (m-30) cc_final: 0.7450 (m-30) REVERT: K 53 LEU cc_start: 0.7132 (pp) cc_final: 0.6903 (pp) REVERT: K 68 THR cc_start: 0.8721 (p) cc_final: 0.8465 (m) REVERT: K 103 MET cc_start: 0.8733 (mtm) cc_final: 0.8358 (mtp) REVERT: K 148 TYR cc_start: 0.8151 (m-80) cc_final: 0.7864 (m-80) REVERT: K 193 ARG cc_start: 0.6444 (mtp-110) cc_final: 0.6075 (mtp-110) REVERT: K 207 MET cc_start: 0.7055 (mtt) cc_final: 0.6676 (mtt) REVERT: L 71 GLU cc_start: 0.7833 (tt0) cc_final: 0.7583 (tp30) REVERT: L 98 GLU cc_start: 0.8691 (tt0) cc_final: 0.8379 (tt0) REVERT: L 136 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8034 (pp) outliers start: 181 outliers final: 150 residues processed: 538 average time/residue: 0.2005 time to fit residues: 178.1578 Evaluate side-chains 545 residues out of total 3539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 372 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 659 GLN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1312 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 874 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1007 ASP Chi-restraints excluded: chain D residue 1019 ASN Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1199 PHE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 445 ASP Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain K residue 40 HIS Chi-restraints excluded: chain K residue 70 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 119 optimal weight: 0.4980 chunk 397 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 413 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN E 72 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117283 restraints weight = 47990.484| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.89 r_work: 0.3185 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34812 Z= 0.184 Angle : 0.626 15.015 47399 Z= 0.322 Chirality : 0.043 0.245 5389 Planarity : 0.004 0.056 5902 Dihedral : 15.332 166.223 5520 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.95 % Rotamer: Outliers : 5.21 % Allowed : 24.21 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.03 % 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: -0.54 (0.13), residues: 4099 helix: 1.10 (0.12), residues: 1779 sheet: -0.70 (0.25), residues: 377 loop : -1.74 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 322 TYR 0.020 0.001 TYR D 144 PHE 0.022 0.002 PHE K 191 TRP 0.026 0.002 TRP K 166 HIS 0.013 0.001 HIS K 104 Details of bonding type rmsd covalent geometry : bond 0.00435 (34804) covalent geometry : angle 0.62466 (47387) hydrogen bonds : bond 0.04250 ( 1569) hydrogen bonds : angle 4.36133 ( 4403) metal coordination : bond 0.00523 ( 8) metal coordination : angle 2.48069 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11092.16 seconds wall clock time: 189 minutes 17.66 seconds (11357.66 seconds total)