Starting phenix.real_space_refine on Sun Sep 13 23:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.map" model { file = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xln_22249/09_2026/6xln_22249.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.132 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 40 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16148 2.51 5 N 4582 2.21 5 O 5077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25956 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10381 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "N" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 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 14513 SG CYS D 70 100.483 41.374 69.547 1.00126.38 S ATOM 14527 SG CYS D 72 100.554 37.839 68.965 1.00129.54 S ATOM 14635 SG CYS D 85 102.971 39.790 67.518 1.00129.74 S ATOM 14659 SG CYS D 88 98.965 40.046 66.652 1.00129.43 S ATOM 20341 SG CYS D 814 88.381 106.087 73.943 1.00 89.97 S ATOM 20906 SG CYS D 888 86.529 103.030 73.832 1.00 91.64 S ATOM 20957 SG CYS D 895 87.888 104.356 76.782 1.00 82.79 S ATOM 20978 SG CYS D 898 85.411 106.176 75.448 1.00 85.12 S Time building chain proxies: 5.08, per 1000 atoms: 0.20 Number of scatterers: 25956 At special positions: 0 Unit cell: (138.632, 151.962, 163.959, 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 106 16.00 P 40 15.00 Mg 1 11.99 O 5077 8.00 N 4582 7.00 C 16148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 876.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 47 sheets defined 38.8% alpha, 18.8% beta 14 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.709A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 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 212 through 228 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.576A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.676A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.679A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.745A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.718A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.675A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.929A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.931A 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 479 removed outlier: 3.520A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 509 removed outlier: 4.034A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.742A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.234A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.525A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 660' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.809A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.569A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.577A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.882A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 4.278A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.355A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 999 " --> pdb=" O ARG C 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.597A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.510A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.878A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.503A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.519A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.032A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.610A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 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 removed outlier: 4.088A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.926A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.725A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.591A pdb=" N ARG D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.527A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.702A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.909A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (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 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.521A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.552A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.773A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.753A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.186A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.701A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.631A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.765A 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 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.651A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1242 removed outlier: 7.530A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1245 No H-bonds generated for 'chain 'D' and resid 1243 through 1245' Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.934A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1372 removed outlier: 3.653A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.637A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 4.093A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.604A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.014A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.421A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.553A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.741A 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 13 through 20 removed outlier: 6.382A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.527A 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 111 removed outlier: 4.319A pdb=" N ALA B 138 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N GLY B 108 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLU B 136 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 11.829A pdb=" N VAL B 110 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N THR B 134 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.357A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.771A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.485A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.581A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.902A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 removed outlier: 7.065A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.893A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.425A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.571A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.417A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.679A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.515A 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 1209 through 1210 removed outlier: 7.586A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.766A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.646A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.217A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.350A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.385A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 255 removed outlier: 3.658A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) 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 703 through 707 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.887A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AE4, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.983A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.105A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.080A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.448A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF1, first strand: chain 'D' and resid 1187 through 1191 removed outlier: 7.056A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 5.546A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7066 1.33 - 1.45: 4299 1.45 - 1.57: 14800 1.57 - 1.69: 77 1.69 - 1.81: 184 Bond restraints: 26426 Sorted by residual: bond pdb=" C4' DT T 8 " pdb=" C3' DT T 8 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.00e-02 1.00e+04 1.35e+01 bond pdb=" C3' DG T 5 " pdb=" O3' DG T 5 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" N9 DG T 11 " pdb=" C4 DG T 11 " ideal model delta sigma weight residual 1.375 1.347 0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DT T 8 " pdb=" O3' DT T 8 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C4' DC T 13 " pdb=" C3' DC T 13 " ideal model delta sigma weight residual 1.529 1.496 0.033 1.00e-02 1.00e+04 1.08e+01 ... (remaining 26421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 34819 2.37 - 4.75: 974 4.75 - 7.12: 72 7.12 - 9.50: 11 9.50 - 11.87: 2 Bond angle restraints: 35878 Sorted by residual: angle pdb=" N ASP C1296 " pdb=" CA ASP C1296 " pdb=" C ASP C1296 " ideal model delta sigma weight residual 111.28 123.15 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O4' DT T 8 " pdb=" C4' DT T 8 " pdb=" C3' DT T 8 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.00e+01 angle pdb=" O4' DC T 9 " pdb=" C4' DC T 9 " pdb=" C3' DC T 9 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O4' DC N 82 " pdb=" C4' DC N 82 " pdb=" C3' DC N 82 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT T 14 " pdb=" C4 DT T 14 " pdb=" O4 DT T 14 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 ... (remaining 35873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14303 17.83 - 35.66: 1449 35.66 - 53.49: 286 53.49 - 71.32: 72 71.32 - 89.15: 20 Dihedral angle restraints: 16130 sinusoidal: 6926 harmonic: 9204 Sorted by residual: dihedral pdb=" CA PHE C1265 " pdb=" C PHE C1265 " pdb=" N GLY C1266 " pdb=" CA GLY C1266 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA SER C1332 " pdb=" C SER C1332 " pdb=" N LEU C1333 " pdb=" CA LEU C1333 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE C 906 " pdb=" C PHE C 906 " pdb=" N GLY C 907 " pdb=" CA GLY C 907 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 16127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3685 0.093 - 0.187: 401 0.187 - 0.280: 23 0.280 - 0.374: 4 0.374 - 0.467: 2 Chirality restraints: 4115 Sorted by residual: chirality pdb=" CA ASP C1296 " pdb=" N ASP C1296 " pdb=" C ASP C1296 " pdb=" CB ASP C1296 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB VAL A 192 " pdb=" CA VAL A 192 " pdb=" CG1 VAL A 192 " pdb=" CG2 VAL A 192 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CG LEU C1101 " pdb=" CB LEU C1101 " pdb=" CD1 LEU C1101 " pdb=" CD2 LEU C1101 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 4112 not shown) Planarity restraints: 4552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.021 2.00e-02 2.50e+03 1.62e-02 6.55e+00 pdb=" CG TRP D 115 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 749 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO D 750 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " -0.029 2.00e-02 2.50e+03 1.57e-02 4.93e+00 pdb=" CG TYR D 75 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " -0.022 2.00e-02 2.50e+03 ... (remaining 4549 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 110 2.44 - 3.05: 16530 3.05 - 3.67: 39002 3.67 - 4.28: 60272 4.28 - 4.90: 102035 Nonbonded interactions: 217949 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.822 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 1.921 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.044 2.170 nonbonded pdb=" O PHE D 17 " pdb=" NH2 ARG D1355 " model vdw 2.196 3.120 nonbonded pdb=" OE1 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.199 3.040 ... (remaining 217944 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 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 30.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.013 0.667 26434 Z= 0.545 Angle : 0.963 22.334 35890 Z= 0.558 Chirality : 0.059 0.467 4115 Planarity : 0.005 0.063 4552 Dihedral : 15.005 89.152 10210 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % Rotamer: Outliers : 0.22 % Allowed : 5.87 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.12), residues: 3191 helix: -2.38 (0.12), residues: 1107 sheet: -1.82 (0.22), residues: 424 loop : -1.64 (0.13), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1262 TYR 0.029 0.003 TYR D 75 PHE 0.020 0.003 PHE D 172 TRP 0.043 0.003 TRP D 115 HIS 0.009 0.002 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.01143 / 0.51 (26426) covalent geometry : angle 0.93498 / 0.56 (35878) hydrogen bonds : bond 0.16584 / 11.20 ( 1071) hydrogen bonds : angle 7.73182 / 5.37 ( 2941) metal coordination : bond 0.32635 / 16.63 ( 8) metal coordination : angle 12.56766 / 7.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 316 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8214 (mp10) cc_final: 0.7917 (pm20) REVERT: A 145 LYS cc_start: 0.8802 (tttt) cc_final: 0.8566 (ttpp) REVERT: A 194 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7194 (tm-30) REVERT: A 205 MET cc_start: 0.8464 (mtp) cc_final: 0.7964 (mtp) REVERT: B 18 GLN cc_start: 0.8005 (mp10) cc_final: 0.7520 (mm-40) REVERT: B 95 LYS cc_start: 0.8695 (mttt) cc_final: 0.8417 (mttt) REVERT: B 127 GLN cc_start: 0.8161 (pm20) cc_final: 0.7919 (pm20) REVERT: B 145 LYS cc_start: 0.8567 (tttt) cc_final: 0.8326 (ttpt) REVERT: B 200 LYS cc_start: 0.8845 (tttt) cc_final: 0.8546 (tmmt) REVERT: C 70 TYR cc_start: 0.8350 (t80) cc_final: 0.8149 (t80) REVERT: C 115 LYS cc_start: 0.7751 (mttt) cc_final: 0.7512 (mttt) REVERT: C 142 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7807 (tt0) REVERT: C 158 ASP cc_start: 0.7224 (t70) cc_final: 0.6977 (t0) REVERT: C 191 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8477 (mmtp) REVERT: C 200 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7892 (mmm160) REVERT: C 222 ASP cc_start: 0.7713 (m-30) cc_final: 0.7365 (m-30) REVERT: C 230 PHE cc_start: 0.7440 (m-80) cc_final: 0.7206 (m-80) REVERT: C 335 THR cc_start: 0.7237 (m) cc_final: 0.6911 (p) REVERT: C 349 GLU cc_start: 0.7639 (mp0) cc_final: 0.6997 (mp0) REVERT: C 422 LYS cc_start: 0.8694 (mttt) cc_final: 0.8457 (mtpt) REVERT: C 439 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8480 (ttmt) REVERT: C 488 MET cc_start: 0.7483 (mmm) cc_final: 0.7122 (tpp) REVERT: C 503 LYS cc_start: 0.8648 (tptp) cc_final: 0.8271 (tttt) REVERT: C 516 ASP cc_start: 0.7825 (t70) cc_final: 0.7599 (t70) REVERT: C 653 MET cc_start: 0.8752 (ttt) cc_final: 0.8322 (ttm) REVERT: C 768 MET cc_start: 0.7797 (mtp) cc_final: 0.7523 (mtp) REVERT: C 943 LYS cc_start: 0.8541 (tppt) cc_final: 0.8321 (tppp) REVERT: C 950 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8129 (tm-30) REVERT: C 955 GLN cc_start: 0.8192 (tp40) cc_final: 0.7527 (tp-100) REVERT: C 965 GLN cc_start: 0.7591 (mt0) cc_final: 0.7353 (mt0) REVERT: C 1025 PHE cc_start: 0.7170 (t80) cc_final: 0.6844 (t80) REVERT: C 1027 LYS cc_start: 0.8831 (tptp) cc_final: 0.8518 (pttt) REVERT: C 1032 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7790 (ptpp) REVERT: C 1167 GLU cc_start: 0.7926 (tp30) cc_final: 0.7357 (tm-30) REVERT: D 74 LYS cc_start: 0.9152 (tttt) cc_final: 0.8891 (ttmm) REVERT: D 151 MET cc_start: 0.6986 (mpp) cc_final: 0.5935 (pp-130) REVERT: D 200 GLN cc_start: 0.8434 (tt0) cc_final: 0.8197 (mt0) REVERT: D 289 ASP cc_start: 0.6950 (m-30) cc_final: 0.6588 (t0) REVERT: D 398 LYS cc_start: 0.8222 (tttm) cc_final: 0.7731 (ttmm) REVERT: D 402 GLU cc_start: 0.8269 (pp20) cc_final: 0.7978 (pp20) REVERT: D 603 LYS cc_start: 0.7844 (tttt) cc_final: 0.7609 (ttpt) REVERT: D 781 LYS cc_start: 0.7792 (tttt) cc_final: 0.7370 (ttpt) REVERT: D 955 LYS cc_start: 0.8569 (pttt) cc_final: 0.8295 (pptt) REVERT: D 1190 ILE cc_start: 0.7765 (mt) cc_final: 0.7540 (mp) REVERT: E 8 ASP cc_start: 0.8413 (m-30) cc_final: 0.7925 (m-30) REVERT: E 11 GLU cc_start: 0.8050 (mp0) cc_final: 0.7644 (mp0) REVERT: E 41 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7183 (tm-30) REVERT: E 42 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 68 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 72 GLN cc_start: 0.8441 (tt0) cc_final: 0.8013 (tm-30) outliers start: 6 outliers final: 3 residues processed: 322 average time/residue: 0.7763 time to fit residues: 282.9312 Evaluate side-chains 228 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 1186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 194 GLN B 93 GLN B 137 ASN C 46 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 518 ASN C 582 ASN C 620 ASN C 628 HIS C 649 GLN C 673 HIS C1134 GLN C1244 HIS C1268 GLN D 80 HIS D 157 GLN D 158 GLN D 209 ASN D 274 ASN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D1244 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089782 restraints weight = 36005.044| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.40 r_work: 0.3044 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26434 Z= 0.161 Angle : 0.640 12.499 35890 Z= 0.337 Chirality : 0.046 0.196 4115 Planarity : 0.005 0.068 4552 Dihedral : 10.232 81.092 3946 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.61 % Allowed : 11.62 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3191 helix: -0.94 (0.14), residues: 1132 sheet: -1.39 (0.24), residues: 402 loop : -1.12 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.019 0.001 TYR D 140 PHE 0.020 0.002 PHE C 337 TRP 0.011 0.001 TRP D 115 HIS 0.005 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (26426) covalent geometry : angle 0.63223 / 0.34 (35878) hydrogen bonds : bond 0.04402 / 3.00 ( 1071) hydrogen bonds : angle 5.54905 / 3.83 ( 2941) metal coordination : bond 0.01441 / 0.60 ( 8) metal coordination : angle 5.51809 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8243 (tpp80) REVERT: A 127 GLN cc_start: 0.8135 (mp10) cc_final: 0.7705 (pm20) REVERT: A 145 LYS cc_start: 0.8169 (tttt) cc_final: 0.7851 (ttpp) REVERT: A 194 GLN cc_start: 0.8410 (tp40) cc_final: 0.7733 (tm-30) REVERT: A 205 MET cc_start: 0.8036 (mtp) cc_final: 0.7399 (mtp) REVERT: B 18 GLN cc_start: 0.7850 (mp10) cc_final: 0.6988 (mm-40) REVERT: B 95 LYS cc_start: 0.8293 (mttt) cc_final: 0.7949 (mttt) REVERT: B 127 GLN cc_start: 0.8015 (pm20) cc_final: 0.7760 (pm20) REVERT: B 143 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.7124 (mtm-85) REVERT: B 170 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7194 (pmt170) REVERT: B 200 LYS cc_start: 0.8187 (tttt) cc_final: 0.7865 (tmmt) REVERT: C 70 TYR cc_start: 0.8113 (t80) cc_final: 0.7691 (t80) REVERT: C 142 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8236 (tt0) REVERT: C 158 ASP cc_start: 0.7443 (t70) cc_final: 0.7224 (t0) REVERT: C 191 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8495 (mmtp) REVERT: C 200 ARG cc_start: 0.7615 (mmm160) cc_final: 0.7274 (mmm160) REVERT: C 222 ASP cc_start: 0.7710 (m-30) cc_final: 0.7257 (m-30) REVERT: C 230 PHE cc_start: 0.6694 (m-80) cc_final: 0.6023 (m-80) REVERT: C 422 LYS cc_start: 0.7970 (mttt) cc_final: 0.7748 (mtpt) REVERT: C 439 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8324 (ttmm) REVERT: C 503 LYS cc_start: 0.8310 (tptp) cc_final: 0.7817 (tttt) REVERT: C 600 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 633 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7367 (tp) REVERT: C 738 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: C 768 MET cc_start: 0.8090 (mtp) cc_final: 0.7705 (mtp) REVERT: C 876 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7746 (tm-30) REVERT: C 924 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7973 (m) REVERT: C 950 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8117 (tm-30) REVERT: C 955 GLN cc_start: 0.8102 (tp40) cc_final: 0.7604 (tp-100) REVERT: C 1025 PHE cc_start: 0.6875 (t80) cc_final: 0.6478 (t80) REVERT: C 1027 LYS cc_start: 0.8791 (tptp) cc_final: 0.8509 (pttt) REVERT: C 1032 LYS cc_start: 0.7476 (ptpp) cc_final: 0.7255 (mttp) REVERT: C 1167 GLU cc_start: 0.7795 (tp30) cc_final: 0.7238 (tm-30) REVERT: C 1174 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: D 60 ARG cc_start: 0.8417 (ttt-90) cc_final: 0.8123 (mtp-110) REVERT: D 74 LYS cc_start: 0.9068 (tttt) cc_final: 0.8754 (ttmm) REVERT: D 80 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6559 (p-80) REVERT: D 151 MET cc_start: 0.7176 (mpp) cc_final: 0.6178 (ppp) REVERT: D 159 ILE cc_start: 0.8694 (pp) cc_final: 0.8385 (pp) REVERT: D 200 GLN cc_start: 0.8109 (tt0) cc_final: 0.7902 (mt0) REVERT: D 237 MET cc_start: 0.9051 (mtm) cc_final: 0.8843 (mtm) REVERT: D 275 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6603 (mtt180) REVERT: D 289 ASP cc_start: 0.6685 (m-30) cc_final: 0.6168 (t0) REVERT: D 312 ARG cc_start: 0.7118 (mmm160) cc_final: 0.6648 (mmm160) REVERT: D 398 LYS cc_start: 0.7665 (tttm) cc_final: 0.7221 (ttmm) REVERT: D 603 LYS cc_start: 0.7196 (tttt) cc_final: 0.6938 (ttmt) REVERT: D 677 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: D 703 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8225 (t) REVERT: D 731 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7492 (tpt-90) REVERT: D 781 LYS cc_start: 0.7477 (tttt) cc_final: 0.7013 (ttpt) REVERT: D 955 LYS cc_start: 0.8231 (pttt) cc_final: 0.7946 (pptt) REVERT: D 1189 MET cc_start: 0.8754 (mtt) cc_final: 0.8439 (mmm) REVERT: D 1195 GLN cc_start: 0.6975 (pm20) cc_final: 0.6201 (pp30) REVERT: E 7 GLN cc_start: 0.7653 (tp40) cc_final: 0.6147 (tp40) REVERT: E 8 ASP cc_start: 0.8554 (m-30) cc_final: 0.8192 (m-30) REVERT: E 11 GLU cc_start: 0.8119 (mp0) cc_final: 0.7463 (mp0) REVERT: E 41 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7220 (tm-30) REVERT: E 68 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6929 (tm-30) REVERT: E 71 GLU cc_start: 0.7245 (pp20) cc_final: 0.7028 (pp20) REVERT: E 72 GLN cc_start: 0.8139 (tt0) cc_final: 0.7698 (tm-30) REVERT: E 76 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7512 (mt-10) outliers start: 44 outliers final: 11 residues processed: 295 average time/residue: 0.6874 time to fit residues: 231.1252 Evaluate side-chains 246 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 215 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN D 80 HIS ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088076 restraints weight = 36361.293| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.38 r_work: 0.3014 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26434 Z= 0.256 Angle : 0.651 10.264 35890 Z= 0.339 Chirality : 0.047 0.236 4115 Planarity : 0.005 0.058 4552 Dihedral : 10.136 80.543 3945 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 13.34 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3191 helix: -0.51 (0.15), residues: 1143 sheet: -1.33 (0.24), residues: 413 loop : -0.95 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 478 TYR 0.016 0.002 TYR D 723 PHE 0.020 0.002 PHE C 906 TRP 0.008 0.001 TRP D 115 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (26426) covalent geometry : angle 0.64598 / 0.34 (35878) hydrogen bonds : bond 0.04370 / 3.03 ( 1071) hydrogen bonds : angle 5.26415 / 3.63 ( 2941) metal coordination : bond 0.01063 / 0.58 ( 8) metal coordination : angle 4.23877 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8199 (tpp80) REVERT: A 127 GLN cc_start: 0.8044 (mp10) cc_final: 0.7626 (pm20) REVERT: A 145 LYS cc_start: 0.8158 (tttt) cc_final: 0.7635 (tttp) REVERT: A 194 GLN cc_start: 0.8501 (tp40) cc_final: 0.7769 (tm-30) REVERT: A 205 MET cc_start: 0.8211 (mtp) cc_final: 0.7646 (mtp) REVERT: B 18 GLN cc_start: 0.7855 (mp10) cc_final: 0.6992 (mm-40) REVERT: B 67 GLU cc_start: 0.7873 (mp0) cc_final: 0.7665 (mp0) REVERT: B 95 LYS cc_start: 0.8299 (mttt) cc_final: 0.7948 (mttt) REVERT: B 127 GLN cc_start: 0.8014 (pm20) cc_final: 0.7766 (pm20) REVERT: B 143 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: B 170 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7164 (pmt170) REVERT: B 200 LYS cc_start: 0.8381 (tttt) cc_final: 0.8118 (tmmt) REVERT: C 70 TYR cc_start: 0.8207 (t80) cc_final: 0.7781 (t80) REVERT: C 142 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8261 (tt0) REVERT: C 191 LYS cc_start: 0.8709 (mmpt) cc_final: 0.8491 (mmtp) REVERT: C 200 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7461 (mmm160) REVERT: C 222 ASP cc_start: 0.7678 (m-30) cc_final: 0.7217 (m-30) REVERT: C 230 PHE cc_start: 0.6743 (m-80) cc_final: 0.6400 (m-80) REVERT: C 422 LYS cc_start: 0.8027 (mttt) cc_final: 0.7769 (mtpt) REVERT: C 439 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8214 (ttmt) REVERT: C 503 LYS cc_start: 0.8302 (tptp) cc_final: 0.7757 (tttt) REVERT: C 600 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 633 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7412 (tp) REVERT: C 694 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7204 (mtm-85) REVERT: C 768 MET cc_start: 0.8148 (mtp) cc_final: 0.7754 (mtp) REVERT: C 876 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 924 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (m) REVERT: C 950 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8098 (tm-30) REVERT: C 955 GLN cc_start: 0.8112 (tp40) cc_final: 0.7625 (tp-100) REVERT: C 1010 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.6222 (pm20) REVERT: C 1025 PHE cc_start: 0.6979 (t80) cc_final: 0.6499 (t80) REVERT: C 1027 LYS cc_start: 0.8772 (tptp) cc_final: 0.8469 (pttt) REVERT: C 1167 GLU cc_start: 0.7818 (tp30) cc_final: 0.7162 (tm-30) REVERT: C 1174 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: D 60 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.8102 (mtp-110) REVERT: D 74 LYS cc_start: 0.8895 (tttt) cc_final: 0.8537 (ttmm) REVERT: D 80 HIS cc_start: 0.7779 (p-80) cc_final: 0.7207 (p-80) REVERT: D 129 ASP cc_start: 0.8028 (t0) cc_final: 0.7770 (t0) REVERT: D 151 MET cc_start: 0.7265 (mpp) cc_final: 0.6266 (ppp) REVERT: D 200 GLN cc_start: 0.8185 (tt0) cc_final: 0.7927 (mt0) REVERT: D 275 ARG cc_start: 0.6880 (mtt180) cc_final: 0.6643 (mtt180) REVERT: D 289 ASP cc_start: 0.6668 (m-30) cc_final: 0.6210 (t0) REVERT: D 312 ARG cc_start: 0.7197 (mmm160) cc_final: 0.6907 (mmm160) REVERT: D 398 LYS cc_start: 0.7737 (tttm) cc_final: 0.7243 (ttmm) REVERT: D 603 LYS cc_start: 0.7198 (tttt) cc_final: 0.6875 (ttmt) REVERT: D 677 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: D 703 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8262 (t) REVERT: D 731 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7599 (tpt-90) REVERT: D 738 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6765 (mtt180) REVERT: D 781 LYS cc_start: 0.7498 (tttt) cc_final: 0.7112 (ttmt) REVERT: D 903 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6896 (mm) REVERT: D 955 LYS cc_start: 0.8144 (pttt) cc_final: 0.7895 (pptt) REVERT: D 993 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: D 1025 MET cc_start: 0.7628 (ttp) cc_final: 0.7403 (ttp) REVERT: D 1189 MET cc_start: 0.8648 (mtt) cc_final: 0.8203 (mmt) REVERT: D 1369 ARG cc_start: 0.6914 (ttt90) cc_final: 0.6693 (mtp85) REVERT: E 7 GLN cc_start: 0.7656 (tp40) cc_final: 0.6108 (tp40) REVERT: E 8 ASP cc_start: 0.8523 (m-30) cc_final: 0.8191 (m-30) REVERT: E 11 GLU cc_start: 0.8148 (mp0) cc_final: 0.7340 (mp0) REVERT: E 41 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7217 (tm-30) REVERT: E 68 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6914 (tm-30) REVERT: E 71 GLU cc_start: 0.7363 (pp20) cc_final: 0.7155 (pp20) REVERT: E 72 GLN cc_start: 0.8163 (tt0) cc_final: 0.7710 (tm-30) REVERT: E 76 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7484 (mt-10) outliers start: 72 outliers final: 23 residues processed: 285 average time/residue: 0.7023 time to fit residues: 228.7318 Evaluate side-chains 258 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 221 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089658 restraints weight = 35966.490| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.40 r_work: 0.3042 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26434 Z= 0.165 Angle : 0.583 10.797 35890 Z= 0.303 Chirality : 0.045 0.189 4115 Planarity : 0.004 0.058 4552 Dihedral : 9.996 81.277 3945 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.71 % Allowed : 14.26 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3191 helix: -0.13 (0.15), residues: 1138 sheet: -1.20 (0.24), residues: 418 loop : -0.76 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 271 TYR 0.017 0.001 TYR D 679 PHE 0.022 0.001 PHE C 906 TRP 0.007 0.001 TRP D 33 HIS 0.004 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (26426) covalent geometry : angle 0.57909 / 0.30 (35878) hydrogen bonds : bond 0.03775 / 2.61 ( 1071) hydrogen bonds : angle 5.02205 / 3.47 ( 2941) metal coordination : bond 0.00585 / 0.33 ( 8) metal coordination : angle 3.51014 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.7992 (tpp80) REVERT: A 51 MET cc_start: 0.8940 (mmt) cc_final: 0.8732 (mmm) REVERT: A 127 GLN cc_start: 0.8031 (mp10) cc_final: 0.7692 (pm20) REVERT: A 145 LYS cc_start: 0.8041 (tttt) cc_final: 0.7722 (ttpp) REVERT: A 186 ASN cc_start: 0.8179 (m-40) cc_final: 0.7905 (m110) REVERT: A 194 GLN cc_start: 0.8489 (tp40) cc_final: 0.7773 (tm-30) REVERT: A 205 MET cc_start: 0.8173 (mtp) cc_final: 0.7506 (mtp) REVERT: B 18 GLN cc_start: 0.7777 (mp10) cc_final: 0.6900 (mm-40) REVERT: B 67 GLU cc_start: 0.8099 (mp0) cc_final: 0.7863 (mp0) REVERT: B 95 LYS cc_start: 0.8289 (mttt) cc_final: 0.7945 (mttt) REVERT: B 127 GLN cc_start: 0.8004 (pm20) cc_final: 0.7760 (pm20) REVERT: B 143 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.7135 (mtm-85) REVERT: B 145 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7652 (ttpp) REVERT: B 158 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.5851 (ttp80) REVERT: B 170 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7035 (pmt170) REVERT: B 188 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: B 200 LYS cc_start: 0.8408 (tttt) cc_final: 0.8079 (tmmt) REVERT: C 70 TYR cc_start: 0.8216 (t80) cc_final: 0.7764 (t80) REVERT: C 142 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8239 (tt0) REVERT: C 191 LYS cc_start: 0.8708 (mmpt) cc_final: 0.8492 (mmtp) REVERT: C 200 ARG cc_start: 0.7671 (mmm160) cc_final: 0.7295 (mmm160) REVERT: C 222 ASP cc_start: 0.7664 (m-30) cc_final: 0.7209 (m-30) REVERT: C 284 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7367 (tt) REVERT: C 370 MET cc_start: 0.7409 (mmm) cc_final: 0.7118 (mmm) REVERT: C 422 LYS cc_start: 0.7986 (mttt) cc_final: 0.7776 (mtmt) REVERT: C 439 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8396 (ttmm) REVERT: C 503 LYS cc_start: 0.8136 (tptp) cc_final: 0.7623 (tttt) REVERT: C 600 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.7862 (p) REVERT: C 633 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7455 (tp) REVERT: C 694 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7135 (mtm-85) REVERT: C 738 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: C 768 MET cc_start: 0.8138 (mtp) cc_final: 0.7655 (mtp) REVERT: C 876 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 924 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8089 (m) REVERT: C 950 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8025 (tm-30) REVERT: C 955 GLN cc_start: 0.8092 (tp40) cc_final: 0.7614 (tp-100) REVERT: C 1025 PHE cc_start: 0.6928 (t80) cc_final: 0.6480 (t80) REVERT: C 1027 LYS cc_start: 0.8789 (tptp) cc_final: 0.8492 (pttt) REVERT: C 1131 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7627 (mtt) REVERT: C 1167 GLU cc_start: 0.7788 (tp30) cc_final: 0.7152 (tm-30) REVERT: C 1174 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: D 60 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.8068 (mtp-110) REVERT: D 74 LYS cc_start: 0.8898 (tttt) cc_final: 0.8550 (ttmm) REVERT: D 80 HIS cc_start: 0.7791 (p-80) cc_final: 0.6910 (p-80) REVERT: D 114 ILE cc_start: 0.8358 (tt) cc_final: 0.8100 (tp) REVERT: D 129 ASP cc_start: 0.8049 (t0) cc_final: 0.7794 (t0) REVERT: D 200 GLN cc_start: 0.8156 (tt0) cc_final: 0.7897 (mt0) REVERT: D 275 ARG cc_start: 0.6835 (mtt180) cc_final: 0.6590 (mtt180) REVERT: D 289 ASP cc_start: 0.6631 (m-30) cc_final: 0.6190 (t0) REVERT: D 304 ASP cc_start: 0.7719 (m-30) cc_final: 0.7278 (t0) REVERT: D 312 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6707 (mmm160) REVERT: D 330 MET cc_start: 0.8155 (mtm) cc_final: 0.7611 (mtp) REVERT: D 348 ASP cc_start: 0.8719 (m-30) cc_final: 0.8420 (m-30) REVERT: D 375 GLU cc_start: 0.8296 (tp30) cc_final: 0.7895 (mm-30) REVERT: D 398 LYS cc_start: 0.7703 (tttm) cc_final: 0.7250 (ttmm) REVERT: D 548 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8128 (m) REVERT: D 572 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 603 LYS cc_start: 0.7390 (tttt) cc_final: 0.6972 (ttmt) REVERT: D 731 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7527 (tpt-90) REVERT: D 738 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6766 (mtt180) REVERT: D 781 LYS cc_start: 0.7470 (tttt) cc_final: 0.7068 (ttmt) REVERT: D 805 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: D 955 LYS cc_start: 0.8158 (pttt) cc_final: 0.7916 (pptt) REVERT: D 980 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7653 (t) REVERT: D 993 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6316 (pp20) REVERT: D 1025 MET cc_start: 0.7696 (ttp) cc_final: 0.7494 (ttp) REVERT: D 1195 GLN cc_start: 0.6971 (pm20) cc_final: 0.6180 (pp30) REVERT: D 1369 ARG cc_start: 0.6865 (ttt90) cc_final: 0.6652 (mtp85) REVERT: E 7 GLN cc_start: 0.7613 (tp40) cc_final: 0.5993 (tp40) REVERT: E 8 ASP cc_start: 0.8517 (m-30) cc_final: 0.8189 (m-30) REVERT: E 11 GLU cc_start: 0.8125 (mp0) cc_final: 0.7408 (mp0) REVERT: E 41 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7326 (tm-30) REVERT: E 68 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6960 (tm-30) REVERT: E 71 GLU cc_start: 0.7343 (pp20) cc_final: 0.7118 (pp20) REVERT: E 72 GLN cc_start: 0.8148 (tt0) cc_final: 0.7671 (tm-30) REVERT: E 76 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7414 (mt-10) outliers start: 74 outliers final: 30 residues processed: 301 average time/residue: 0.7253 time to fit residues: 250.3995 Evaluate side-chains 279 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 293 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 116 optimal weight: 0.1980 chunk 218 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091585 restraints weight = 35828.044| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.41 r_work: 0.3070 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26434 Z= 0.121 Angle : 0.546 10.013 35890 Z= 0.286 Chirality : 0.044 0.182 4115 Planarity : 0.004 0.057 4552 Dihedral : 9.845 81.581 3945 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.30 % Allowed : 14.74 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3191 helix: 0.22 (0.16), residues: 1139 sheet: -0.99 (0.25), residues: 403 loop : -0.60 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 322 TYR 0.018 0.001 TYR D1365 PHE 0.024 0.001 PHE C 906 TRP 0.007 0.001 TRP D 33 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26426) covalent geometry : angle 0.54426 / 0.29 (35878) hydrogen bonds : bond 0.03430 / 2.36 ( 1071) hydrogen bonds : angle 4.83412 / 3.34 ( 2941) metal coordination : bond 0.00362 / 0.20 ( 8) metal coordination : angle 2.71355 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 257 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.7974 (tpp80) REVERT: A 51 MET cc_start: 0.8925 (mmt) cc_final: 0.8639 (mmt) REVERT: A 127 GLN cc_start: 0.8028 (mp10) cc_final: 0.7663 (pm20) REVERT: A 145 LYS cc_start: 0.7992 (tttt) cc_final: 0.7685 (ttpp) REVERT: A 186 ASN cc_start: 0.8174 (m-40) cc_final: 0.7824 (m110) REVERT: A 194 GLN cc_start: 0.8352 (tp40) cc_final: 0.7653 (tm-30) REVERT: A 204 GLU cc_start: 0.7972 (tt0) cc_final: 0.7382 (mt-10) REVERT: A 205 MET cc_start: 0.8138 (mtp) cc_final: 0.7444 (mtp) REVERT: B 18 GLN cc_start: 0.7744 (mp10) cc_final: 0.6861 (mm-40) REVERT: B 67 GLU cc_start: 0.8092 (mp0) cc_final: 0.7813 (mp0) REVERT: B 95 LYS cc_start: 0.8126 (mttt) cc_final: 0.7791 (mttt) REVERT: B 127 GLN cc_start: 0.8002 (pm20) cc_final: 0.7781 (pm20) REVERT: B 143 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: B 170 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7005 (pmt170) REVERT: B 188 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: B 200 LYS cc_start: 0.8397 (tttt) cc_final: 0.8076 (tmmt) REVERT: C 70 TYR cc_start: 0.8239 (t80) cc_final: 0.7797 (t80) REVERT: C 142 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8185 (tt0) REVERT: C 191 LYS cc_start: 0.8638 (mmpt) cc_final: 0.8389 (mmtp) REVERT: C 200 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7331 (mmm160) REVERT: C 370 MET cc_start: 0.7536 (mmm) cc_final: 0.7275 (mmm) REVERT: C 439 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8373 (ttmt) REVERT: C 503 LYS cc_start: 0.8130 (tptp) cc_final: 0.7600 (tttt) REVERT: C 600 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7773 (p) REVERT: C 694 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7177 (mtm-85) REVERT: C 738 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: C 768 MET cc_start: 0.8127 (mtp) cc_final: 0.7625 (mtp) REVERT: C 791 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 876 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7493 (tm-30) REVERT: C 950 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8047 (tm-30) REVERT: C 955 GLN cc_start: 0.8075 (tp40) cc_final: 0.7618 (tp-100) REVERT: C 1010 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6603 (pp30) REVERT: C 1025 PHE cc_start: 0.6847 (t80) cc_final: 0.6404 (t80) REVERT: C 1027 LYS cc_start: 0.8745 (tptp) cc_final: 0.8430 (pttm) REVERT: C 1131 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: C 1137 GLU cc_start: 0.7067 (mp0) cc_final: 0.6860 (mp0) REVERT: C 1167 GLU cc_start: 0.7771 (tp30) cc_final: 0.7338 (tm-30) REVERT: C 1174 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: D 60 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.7932 (mtp-110) REVERT: D 74 LYS cc_start: 0.8895 (tttt) cc_final: 0.8630 (ttmm) REVERT: D 80 HIS cc_start: 0.7529 (p-80) cc_final: 0.6621 (p-80) REVERT: D 114 ILE cc_start: 0.8315 (tt) cc_final: 0.8017 (tp) REVERT: D 129 ASP cc_start: 0.8036 (t0) cc_final: 0.7795 (t0) REVERT: D 151 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6110 (ppp) REVERT: D 237 MET cc_start: 0.9140 (mtp) cc_final: 0.8722 (mtp) REVERT: D 275 ARG cc_start: 0.6775 (mtt180) cc_final: 0.6531 (mtt180) REVERT: D 289 ASP cc_start: 0.6634 (m-30) cc_final: 0.6144 (t0) REVERT: D 304 ASP cc_start: 0.7612 (m-30) cc_final: 0.7153 (t0) REVERT: D 312 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6422 (mmm-85) REVERT: D 330 MET cc_start: 0.8058 (mtm) cc_final: 0.7589 (mtp) REVERT: D 348 ASP cc_start: 0.8657 (m-30) cc_final: 0.8333 (m-30) REVERT: D 371 LYS cc_start: 0.8763 (mttt) cc_final: 0.8322 (mmpt) REVERT: D 375 GLU cc_start: 0.8324 (tp30) cc_final: 0.7902 (mm-30) REVERT: D 398 LYS cc_start: 0.7685 (tttm) cc_final: 0.7238 (ttmm) REVERT: D 525 MET cc_start: 0.8322 (ptp) cc_final: 0.8112 (ptp) REVERT: D 603 LYS cc_start: 0.7318 (tttt) cc_final: 0.6904 (ttmt) REVERT: D 649 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7386 (mtpp) REVERT: D 703 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8336 (t) REVERT: D 731 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7680 (tpt-90) REVERT: D 738 ARG cc_start: 0.7152 (ttm170) cc_final: 0.6622 (mtt180) REVERT: D 781 LYS cc_start: 0.7412 (tttt) cc_final: 0.7037 (ttmt) REVERT: D 805 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: D 955 LYS cc_start: 0.8076 (pttt) cc_final: 0.7843 (pptt) REVERT: D 980 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7689 (t) REVERT: D 1025 MET cc_start: 0.7718 (ttp) cc_final: 0.7515 (ttp) REVERT: D 1195 GLN cc_start: 0.6963 (pm20) cc_final: 0.6145 (pp30) REVERT: E 7 GLN cc_start: 0.7588 (tp40) cc_final: 0.5894 (tp40) REVERT: E 8 ASP cc_start: 0.8507 (m-30) cc_final: 0.8195 (m-30) REVERT: E 11 GLU cc_start: 0.8069 (mp0) cc_final: 0.7321 (mp0) REVERT: E 41 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7214 (tm-30) REVERT: E 68 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6915 (tm-30) REVERT: E 72 GLN cc_start: 0.8183 (tt0) cc_final: 0.7773 (tm-30) outliers start: 90 outliers final: 30 residues processed: 318 average time/residue: 0.7044 time to fit residues: 257.1277 Evaluate side-chains 271 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 78 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088183 restraints weight = 36060.818| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.40 r_work: 0.3020 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 26434 Z= 0.260 Angle : 0.624 10.719 35890 Z= 0.321 Chirality : 0.047 0.179 4115 Planarity : 0.005 0.077 4552 Dihedral : 9.898 80.496 3945 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.93 % Allowed : 16.20 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3191 helix: 0.17 (0.15), residues: 1138 sheet: -1.13 (0.24), residues: 427 loop : -0.60 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 271 TYR 0.016 0.002 TYR C1018 PHE 0.022 0.002 PHE C 906 TRP 0.006 0.001 TRP C1276 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (26426) covalent geometry : angle 0.62148 / 0.32 (35878) hydrogen bonds : bond 0.03896 / 2.71 ( 1071) hydrogen bonds : angle 4.90125 / 3.39 ( 2941) metal coordination : bond 0.00912 / 0.51 ( 8) metal coordination : angle 2.84777 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 234 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8151 (tpp80) REVERT: A 51 MET cc_start: 0.8963 (mmt) cc_final: 0.8694 (mmt) REVERT: A 93 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 127 GLN cc_start: 0.8019 (mp10) cc_final: 0.7696 (pm20) REVERT: A 145 LYS cc_start: 0.8113 (tttt) cc_final: 0.7887 (ttpp) REVERT: A 186 ASN cc_start: 0.8184 (m-40) cc_final: 0.7814 (m110) REVERT: A 194 GLN cc_start: 0.8447 (tp40) cc_final: 0.7681 (tm-30) REVERT: A 204 GLU cc_start: 0.8011 (tt0) cc_final: 0.7360 (mt-10) REVERT: A 205 MET cc_start: 0.8141 (mtp) cc_final: 0.7463 (mtp) REVERT: B 12 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7013 (ptt180) REVERT: B 18 GLN cc_start: 0.7769 (mp10) cc_final: 0.6872 (mm-40) REVERT: B 67 GLU cc_start: 0.8120 (mp0) cc_final: 0.7864 (mp0) REVERT: B 95 LYS cc_start: 0.8319 (mttt) cc_final: 0.8012 (mttt) REVERT: B 127 GLN cc_start: 0.8002 (pm20) cc_final: 0.7756 (pm20) REVERT: B 143 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: B 145 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7662 (ttpp) REVERT: B 170 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7009 (pmt170) REVERT: B 188 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: B 200 LYS cc_start: 0.8308 (tttt) cc_final: 0.7960 (tmmt) REVERT: C 70 TYR cc_start: 0.8268 (t80) cc_final: 0.7826 (t80) REVERT: C 191 LYS cc_start: 0.8694 (mmpt) cc_final: 0.8438 (mmtp) REVERT: C 370 MET cc_start: 0.7526 (mmm) cc_final: 0.7261 (mmm) REVERT: C 439 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8329 (ttmt) REVERT: C 503 LYS cc_start: 0.8145 (tptp) cc_final: 0.7623 (tttt) REVERT: C 600 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.7833 (p) REVERT: C 694 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7169 (mtm-85) REVERT: C 738 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: C 768 MET cc_start: 0.8109 (mtp) cc_final: 0.7693 (mtp) REVERT: C 800 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: C 876 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 950 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7980 (tm-30) REVERT: C 955 GLN cc_start: 0.8087 (tp40) cc_final: 0.7614 (tp-100) REVERT: C 1010 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6723 (pp30) REVERT: C 1025 PHE cc_start: 0.6874 (t80) cc_final: 0.6421 (t80) REVERT: C 1027 LYS cc_start: 0.8760 (tptp) cc_final: 0.8458 (pttm) REVERT: C 1106 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7328 (ptp-170) REVERT: C 1131 MET cc_start: 0.7740 (mtt) cc_final: 0.7502 (mtt) REVERT: C 1137 GLU cc_start: 0.7057 (mp0) cc_final: 0.6823 (mp0) REVERT: C 1167 GLU cc_start: 0.7781 (tp30) cc_final: 0.7134 (tm-30) REVERT: C 1174 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: D 60 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.8024 (mtp-110) REVERT: D 74 LYS cc_start: 0.8879 (tttt) cc_final: 0.8577 (ttmm) REVERT: D 129 ASP cc_start: 0.8063 (t0) cc_final: 0.7807 (t0) REVERT: D 237 MET cc_start: 0.9054 (mtp) cc_final: 0.8828 (mtp) REVERT: D 275 ARG cc_start: 0.6911 (mtt180) cc_final: 0.6660 (mtt180) REVERT: D 289 ASP cc_start: 0.6732 (m-30) cc_final: 0.6223 (t0) REVERT: D 312 ARG cc_start: 0.7163 (mmm160) cc_final: 0.6414 (mmm-85) REVERT: D 330 MET cc_start: 0.8186 (mtm) cc_final: 0.7668 (mtp) REVERT: D 348 ASP cc_start: 0.8707 (m-30) cc_final: 0.8408 (m-30) REVERT: D 371 LYS cc_start: 0.8773 (mttt) cc_final: 0.8338 (mmpt) REVERT: D 375 GLU cc_start: 0.8242 (tp30) cc_final: 0.7800 (mm-30) REVERT: D 398 LYS cc_start: 0.7729 (tttm) cc_final: 0.7283 (ttmm) REVERT: D 548 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8158 (m) REVERT: D 603 LYS cc_start: 0.7319 (tttt) cc_final: 0.6921 (ttmt) REVERT: D 649 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7357 (mtmm) REVERT: D 703 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8256 (t) REVERT: D 738 ARG cc_start: 0.7217 (ttm170) cc_final: 0.6683 (mtt180) REVERT: D 781 LYS cc_start: 0.7439 (tttt) cc_final: 0.7032 (ttpt) REVERT: D 805 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: D 955 LYS cc_start: 0.8068 (pttt) cc_final: 0.7845 (pptt) REVERT: D 1195 GLN cc_start: 0.7022 (pm20) cc_final: 0.6294 (pp30) REVERT: E 7 GLN cc_start: 0.7556 (tp40) cc_final: 0.5869 (tp40) REVERT: E 8 ASP cc_start: 0.8483 (m-30) cc_final: 0.8161 (m-30) REVERT: E 11 GLU cc_start: 0.8089 (mp0) cc_final: 0.7403 (mp0) REVERT: E 41 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 68 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6981 (tm-30) REVERT: E 72 GLN cc_start: 0.8091 (tt0) cc_final: 0.7685 (tm-30) outliers start: 80 outliers final: 41 residues processed: 291 average time/residue: 0.7230 time to fit residues: 240.9204 Evaluate side-chains 276 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 263 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089942 restraints weight = 35953.325| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.34 r_work: 0.3044 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26434 Z= 0.191 Angle : 0.585 10.689 35890 Z= 0.303 Chirality : 0.045 0.177 4115 Planarity : 0.004 0.062 4552 Dihedral : 9.874 81.432 3945 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.71 % Allowed : 16.97 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3191 helix: 0.27 (0.16), residues: 1139 sheet: -1.11 (0.25), residues: 425 loop : -0.55 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 271 TYR 0.016 0.001 TYR D 679 PHE 0.022 0.001 PHE C 906 TRP 0.005 0.001 TRP D 115 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (26426) covalent geometry : angle 0.58301 / 0.30 (35878) hydrogen bonds : bond 0.03643 / 2.53 ( 1071) hydrogen bonds : angle 4.83925 / 3.35 ( 2941) metal coordination : bond 0.00675 / 0.38 ( 8) metal coordination : angle 2.89929 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8181 (tpp80) REVERT: A 51 MET cc_start: 0.9001 (mmt) cc_final: 0.8706 (mmt) REVERT: A 93 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 127 GLN cc_start: 0.8049 (mp10) cc_final: 0.7710 (pm20) REVERT: A 145 LYS cc_start: 0.8068 (tttt) cc_final: 0.7762 (ttpp) REVERT: A 186 ASN cc_start: 0.8211 (m-40) cc_final: 0.7840 (m110) REVERT: A 194 GLN cc_start: 0.8433 (tp40) cc_final: 0.7673 (tm-30) REVERT: A 204 GLU cc_start: 0.8013 (tt0) cc_final: 0.7384 (mt-10) REVERT: A 205 MET cc_start: 0.8159 (mtp) cc_final: 0.7505 (mtp) REVERT: B 12 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7004 (ptt180) REVERT: B 18 GLN cc_start: 0.7796 (mp10) cc_final: 0.6905 (mm-40) REVERT: B 41 ASN cc_start: 0.7686 (t0) cc_final: 0.7361 (t0) REVERT: B 67 GLU cc_start: 0.8143 (mp0) cc_final: 0.7874 (mp0) REVERT: B 127 GLN cc_start: 0.8025 (pm20) cc_final: 0.7802 (pm20) REVERT: B 143 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7145 (mtm-85) REVERT: B 145 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7697 (ttpp) REVERT: B 170 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.6993 (pmt170) REVERT: B 188 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: B 200 LYS cc_start: 0.8433 (tttt) cc_final: 0.8097 (tmmt) REVERT: C 70 TYR cc_start: 0.8286 (t80) cc_final: 0.7761 (t80) REVERT: C 191 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8429 (mmtp) REVERT: C 200 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7778 (mmm160) REVERT: C 370 MET cc_start: 0.7499 (mmm) cc_final: 0.7220 (mmm) REVERT: C 439 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8349 (ttmt) REVERT: C 503 LYS cc_start: 0.8176 (tptp) cc_final: 0.7644 (tttt) REVERT: C 600 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.7870 (p) REVERT: C 694 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7179 (mtm-85) REVERT: C 738 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: C 768 MET cc_start: 0.8143 (mtp) cc_final: 0.7687 (mtp) REVERT: C 791 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8132 (tp) REVERT: C 876 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 950 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8005 (tm-30) REVERT: C 955 GLN cc_start: 0.8101 (tp40) cc_final: 0.7634 (tp-100) REVERT: C 965 GLN cc_start: 0.6066 (mt0) cc_final: 0.5817 (mp10) REVERT: C 1025 PHE cc_start: 0.6875 (t80) cc_final: 0.6440 (t80) REVERT: C 1027 LYS cc_start: 0.8765 (tptp) cc_final: 0.8446 (pttm) REVERT: C 1106 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7408 (ptp-170) REVERT: C 1131 MET cc_start: 0.7782 (mtt) cc_final: 0.7562 (mtt) REVERT: C 1137 GLU cc_start: 0.7095 (mp0) cc_final: 0.6850 (mp0) REVERT: C 1167 GLU cc_start: 0.7817 (tp30) cc_final: 0.7170 (tm-30) REVERT: C 1174 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: D 60 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7932 (mtp-110) REVERT: D 74 LYS cc_start: 0.8903 (tttt) cc_final: 0.8636 (ttmm) REVERT: D 129 ASP cc_start: 0.8045 (t0) cc_final: 0.7796 (t0) REVERT: D 237 MET cc_start: 0.9084 (mtp) cc_final: 0.8798 (mtp) REVERT: D 275 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6688 (mtt180) REVERT: D 289 ASP cc_start: 0.6839 (m-30) cc_final: 0.6412 (t0) REVERT: D 312 ARG cc_start: 0.7170 (mmm160) cc_final: 0.6408 (mmm-85) REVERT: D 330 MET cc_start: 0.8208 (mtm) cc_final: 0.7685 (mtp) REVERT: D 348 ASP cc_start: 0.8697 (m-30) cc_final: 0.8393 (m-30) REVERT: D 371 LYS cc_start: 0.8781 (mttt) cc_final: 0.8357 (mmpt) REVERT: D 375 GLU cc_start: 0.8325 (tp30) cc_final: 0.7882 (mm-30) REVERT: D 398 LYS cc_start: 0.7770 (tttm) cc_final: 0.7317 (ttmm) REVERT: D 603 LYS cc_start: 0.7373 (tttt) cc_final: 0.6966 (ttmt) REVERT: D 649 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7416 (mtmm) REVERT: D 703 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8301 (t) REVERT: D 731 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7935 (tpt90) REVERT: D 738 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6729 (mtt180) REVERT: D 781 LYS cc_start: 0.7465 (tttt) cc_final: 0.7047 (ttpt) REVERT: D 805 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: D 955 LYS cc_start: 0.8044 (pttt) cc_final: 0.7716 (pptt) REVERT: D 1189 MET cc_start: 0.8789 (mtt) cc_final: 0.8545 (mmm) REVERT: D 1195 GLN cc_start: 0.6928 (pm20) cc_final: 0.6208 (pp30) REVERT: E 7 GLN cc_start: 0.7678 (tp40) cc_final: 0.6004 (tp40) REVERT: E 8 ASP cc_start: 0.8505 (m-30) cc_final: 0.8201 (m-30) REVERT: E 11 GLU cc_start: 0.8092 (mp0) cc_final: 0.7401 (mp0) REVERT: E 41 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7268 (tm-30) REVERT: E 68 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6978 (tm-30) REVERT: E 72 GLN cc_start: 0.8147 (tt0) cc_final: 0.7691 (tm-30) outliers start: 74 outliers final: 41 residues processed: 284 average time/residue: 0.7305 time to fit residues: 238.0016 Evaluate side-chains 273 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C1013 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089926 restraints weight = 35996.839| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.35 r_work: 0.3044 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26434 Z= 0.191 Angle : 0.590 11.204 35890 Z= 0.303 Chirality : 0.045 0.181 4115 Planarity : 0.004 0.066 4552 Dihedral : 9.849 81.545 3945 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.82 % Allowed : 17.30 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 3191 helix: 0.36 (0.16), residues: 1135 sheet: -1.06 (0.25), residues: 427 loop : -0.49 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 322 TYR 0.017 0.001 TYR C1018 PHE 0.022 0.001 PHE C 906 TRP 0.005 0.001 TRP D 115 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (26426) covalent geometry : angle 0.58828 / 0.30 (35878) hydrogen bonds : bond 0.03616 / 2.51 ( 1071) hydrogen bonds : angle 4.80521 / 3.33 ( 2941) metal coordination : bond 0.00681 / 0.38 ( 8) metal coordination : angle 2.82958 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 225 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8193 (tpp80) REVERT: A 51 MET cc_start: 0.9004 (mmt) cc_final: 0.8693 (mmt) REVERT: A 93 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 127 GLN cc_start: 0.8042 (mp10) cc_final: 0.7713 (pm20) REVERT: A 145 LYS cc_start: 0.8062 (tttt) cc_final: 0.7759 (ttpp) REVERT: A 186 ASN cc_start: 0.8247 (m-40) cc_final: 0.7829 (m110) REVERT: A 194 GLN cc_start: 0.8491 (tp40) cc_final: 0.7810 (tm-30) REVERT: A 204 GLU cc_start: 0.8029 (tt0) cc_final: 0.7399 (mt-10) REVERT: A 205 MET cc_start: 0.8156 (mtp) cc_final: 0.7502 (mtp) REVERT: B 12 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7031 (ptt180) REVERT: B 18 GLN cc_start: 0.7787 (mp10) cc_final: 0.6882 (mm-40) REVERT: B 41 ASN cc_start: 0.7541 (t0) cc_final: 0.7251 (t0) REVERT: B 67 GLU cc_start: 0.8144 (mp0) cc_final: 0.7866 (mp0) REVERT: B 95 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7924 (mttt) REVERT: B 127 GLN cc_start: 0.8032 (pm20) cc_final: 0.7808 (pm20) REVERT: B 170 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.6983 (pmt170) REVERT: B 188 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 200 LYS cc_start: 0.8421 (tttt) cc_final: 0.8077 (tmmt) REVERT: C 70 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 191 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8380 (mmtp) REVERT: C 200 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7789 (mmm160) REVERT: C 370 MET cc_start: 0.7442 (mmm) cc_final: 0.7233 (mmm) REVERT: C 387 ASN cc_start: 0.7043 (p0) cc_final: 0.6805 (m-40) REVERT: C 439 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8399 (ttmm) REVERT: C 503 LYS cc_start: 0.8182 (tptp) cc_final: 0.7647 (tttt) REVERT: C 600 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.7861 (p) REVERT: C 694 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7201 (mtm-85) REVERT: C 738 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: C 768 MET cc_start: 0.8135 (mtp) cc_final: 0.7681 (mtp) REVERT: C 791 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8116 (tp) REVERT: C 876 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 950 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8047 (tm-30) REVERT: C 955 GLN cc_start: 0.8102 (tp40) cc_final: 0.7636 (tp-100) REVERT: C 965 GLN cc_start: 0.6070 (mt0) cc_final: 0.5825 (mt0) REVERT: C 1025 PHE cc_start: 0.6866 (t80) cc_final: 0.6438 (t80) REVERT: C 1027 LYS cc_start: 0.8763 (tptp) cc_final: 0.8439 (pttm) REVERT: C 1032 LYS cc_start: 0.7813 (mppt) cc_final: 0.7596 (mppt) REVERT: C 1106 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7538 (ptp-170) REVERT: C 1131 MET cc_start: 0.7779 (mtt) cc_final: 0.7518 (mtt) REVERT: C 1137 GLU cc_start: 0.7093 (mp0) cc_final: 0.6836 (mp0) REVERT: C 1167 GLU cc_start: 0.7817 (tp30) cc_final: 0.7168 (tm-30) REVERT: C 1174 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: D 60 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.7919 (mtp-110) REVERT: D 74 LYS cc_start: 0.8867 (tttt) cc_final: 0.8625 (ttmm) REVERT: D 129 ASP cc_start: 0.8035 (t0) cc_final: 0.7790 (t0) REVERT: D 237 MET cc_start: 0.9064 (mtp) cc_final: 0.8812 (mtp) REVERT: D 275 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6685 (mtt180) REVERT: D 289 ASP cc_start: 0.6787 (m-30) cc_final: 0.6357 (t0) REVERT: D 312 ARG cc_start: 0.7172 (mmm160) cc_final: 0.6393 (mmm-85) REVERT: D 330 MET cc_start: 0.8210 (mtm) cc_final: 0.7706 (mtp) REVERT: D 348 ASP cc_start: 0.8684 (m-30) cc_final: 0.8380 (m-30) REVERT: D 371 LYS cc_start: 0.8773 (mttt) cc_final: 0.8359 (mmpt) REVERT: D 375 GLU cc_start: 0.8325 (tp30) cc_final: 0.7900 (mm-30) REVERT: D 398 LYS cc_start: 0.7777 (tttm) cc_final: 0.7324 (ttmm) REVERT: D 547 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7673 (mtm110) REVERT: D 603 LYS cc_start: 0.7287 (tttt) cc_final: 0.6971 (ttmt) REVERT: D 649 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7411 (mtmm) REVERT: D 703 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8296 (t) REVERT: D 731 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7934 (tpt90) REVERT: D 738 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6728 (mtt180) REVERT: D 781 LYS cc_start: 0.7473 (tttt) cc_final: 0.7055 (ttpt) REVERT: D 805 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: D 853 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7736 (t) REVERT: D 955 LYS cc_start: 0.8018 (pttt) cc_final: 0.7703 (pptt) REVERT: D 1189 MET cc_start: 0.8765 (mtt) cc_final: 0.8552 (mmm) REVERT: D 1195 GLN cc_start: 0.6893 (pm20) cc_final: 0.6197 (pp30) REVERT: E 7 GLN cc_start: 0.7673 (tp40) cc_final: 0.5969 (tp40) REVERT: E 8 ASP cc_start: 0.8451 (m-30) cc_final: 0.8149 (m-30) REVERT: E 11 GLU cc_start: 0.8069 (mp0) cc_final: 0.7377 (mp0) REVERT: E 41 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7262 (tm-30) REVERT: E 68 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6974 (tm-30) REVERT: E 72 GLN cc_start: 0.8138 (tt0) cc_final: 0.7685 (tm-30) outliers start: 77 outliers final: 46 residues processed: 279 average time/residue: 0.7738 time to fit residues: 247.3419 Evaluate side-chains 279 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 731 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 253 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 257 optimal weight: 0.1980 chunk 165 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091285 restraints weight = 35750.169| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.40 r_work: 0.3071 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26434 Z= 0.133 Angle : 0.553 11.124 35890 Z= 0.287 Chirality : 0.044 0.170 4115 Planarity : 0.004 0.067 4552 Dihedral : 9.778 82.761 3945 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.38 % Allowed : 18.00 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3191 helix: 0.59 (0.16), residues: 1131 sheet: -1.02 (0.25), residues: 433 loop : -0.39 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 368 TYR 0.017 0.001 TYR D 679 PHE 0.023 0.001 PHE C 906 TRP 0.008 0.001 TRP C 807 HIS 0.003 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (26426) covalent geometry : angle 0.55165 / 0.29 (35878) hydrogen bonds : bond 0.03332 / 2.30 ( 1071) hydrogen bonds : angle 4.68165 / 3.24 ( 2941) metal coordination : bond 0.00408 / 0.23 ( 8) metal coordination : angle 2.49819 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8162 (tpp80) REVERT: A 51 MET cc_start: 0.8983 (mmt) cc_final: 0.8694 (mmm) REVERT: A 127 GLN cc_start: 0.8011 (mp10) cc_final: 0.7683 (pm20) REVERT: A 145 LYS cc_start: 0.7972 (tttt) cc_final: 0.7687 (ttpp) REVERT: A 186 ASN cc_start: 0.8212 (m-40) cc_final: 0.7791 (m110) REVERT: A 194 GLN cc_start: 0.8518 (tp40) cc_final: 0.7826 (tm-30) REVERT: A 204 GLU cc_start: 0.7968 (tt0) cc_final: 0.7347 (mt-10) REVERT: A 205 MET cc_start: 0.8050 (mtp) cc_final: 0.7351 (mtp) REVERT: B 12 ARG cc_start: 0.7500 (ttm110) cc_final: 0.6985 (ptt180) REVERT: B 18 GLN cc_start: 0.7736 (mp10) cc_final: 0.6831 (mm-40) REVERT: B 41 ASN cc_start: 0.7543 (t0) cc_final: 0.7230 (t0) REVERT: B 67 GLU cc_start: 0.8103 (mp0) cc_final: 0.7814 (mp0) REVERT: B 95 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7809 (mttt) REVERT: B 127 GLN cc_start: 0.8014 (pm20) cc_final: 0.7792 (pm20) REVERT: B 145 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7751 (ttpp) REVERT: B 170 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.6941 (pmt170) REVERT: B 188 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: B 200 LYS cc_start: 0.8323 (tttt) cc_final: 0.7950 (tmmt) REVERT: C 70 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 191 LYS cc_start: 0.8603 (mmpt) cc_final: 0.8354 (mmtp) REVERT: C 200 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7813 (mmm160) REVERT: C 370 MET cc_start: 0.7470 (mmm) cc_final: 0.7167 (mmm) REVERT: C 439 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8380 (ttmm) REVERT: C 503 LYS cc_start: 0.8042 (tptp) cc_final: 0.7511 (tttt) REVERT: C 600 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7756 (p) REVERT: C 694 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7169 (mtm-85) REVERT: C 738 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: C 768 MET cc_start: 0.8062 (mtp) cc_final: 0.7606 (mtp) REVERT: C 791 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (tp) REVERT: C 876 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 901 LEU cc_start: 0.3194 (OUTLIER) cc_final: 0.2748 (tt) REVERT: C 950 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8069 (tm-30) REVERT: C 955 GLN cc_start: 0.8068 (tp40) cc_final: 0.7614 (tp-100) REVERT: C 1025 PHE cc_start: 0.6813 (t80) cc_final: 0.6407 (t80) REVERT: C 1027 LYS cc_start: 0.8777 (tptp) cc_final: 0.8448 (pttm) REVERT: C 1032 LYS cc_start: 0.7795 (mppt) cc_final: 0.7586 (mttp) REVERT: C 1131 MET cc_start: 0.7630 (mtt) cc_final: 0.7421 (mtt) REVERT: C 1137 GLU cc_start: 0.7044 (mp0) cc_final: 0.6461 (tt0) REVERT: C 1167 GLU cc_start: 0.7778 (tp30) cc_final: 0.7192 (tm-30) REVERT: C 1174 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: D 60 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.7912 (mtp-110) REVERT: D 74 LYS cc_start: 0.8879 (tttt) cc_final: 0.8627 (ttmm) REVERT: D 114 ILE cc_start: 0.8273 (tt) cc_final: 0.7985 (tp) REVERT: D 129 ASP cc_start: 0.7993 (t0) cc_final: 0.7714 (t0) REVERT: D 237 MET cc_start: 0.9038 (mtp) cc_final: 0.8791 (mtp) REVERT: D 275 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6600 (mtt180) REVERT: D 289 ASP cc_start: 0.6622 (m-30) cc_final: 0.6255 (t0) REVERT: D 304 ASP cc_start: 0.7622 (m-30) cc_final: 0.7165 (t0) REVERT: D 312 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6744 (mmm160) REVERT: D 330 MET cc_start: 0.8030 (mtm) cc_final: 0.7659 (mtp) REVERT: D 348 ASP cc_start: 0.8619 (m-30) cc_final: 0.8308 (m-30) REVERT: D 371 LYS cc_start: 0.8714 (mttt) cc_final: 0.8316 (mmpt) REVERT: D 375 GLU cc_start: 0.8276 (tp30) cc_final: 0.7871 (mm-30) REVERT: D 398 LYS cc_start: 0.7684 (tttm) cc_final: 0.7237 (ttmm) REVERT: D 603 LYS cc_start: 0.7204 (tttt) cc_final: 0.6889 (ttmt) REVERT: D 649 LYS cc_start: 0.7510 (mmmt) cc_final: 0.7210 (mtpp) REVERT: D 703 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8224 (t) REVERT: D 738 ARG cc_start: 0.7063 (ttm170) cc_final: 0.6558 (mtt180) REVERT: D 754 ILE cc_start: 0.7282 (pt) cc_final: 0.7012 (pp) REVERT: D 781 LYS cc_start: 0.7363 (tttt) cc_final: 0.6952 (ttpt) REVERT: D 805 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: D 853 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7622 (t) REVERT: D 873 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7899 (tt0) REVERT: D 955 LYS cc_start: 0.8009 (pttt) cc_final: 0.7699 (pptt) REVERT: D 1189 MET cc_start: 0.8611 (mtt) cc_final: 0.8393 (mmm) REVERT: D 1195 GLN cc_start: 0.6796 (pm20) cc_final: 0.6344 (pp30) REVERT: E 8 ASP cc_start: 0.8464 (m-30) cc_final: 0.8188 (m-30) REVERT: E 11 GLU cc_start: 0.8086 (mp0) cc_final: 0.7506 (mp0) REVERT: E 41 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7184 (tm-30) REVERT: E 68 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6949 (tm-30) REVERT: E 71 GLU cc_start: 0.7166 (pp20) cc_final: 0.6791 (pp20) REVERT: E 72 GLN cc_start: 0.8056 (tt0) cc_final: 0.7666 (tm-30) REVERT: E 74 GLU cc_start: 0.7530 (pp20) cc_final: 0.7116 (pp20) outliers start: 65 outliers final: 31 residues processed: 282 average time/residue: 0.7672 time to fit residues: 247.2917 Evaluate side-chains 263 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 223 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN C 69 GLN C 490 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091452 restraints weight = 35755.768| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.40 r_work: 0.3070 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26434 Z= 0.134 Angle : 0.557 11.744 35890 Z= 0.287 Chirality : 0.044 0.195 4115 Planarity : 0.004 0.073 4552 Dihedral : 9.735 83.325 3945 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 18.88 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3191 helix: 0.72 (0.16), residues: 1130 sheet: -0.91 (0.25), residues: 423 loop : -0.35 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 322 TYR 0.022 0.001 TYR C1231 PHE 0.023 0.001 PHE C 906 TRP 0.006 0.001 TRP D 33 HIS 0.003 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (26426) covalent geometry : angle 0.55621 / 0.29 (35878) hydrogen bonds : bond 0.03295 / 2.28 ( 1071) hydrogen bonds : angle 4.64529 / 3.21 ( 2941) metal coordination : bond 0.00439 / 0.25 ( 8) metal coordination : angle 2.14152 / 1.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8159 (tpp80) REVERT: A 51 MET cc_start: 0.8969 (mmt) cc_final: 0.8749 (mmm) REVERT: A 127 GLN cc_start: 0.8011 (mp10) cc_final: 0.7685 (pm20) REVERT: A 145 LYS cc_start: 0.7987 (tttt) cc_final: 0.7694 (ttpp) REVERT: A 186 ASN cc_start: 0.8185 (m-40) cc_final: 0.7799 (m110) REVERT: A 194 GLN cc_start: 0.8529 (tp40) cc_final: 0.7820 (tm-30) REVERT: A 204 GLU cc_start: 0.8071 (tt0) cc_final: 0.7379 (mt-10) REVERT: A 205 MET cc_start: 0.8007 (mtp) cc_final: 0.7293 (mtp) REVERT: B 12 ARG cc_start: 0.7492 (ttm110) cc_final: 0.6989 (ptt180) REVERT: B 18 GLN cc_start: 0.7743 (mp10) cc_final: 0.6861 (mm-40) REVERT: B 41 ASN cc_start: 0.7560 (t0) cc_final: 0.7249 (t0) REVERT: B 67 GLU cc_start: 0.8117 (mp0) cc_final: 0.7820 (mp0) REVERT: B 95 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7603 (ptpt) REVERT: B 127 GLN cc_start: 0.8023 (pm20) cc_final: 0.7800 (pm20) REVERT: B 145 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7714 (ttpp) REVERT: B 170 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.6935 (pmt170) REVERT: B 188 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: B 200 LYS cc_start: 0.8358 (tttt) cc_final: 0.8000 (tmmt) REVERT: C 70 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 191 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8350 (mmtp) REVERT: C 200 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7527 (mmm160) REVERT: C 201 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.7147 (ptm160) REVERT: C 439 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8381 (ttmm) REVERT: C 503 LYS cc_start: 0.8188 (tptp) cc_final: 0.7694 (tttt) REVERT: C 600 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7762 (p) REVERT: C 694 ARG cc_start: 0.8212 (mmt90) cc_final: 0.7190 (mtm-85) REVERT: C 738 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: C 768 MET cc_start: 0.8118 (mtp) cc_final: 0.7650 (mtp) REVERT: C 791 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8128 (tp) REVERT: C 851 THR cc_start: 0.8302 (t) cc_final: 0.8062 (p) REVERT: C 876 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 950 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8098 (tm-30) REVERT: C 955 GLN cc_start: 0.8070 (tp40) cc_final: 0.7616 (tp-100) REVERT: C 1025 PHE cc_start: 0.6806 (t80) cc_final: 0.6409 (t80) REVERT: C 1027 LYS cc_start: 0.8769 (tptp) cc_final: 0.8446 (pttm) REVERT: C 1032 LYS cc_start: 0.7829 (mppt) cc_final: 0.7602 (mttp) REVERT: C 1137 GLU cc_start: 0.7000 (mp0) cc_final: 0.6492 (tt0) REVERT: C 1167 GLU cc_start: 0.7775 (tp30) cc_final: 0.7166 (tm-30) REVERT: C 1174 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: D 60 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7913 (mtp-110) REVERT: D 74 LYS cc_start: 0.8869 (tttt) cc_final: 0.8617 (ttmm) REVERT: D 129 ASP cc_start: 0.7984 (t0) cc_final: 0.7708 (t0) REVERT: D 237 MET cc_start: 0.9020 (mtp) cc_final: 0.8800 (mtp) REVERT: D 275 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6619 (mtt180) REVERT: D 289 ASP cc_start: 0.6668 (m-30) cc_final: 0.6391 (t0) REVERT: D 312 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6450 (mmm-85) REVERT: D 348 ASP cc_start: 0.8647 (m-30) cc_final: 0.8350 (m-30) REVERT: D 371 LYS cc_start: 0.8702 (mttt) cc_final: 0.8346 (mmpt) REVERT: D 375 GLU cc_start: 0.8308 (tp30) cc_final: 0.7875 (mm-30) REVERT: D 398 LYS cc_start: 0.7691 (tttm) cc_final: 0.7244 (ttmm) REVERT: D 603 LYS cc_start: 0.7429 (tttt) cc_final: 0.7101 (ttmt) REVERT: D 649 LYS cc_start: 0.7542 (mmmt) cc_final: 0.7249 (mtpp) REVERT: D 698 MET cc_start: 0.7877 (tpt) cc_final: 0.7470 (mmm) REVERT: D 703 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8244 (t) REVERT: D 738 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6557 (mtt180) REVERT: D 754 ILE cc_start: 0.7256 (pt) cc_final: 0.6978 (pp) REVERT: D 781 LYS cc_start: 0.7374 (tttt) cc_final: 0.6964 (ttpt) REVERT: D 805 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: D 853 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7593 (t) REVERT: D 873 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7855 (tt0) REVERT: D 955 LYS cc_start: 0.7997 (pttt) cc_final: 0.7689 (pptt) REVERT: D 980 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7512 (m) REVERT: D 1189 MET cc_start: 0.8500 (mtt) cc_final: 0.8277 (mmm) REVERT: D 1195 GLN cc_start: 0.6722 (pm20) cc_final: 0.6332 (pp30) REVERT: E 3 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8086 (ttm-80) REVERT: E 8 ASP cc_start: 0.8451 (m-30) cc_final: 0.8157 (m-30) REVERT: E 11 GLU cc_start: 0.8066 (mp0) cc_final: 0.7492 (mp0) REVERT: E 41 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7126 (tm-30) REVERT: E 68 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6962 (tm-30) REVERT: E 72 GLN cc_start: 0.8121 (tt0) cc_final: 0.7712 (tm-30) outliers start: 47 outliers final: 27 residues processed: 268 average time/residue: 0.7300 time to fit residues: 222.9146 Evaluate side-chains 265 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 217 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN C 490 GLN ** D 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092146 restraints weight = 35562.622| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.40 r_work: 0.3082 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26434 Z= 0.128 Angle : 0.553 11.500 35890 Z= 0.285 Chirality : 0.043 0.160 4115 Planarity : 0.004 0.070 4552 Dihedral : 9.720 84.241 3945 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 18.91 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3191 helix: 0.87 (0.16), residues: 1125 sheet: -0.89 (0.25), residues: 413 loop : -0.32 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 322 TYR 0.021 0.001 TYR C1018 PHE 0.023 0.001 PHE C 906 TRP 0.006 0.001 TRP C 807 HIS 0.003 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26426) covalent geometry : angle 0.55175 / 0.28 (35878) hydrogen bonds : bond 0.03216 / 2.22 ( 1071) hydrogen bonds : angle 4.60128 / 3.18 ( 2941) metal coordination : bond 0.00380 / 0.22 ( 8) metal coordination : angle 2.06596 / 0.98 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10564.42 seconds wall clock time: 180 minutes 5.64 seconds (10805.64 seconds total)