Starting phenix.real_space_refine on Tue Sep 15 16:53:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vkq_8702/09_2026/5vkq_8702.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 188 5.16 5 C 26900 2.51 5 N 7352 2.21 5 O 7428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.16s 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: 41900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 33, 'TYR:plan': 6, 'ASP:plan': 51, 'ARG:plan': 27, 'GLU:plan': 52, 'HIS:plan': 8, 'PHE:plan': 7, 'GLN:plan1': 18, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 809 Chain: "B" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 33, 'TYR:plan': 6, 'ASP:plan': 51, 'ARG:plan': 27, 'GLU:plan': 52, 'HIS:plan': 8, 'PHE:plan': 7, 'GLN:plan1': 18, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 809 Chain: "C" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 33, 'TYR:plan': 6, 'ASP:plan': 51, 'ARG:plan': 27, 'GLU:plan': 52, 'HIS:plan': 8, 'PHE:plan': 7, 'GLN:plan1': 18, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 809 Chain: "D" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'ASN:plan1': 33, 'TYR:plan': 6, 'ASP:plan': 51, 'ARG:plan': 27, 'GLU:plan': 52, 'HIS:plan': 8, 'PHE:plan': 7, 'GLN:plan1': 18, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 809 Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 151 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 151 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 151 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 151 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.28, per 1000 atoms: 0.22 Number of scatterers: 41900 At special positions: 0 Unit cell: (176.262, 176.262, 260.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 188 16.00 P 32 15.00 O 7428 8.00 N 7352 7.00 C 26900 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11184 Finding SS restraints... Secondary structure from input PDB file: 356 helices and 0 sheets defined 67.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 200 through 208 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.533A pdb=" N LEU A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.800A pdb=" N MET A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.547A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 445 removed outlier: 4.571A pdb=" N GLU A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 481 through 491 removed outlier: 4.463A pdb=" N LEU A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N MET A 487 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 513 removed outlier: 3.617A pdb=" N GLY A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.650A pdb=" N LEU A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 545 removed outlier: 3.550A pdb=" N MET A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 545 " --> pdb=" O MET A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.730A pdb=" N GLU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 4.144A pdb=" N LYS A 566 " --> pdb=" O HIS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.541A pdb=" N ALA A 579 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.736A pdb=" N CYS A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 609 removed outlier: 3.637A pdb=" N GLN A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 609 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.974A pdb=" N TYR A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 647 through 654 removed outlier: 3.994A pdb=" N LYS A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 695 through 704 Processing helix chain 'A' and resid 705 through 715 removed outlier: 3.628A pdb=" N CYS A 709 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.818A pdb=" N SER A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 795 through 803 removed outlier: 3.799A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.502A pdb=" N ALA A 809 " --> pdb=" O TYR A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 4.190A pdb=" N ALA A 822 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 838 removed outlier: 3.622A pdb=" N ILE A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 856 removed outlier: 8.170A pdb=" N SER A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 856 " --> pdb=" O SER A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 874 Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.538A pdb=" N VAL A 879 " --> pdb=" O HIS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 908 through 919 removed outlier: 4.022A pdb=" N THR A 918 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 941 through 952 removed outlier: 3.691A pdb=" N VAL A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 986 removed outlier: 3.782A pdb=" N LEU A 981 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1012 through 1019 Processing helix chain 'A' and resid 1022 through 1033 Processing helix chain 'A' and resid 1046 through 1054 removed outlier: 3.596A pdb=" N ILE A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.523A pdb=" N GLY A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1089 through 1099 Processing helix chain 'A' and resid 1112 through 1120 removed outlier: 4.036A pdb=" N PHE A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A1120 " --> pdb=" O PHE A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1142 through 1156 Processing helix chain 'A' and resid 1158 through 1168 removed outlier: 3.846A pdb=" N GLN A1162 " --> pdb=" O ASN A1158 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1189 removed outlier: 3.653A pdb=" N THR A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1216 removed outlier: 3.747A pdb=" N LEU A1196 " --> pdb=" O ARG A1192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A1197 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1225 removed outlier: 3.587A pdb=" N ILE A1223 " --> pdb=" O SER A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1241 Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1249 through 1262 Processing helix chain 'A' and resid 1269 through 1281 removed outlier: 3.917A pdb=" N VAL A1276 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1290 removed outlier: 3.508A pdb=" N TRP A1285 " --> pdb=" O CYS A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1323 removed outlier: 3.667A pdb=" N LYS A1303 " --> pdb=" O VAL A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1357 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1365 through 1387 removed outlier: 3.839A pdb=" N VAL A1369 " --> pdb=" O GLY A1365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1377 " --> pdb=" O LEU A1373 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A1384 " --> pdb=" O GLY A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1419 Processing helix chain 'A' and resid 1428 through 1460 removed outlier: 4.409A pdb=" N GLY A1434 " --> pdb=" O ALA A1430 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A1439 " --> pdb=" O ASP A1435 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A1446 " --> pdb=" O ARG A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1475 removed outlier: 3.757A pdb=" N ARG A1474 " --> pdb=" O PRO A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1501 Processing helix chain 'A' and resid 1502 through 1504 No H-bonds generated for 'chain 'A' and resid 1502 through 1504' Processing helix chain 'A' and resid 1514 through 1519 Processing helix chain 'A' and resid 1530 through 1548 Processing helix chain 'A' and resid 1548 through 1585 removed outlier: 4.786A pdb=" N ARG A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA A1566 " --> pdb=" O GLN A1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN A1567 " --> pdb=" O ARG A1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A1570 " --> pdb=" O ALA A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1600 Processing helix chain 'A' and resid 1670 through 1674 removed outlier: 3.760A pdb=" N ASN A1673 " --> pdb=" O ARG A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1689 Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 200 through 208 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.533A pdb=" N LEU B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 380 through 390 removed outlier: 3.799A pdb=" N MET B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 413 through 424 removed outlier: 3.546A pdb=" N ILE B 417 " --> pdb=" O HIS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 445 removed outlier: 4.571A pdb=" N GLU B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 471 through 476 Processing helix chain 'B' and resid 481 through 491 removed outlier: 4.463A pdb=" N LEU B 486 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N MET B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 removed outlier: 3.618A pdb=" N GLY B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 524 removed outlier: 3.649A pdb=" N LEU B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 545 removed outlier: 3.551A pdb=" N MET B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 545 " --> pdb=" O MET B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 562 removed outlier: 3.730A pdb=" N GLU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 4.145A pdb=" N LYS B 566 " --> pdb=" O HIS B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.541A pdb=" N ALA B 579 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 removed outlier: 3.737A pdb=" N CYS B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 609 removed outlier: 3.636A pdb=" N GLN B 601 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.975A pdb=" N TYR B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 647 through 654 removed outlier: 3.994A pdb=" N LYS B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 671 Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 695 through 704 Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.628A pdb=" N CYS B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 762 through 771 removed outlier: 3.818A pdb=" N SER B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 783 Processing helix chain 'B' and resid 795 through 803 removed outlier: 3.799A pdb=" N VAL B 799 " --> pdb=" O LYS B 795 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 815 removed outlier: 3.503A pdb=" N ALA B 809 " --> pdb=" O TYR B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 removed outlier: 4.189A pdb=" N ALA B 822 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 838 removed outlier: 3.622A pdb=" N ILE B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 856 removed outlier: 8.169A pdb=" N SER B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY B 853 " --> pdb=" O PHE B 849 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 874 Processing helix chain 'B' and resid 875 through 886 removed outlier: 3.537A pdb=" N VAL B 879 " --> pdb=" O HIS B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 907 Processing helix chain 'B' and resid 908 through 919 removed outlier: 4.022A pdb=" N THR B 918 " --> pdb=" O VAL B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 939 Processing helix chain 'B' and resid 941 through 952 removed outlier: 3.691A pdb=" N VAL B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 986 removed outlier: 3.781A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 986 " --> pdb=" O ALA B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1012 through 1019 Processing helix chain 'B' and resid 1022 through 1033 Processing helix chain 'B' and resid 1046 through 1054 removed outlier: 3.595A pdb=" N ILE B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1067 removed outlier: 3.523A pdb=" N GLY B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1088 Processing helix chain 'B' and resid 1089 through 1099 Processing helix chain 'B' and resid 1112 through 1120 removed outlier: 4.036A pdb=" N PHE B1116 " --> pdb=" O ALA B1112 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B1120 " --> pdb=" O PHE B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1132 Processing helix chain 'B' and resid 1135 through 1140 Processing helix chain 'B' and resid 1142 through 1156 Processing helix chain 'B' and resid 1158 through 1168 removed outlier: 3.847A pdb=" N GLN B1162 " --> pdb=" O ASN B1158 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B1168 " --> pdb=" O PHE B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1189 removed outlier: 3.652A pdb=" N THR B1187 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1216 removed outlier: 3.746A pdb=" N LEU B1196 " --> pdb=" O ARG B1192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B1197 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B1198 " --> pdb=" O LYS B1194 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B1216 " --> pdb=" O ALA B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1225 removed outlier: 3.587A pdb=" N ILE B1223 " --> pdb=" O SER B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1233 through 1241 Processing helix chain 'B' and resid 1243 through 1248 Processing helix chain 'B' and resid 1249 through 1262 Processing helix chain 'B' and resid 1269 through 1281 removed outlier: 3.917A pdb=" N VAL B1276 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS B1281 " --> pdb=" O ALA B1277 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1290 removed outlier: 3.508A pdb=" N TRP B1285 " --> pdb=" O CYS B1281 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1323 removed outlier: 3.668A pdb=" N LYS B1303 " --> pdb=" O VAL B1299 " (cutoff:3.500A) Processing helix chain 'B' and resid 1337 through 1357 Processing helix chain 'B' and resid 1362 through 1364 No H-bonds generated for 'chain 'B' and resid 1362 through 1364' Processing helix chain 'B' and resid 1365 through 1387 removed outlier: 3.839A pdb=" N VAL B1369 " --> pdb=" O GLY B1365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B1377 " --> pdb=" O LEU B1373 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER B1384 " --> pdb=" O GLY B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1419 Processing helix chain 'B' and resid 1428 through 1460 removed outlier: 4.410A pdb=" N GLY B1434 " --> pdb=" O ALA B1430 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B1439 " --> pdb=" O ASP B1435 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1469 through 1475 removed outlier: 3.757A pdb=" N ARG B1474 " --> pdb=" O PRO B1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 1492 through 1501 Processing helix chain 'B' and resid 1502 through 1504 No H-bonds generated for 'chain 'B' and resid 1502 through 1504' Processing helix chain 'B' and resid 1514 through 1519 Processing helix chain 'B' and resid 1530 through 1548 Processing helix chain 'B' and resid 1548 through 1585 removed outlier: 4.786A pdb=" N ARG B1563 " --> pdb=" O ASP B1559 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B1566 " --> pdb=" O GLN B1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN B1567 " --> pdb=" O ARG B1563 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B1570 " --> pdb=" O ALA B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1595 through 1600 Processing helix chain 'B' and resid 1670 through 1674 removed outlier: 3.760A pdb=" N ASN B1673 " --> pdb=" O ARG B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1676 through 1689 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.533A pdb=" N LEU C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.800A pdb=" N MET C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.547A pdb=" N ILE C 417 " --> pdb=" O HIS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 445 removed outlier: 4.571A pdb=" N GLU C 443 " --> pdb=" O HIS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 457 Processing helix chain 'C' and resid 471 through 476 Processing helix chain 'C' and resid 481 through 491 removed outlier: 4.463A pdb=" N LEU C 486 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N MET C 487 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 491 " --> pdb=" O MET C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.617A pdb=" N GLY C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 524 removed outlier: 3.649A pdb=" N LEU C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 545 removed outlier: 3.551A pdb=" N MET C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 545 " --> pdb=" O MET C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.729A pdb=" N GLU C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 removed outlier: 4.144A pdb=" N LYS C 566 " --> pdb=" O HIS C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 579 removed outlier: 3.541A pdb=" N ALA C 579 " --> pdb=" O GLU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 removed outlier: 3.735A pdb=" N CYS C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN C 587 " --> pdb=" O HIS C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 609 removed outlier: 3.637A pdb=" N GLN C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 609 " --> pdb=" O MET C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 632 removed outlier: 3.974A pdb=" N TYR C 627 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS C 628 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 647 through 654 removed outlier: 3.994A pdb=" N LYS C 651 " --> pdb=" O THR C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 Processing helix chain 'C' and resid 672 through 682 Processing helix chain 'C' and resid 695 through 704 Processing helix chain 'C' and resid 705 through 715 removed outlier: 3.627A pdb=" N CYS C 709 " --> pdb=" O TYR C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 738 through 750 Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.818A pdb=" N SER C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 795 through 803 removed outlier: 3.799A pdb=" N VAL C 799 " --> pdb=" O LYS C 795 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 803 " --> pdb=" O VAL C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 815 removed outlier: 3.503A pdb=" N ALA C 809 " --> pdb=" O TYR C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 823 removed outlier: 4.190A pdb=" N ALA C 822 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 838 removed outlier: 3.622A pdb=" N ILE C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 856 removed outlier: 8.170A pdb=" N SER C 852 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY C 853 " --> pdb=" O PHE C 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 874 Processing helix chain 'C' and resid 875 through 886 removed outlier: 3.538A pdb=" N VAL C 879 " --> pdb=" O HIS C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 Processing helix chain 'C' and resid 908 through 919 removed outlier: 4.022A pdb=" N THR C 918 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 939 Processing helix chain 'C' and resid 941 through 952 removed outlier: 3.690A pdb=" N VAL C 945 " --> pdb=" O GLN C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 986 removed outlier: 3.781A pdb=" N LEU C 981 " --> pdb=" O THR C 977 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 986 " --> pdb=" O ALA C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1012 through 1019 Processing helix chain 'C' and resid 1022 through 1033 Processing helix chain 'C' and resid 1046 through 1054 removed outlier: 3.596A pdb=" N ILE C1050 " --> pdb=" O THR C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1067 removed outlier: 3.522A pdb=" N GLY C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1088 Processing helix chain 'C' and resid 1089 through 1099 Processing helix chain 'C' and resid 1112 through 1120 removed outlier: 4.037A pdb=" N PHE C1116 " --> pdb=" O ALA C1112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C1120 " --> pdb=" O PHE C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1132 Processing helix chain 'C' and resid 1135 through 1140 Processing helix chain 'C' and resid 1142 through 1156 Processing helix chain 'C' and resid 1158 through 1168 removed outlier: 3.846A pdb=" N GLN C1162 " --> pdb=" O ASN C1158 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C1168 " --> pdb=" O PHE C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1170 through 1189 removed outlier: 3.652A pdb=" N THR C1187 " --> pdb=" O ILE C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1216 removed outlier: 3.747A pdb=" N LEU C1196 " --> pdb=" O ARG C1192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C1197 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C1198 " --> pdb=" O LYS C1194 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1225 removed outlier: 3.587A pdb=" N ILE C1223 " --> pdb=" O SER C1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 1233 through 1241 Processing helix chain 'C' and resid 1243 through 1248 Processing helix chain 'C' and resid 1249 through 1262 Processing helix chain 'C' and resid 1269 through 1281 removed outlier: 3.918A pdb=" N VAL C1276 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1290 removed outlier: 3.508A pdb=" N TRP C1285 " --> pdb=" O CYS C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1323 removed outlier: 3.667A pdb=" N LYS C1303 " --> pdb=" O VAL C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1337 through 1357 Processing helix chain 'C' and resid 1362 through 1364 No H-bonds generated for 'chain 'C' and resid 1362 through 1364' Processing helix chain 'C' and resid 1365 through 1387 removed outlier: 3.839A pdb=" N VAL C1369 " --> pdb=" O GLY C1365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C1377 " --> pdb=" O LEU C1373 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER C1384 " --> pdb=" O GLY C1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 1395 through 1419 Processing helix chain 'C' and resid 1428 through 1460 removed outlier: 4.409A pdb=" N GLY C1434 " --> pdb=" O ALA C1430 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP C1439 " --> pdb=" O ASP C1435 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL C1446 " --> pdb=" O ARG C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1469 through 1475 removed outlier: 3.757A pdb=" N ARG C1474 " --> pdb=" O PRO C1470 " (cutoff:3.500A) Processing helix chain 'C' and resid 1492 through 1501 Processing helix chain 'C' and resid 1502 through 1504 No H-bonds generated for 'chain 'C' and resid 1502 through 1504' Processing helix chain 'C' and resid 1514 through 1519 Processing helix chain 'C' and resid 1530 through 1548 Processing helix chain 'C' and resid 1548 through 1585 removed outlier: 4.787A pdb=" N ARG C1563 " --> pdb=" O ASP C1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C1566 " --> pdb=" O GLN C1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C1567 " --> pdb=" O ARG C1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C1570 " --> pdb=" O ALA C1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 1595 through 1600 Processing helix chain 'C' and resid 1670 through 1674 removed outlier: 3.761A pdb=" N ASN C1673 " --> pdb=" O ARG C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1676 through 1689 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 144 through 157 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.533A pdb=" N LEU D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 313 through 323 Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 371 through 379 Processing helix chain 'D' and resid 380 through 390 removed outlier: 3.800A pdb=" N MET D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.546A pdb=" N ILE D 417 " --> pdb=" O HIS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 445 removed outlier: 4.571A pdb=" N GLU D 443 " --> pdb=" O HIS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 Processing helix chain 'D' and resid 471 through 476 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.463A pdb=" N LEU D 486 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N MET D 487 " --> pdb=" O ARG D 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.617A pdb=" N GLY D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 removed outlier: 3.650A pdb=" N LEU D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 545 removed outlier: 3.551A pdb=" N MET D 541 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 545 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 562 removed outlier: 3.729A pdb=" N GLU D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 4.144A pdb=" N LYS D 566 " --> pdb=" O HIS D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 579 removed outlier: 3.541A pdb=" N ALA D 579 " --> pdb=" O GLU D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 587 removed outlier: 3.736A pdb=" N CYS D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 609 removed outlier: 3.637A pdb=" N GLN D 601 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 632 removed outlier: 3.974A pdb=" N TYR D 627 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 628 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 647 through 654 removed outlier: 3.994A pdb=" N LYS D 651 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 672 through 682 Processing helix chain 'D' and resid 695 through 704 Processing helix chain 'D' and resid 705 through 715 removed outlier: 3.628A pdb=" N CYS D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'D' and resid 738 through 750 Processing helix chain 'D' and resid 762 through 771 removed outlier: 3.818A pdb=" N SER D 770 " --> pdb=" O LEU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 783 Processing helix chain 'D' and resid 795 through 803 removed outlier: 3.799A pdb=" N VAL D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 803 " --> pdb=" O VAL D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 815 removed outlier: 3.502A pdb=" N ALA D 809 " --> pdb=" O TYR D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 823 removed outlier: 4.190A pdb=" N ALA D 822 " --> pdb=" O LEU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 838 removed outlier: 3.622A pdb=" N ILE D 833 " --> pdb=" O THR D 829 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 856 removed outlier: 8.169A pdb=" N SER D 852 " --> pdb=" O LYS D 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 875 through 886 removed outlier: 3.537A pdb=" N VAL D 879 " --> pdb=" O HIS D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 907 Processing helix chain 'D' and resid 908 through 919 removed outlier: 4.022A pdb=" N THR D 918 " --> pdb=" O VAL D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 939 Processing helix chain 'D' and resid 941 through 952 removed outlier: 3.691A pdb=" N VAL D 945 " --> pdb=" O GLN D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 986 removed outlier: 3.781A pdb=" N LEU D 981 " --> pdb=" O THR D 977 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 986 " --> pdb=" O ALA D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1012 through 1019 Processing helix chain 'D' and resid 1022 through 1033 Processing helix chain 'D' and resid 1046 through 1054 removed outlier: 3.596A pdb=" N ILE D1050 " --> pdb=" O THR D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1067 removed outlier: 3.522A pdb=" N GLY D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1088 Processing helix chain 'D' and resid 1089 through 1099 Processing helix chain 'D' and resid 1112 through 1120 removed outlier: 4.036A pdb=" N PHE D1116 " --> pdb=" O ALA D1112 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D1120 " --> pdb=" O PHE D1116 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1132 Processing helix chain 'D' and resid 1135 through 1140 Processing helix chain 'D' and resid 1142 through 1156 Processing helix chain 'D' and resid 1158 through 1168 removed outlier: 3.846A pdb=" N GLN D1162 " --> pdb=" O ASN D1158 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER D1168 " --> pdb=" O PHE D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1170 through 1189 removed outlier: 3.653A pdb=" N THR D1187 " --> pdb=" O ILE D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1216 removed outlier: 3.747A pdb=" N LEU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D1197 " --> pdb=" O ALA D1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D1198 " --> pdb=" O LYS D1194 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D1216 " --> pdb=" O ALA D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.587A pdb=" N ILE D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1233 through 1241 Processing helix chain 'D' and resid 1243 through 1248 Processing helix chain 'D' and resid 1249 through 1262 Processing helix chain 'D' and resid 1269 through 1281 removed outlier: 3.918A pdb=" N VAL D1276 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS D1281 " --> pdb=" O ALA D1277 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1290 removed outlier: 3.508A pdb=" N TRP D1285 " --> pdb=" O CYS D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1299 through 1323 removed outlier: 3.667A pdb=" N LYS D1303 " --> pdb=" O VAL D1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 1337 through 1357 Processing helix chain 'D' and resid 1362 through 1364 No H-bonds generated for 'chain 'D' and resid 1362 through 1364' Processing helix chain 'D' and resid 1365 through 1387 removed outlier: 3.839A pdb=" N VAL D1369 " --> pdb=" O GLY D1365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D1377 " --> pdb=" O LEU D1373 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER D1384 " --> pdb=" O GLY D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1395 through 1419 Processing helix chain 'D' and resid 1428 through 1460 removed outlier: 4.409A pdb=" N GLY D1434 " --> pdb=" O ALA D1430 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D1439 " --> pdb=" O ASP D1435 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D1446 " --> pdb=" O ARG D1442 " (cutoff:3.500A) Processing helix chain 'D' and resid 1469 through 1475 removed outlier: 3.756A pdb=" N ARG D1474 " --> pdb=" O PRO D1470 " (cutoff:3.500A) Processing helix chain 'D' and resid 1492 through 1501 Processing helix chain 'D' and resid 1502 through 1504 No H-bonds generated for 'chain 'D' and resid 1502 through 1504' Processing helix chain 'D' and resid 1514 through 1519 Processing helix chain 'D' and resid 1530 through 1548 Processing helix chain 'D' and resid 1548 through 1585 removed outlier: 4.787A pdb=" N ARG D1563 " --> pdb=" O ASP D1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA D1566 " --> pdb=" O GLN D1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN D1567 " --> pdb=" O ARG D1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D1570 " --> pdb=" O ALA D1566 " (cutoff:3.500A) Processing helix chain 'D' and resid 1595 through 1600 Processing helix chain 'D' and resid 1670 through 1674 removed outlier: 3.760A pdb=" N ASN D1673 " --> pdb=" O ARG D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1676 through 1689 2352 hydrogen bonds defined for protein. 7020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.79 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7784 1.33 - 1.45: 9955 1.45 - 1.57: 24509 1.57 - 1.69: 100 1.69 - 1.82: 304 Bond restraints: 42652 Sorted by residual: bond pdb=" O14 PCF C1804 " pdb=" P PCF C1804 " ideal model delta sigma weight residual 1.492 1.619 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" O14 PCF C1801 " pdb=" P PCF C1801 " ideal model delta sigma weight residual 1.492 1.619 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" O14 PCF A1807 " pdb=" P PCF A1807 " ideal model delta sigma weight residual 1.492 1.619 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" O14 PCF D1808 " pdb=" P PCF D1808 " ideal model delta sigma weight residual 1.492 1.618 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" O14 PCF A1803 " pdb=" P PCF A1803 " ideal model delta sigma weight residual 1.492 1.618 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 42647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 55093 2.41 - 4.81: 2447 4.81 - 7.22: 501 7.22 - 9.63: 174 9.63 - 12.04: 69 Bond angle restraints: 58284 Sorted by residual: angle pdb=" N ASN A 924 " pdb=" CA ASN A 924 " pdb=" C ASN A 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN C 924 " pdb=" CA ASN C 924 " pdb=" C ASN C 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN B 924 " pdb=" CA ASN B 924 " pdb=" C ASN B 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN D 924 " pdb=" CA ASN D 924 " pdb=" C ASN D 924 " ideal model delta sigma weight residual 110.24 119.97 -9.73 1.47e+00 4.63e-01 4.38e+01 angle pdb=" C ASN C 803 " pdb=" N ASN C 804 " pdb=" CA ASN C 804 " ideal model delta sigma weight residual 122.46 130.70 -8.24 1.41e+00 5.03e-01 3.42e+01 ... (remaining 58279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.98: 24616 27.98 - 55.96: 712 55.96 - 83.94: 48 83.94 - 111.92: 8 111.92 - 139.90: 24 Dihedral angle restraints: 25408 sinusoidal: 8112 harmonic: 17296 Sorted by residual: dihedral pdb=" CA HIS A 461 " pdb=" C HIS A 461 " pdb=" N VAL A 462 " pdb=" CA VAL A 462 " ideal model delta harmonic sigma weight residual -180.00 -131.35 -48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA HIS B 461 " pdb=" C HIS B 461 " pdb=" N VAL B 462 " pdb=" CA VAL B 462 " ideal model delta harmonic sigma weight residual -180.00 -131.37 -48.63 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA HIS D 461 " pdb=" C HIS D 461 " pdb=" N VAL D 462 " pdb=" CA VAL D 462 " ideal model delta harmonic sigma weight residual -180.00 -131.39 -48.61 0 5.00e+00 4.00e-02 9.45e+01 ... (remaining 25405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5520 0.057 - 0.114: 1345 0.114 - 0.172: 196 0.172 - 0.229: 35 0.229 - 0.286: 20 Chirality restraints: 7116 Sorted by residual: chirality pdb=" CB ILE D1564 " pdb=" CA ILE D1564 " pdb=" CG1 ILE D1564 " pdb=" CG2 ILE D1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE C1564 " pdb=" CA ILE C1564 " pdb=" CG1 ILE C1564 " pdb=" CG2 ILE C1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE A1564 " pdb=" CA ILE A1564 " pdb=" CG1 ILE A1564 " pdb=" CG2 ILE A1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 7113 not shown) Planarity restraints: 7384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B1591 " -0.065 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO B1592 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B1592 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B1592 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D1591 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO D1592 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D1592 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D1592 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C1591 " -0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO C1592 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C1592 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C1592 " -0.056 5.00e-02 4.00e+02 ... (remaining 7381 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 400 2.63 - 3.19: 37501 3.19 - 3.76: 65203 3.76 - 4.33: 89413 4.33 - 4.90: 141040 Nonbonded interactions: 333557 Sorted by model distance: nonbonded pdb=" OH TYR C1532 " pdb=" O11 PCF C1801 " model vdw 2.057 3.040 nonbonded pdb=" OH TYR A1532 " pdb=" O11 PCF A1803 " model vdw 2.059 3.040 nonbonded pdb=" CE2 TYR C1532 " pdb=" C22 PCF C1801 " model vdw 2.097 3.740 nonbonded pdb=" CB GLU C1498 " pdb=" C35 PCF D1801 " model vdw 2.200 3.840 nonbonded pdb=" CB GLU A1498 " pdb=" C35 PCF B1808 " model vdw 2.206 3.840 ... (remaining 333552 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 1 \ 802 or (resid 1803 through 1804 and (name C1 or name C2 or name C21 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1805 and (name C1 or name C2 or name C21 or name C22 or name C \ 23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid \ 1806 or (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or na \ me C37 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O1 \ 1 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or nam \ e O32 or name P )))) selection = (chain 'B' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r resid 1807 or (resid 1808 and (name C1 or name C2 or name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or name O \ 13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) selection = (chain 'D' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.650 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.009 0.880 42654 Z= 0.610 Angle : 1.283 12.037 58284 Z= 0.672 Chirality : 0.052 0.286 7116 Planarity : 0.007 0.099 7384 Dihedral : 14.038 139.903 14224 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.90 % Favored : 90.77 % Rotamer: Outliers : 0.72 % Allowed : 4.19 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.41 % 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: -5.28 (0.08), residues: 5980 helix: -3.43 (0.05), residues: 3608 sheet: None (None), residues: 0 loop : -3.41 (0.10), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1331 TYR 0.035 0.003 TYR C1327 PHE 0.037 0.003 PHE B1505 TRP 0.043 0.004 TRP D1429 HIS 0.018 0.003 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.34 (42652) covalent geometry : angle 1.28266 / 0.67 (58284) hydrogen bonds : bond 0.16486 / 11.84 ( 2352) hydrogen bonds : angle 11.47221 / 8.19 ( 7020) Misc. bond : bond 0.73506 / 37.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 763 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8261 (mmm) cc_final: 0.7075 (ppp) REVERT: A 621 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 1104 LYS cc_start: 0.8574 (mttt) cc_final: 0.7946 (mtmm) REVERT: A 1294 HIS cc_start: 0.5734 (t-90) cc_final: 0.5205 (t-90) REVERT: A 1348 SER cc_start: 0.8480 (t) cc_final: 0.8259 (p) REVERT: A 1399 TYR cc_start: 0.8864 (t80) cc_final: 0.8567 (t80) REVERT: A 1553 LEU cc_start: 0.9018 (tt) cc_final: 0.8785 (tt) REVERT: A 1592 PRO cc_start: 0.8145 (Cg_endo) cc_final: 0.7500 (Cg_exo) REVERT: B 386 MET cc_start: 0.8227 (mmm) cc_final: 0.7099 (ppp) REVERT: B 570 TYR cc_start: 0.8725 (t80) cc_final: 0.8419 (t80) REVERT: B 621 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 1292 MET cc_start: 0.5213 (pp-130) cc_final: 0.3840 (tmm) REVERT: B 1312 ILE cc_start: 0.9291 (mt) cc_final: 0.9090 (mt) REVERT: B 1592 PRO cc_start: 0.8135 (Cg_endo) cc_final: 0.7639 (Cg_exo) REVERT: C 386 MET cc_start: 0.7963 (mmm) cc_final: 0.6902 (ppp) REVERT: C 387 LEU cc_start: 0.8951 (tp) cc_final: 0.8726 (tp) REVERT: C 621 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9012 (tt) REVERT: C 943 ASP cc_start: 0.8042 (m-30) cc_final: 0.7793 (p0) REVERT: C 1104 LYS cc_start: 0.8623 (mttt) cc_final: 0.8019 (mtmm) REVERT: C 1292 MET cc_start: 0.4329 (pp-130) cc_final: 0.3552 (ttt) REVERT: C 1364 LEU cc_start: 0.8399 (mp) cc_final: 0.8185 (mt) REVERT: C 1368 LYS cc_start: 0.9088 (mttt) cc_final: 0.8798 (mtpp) REVERT: C 1456 MET cc_start: 0.7741 (mmm) cc_final: 0.7444 (mmt) REVERT: C 1592 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: D 386 MET cc_start: 0.8428 (mmm) cc_final: 0.7238 (ppp) REVERT: D 621 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8932 (tp) REVERT: D 1104 LYS cc_start: 0.8392 (mttt) cc_final: 0.8028 (mttp) REVERT: D 1292 MET cc_start: 0.4178 (pp-130) cc_final: 0.3385 (ttt) REVERT: D 1364 LEU cc_start: 0.8406 (mp) cc_final: 0.8177 (mt) REVERT: D 1368 LYS cc_start: 0.9119 (mttt) cc_final: 0.8914 (mtpp) REVERT: D 1376 MET cc_start: 0.7580 (mtt) cc_final: 0.7365 (mtp) REVERT: D 1592 PRO cc_start: 0.8171 (Cg_endo) cc_final: 0.7624 (Cg_exo) outliers start: 24 outliers final: 8 residues processed: 783 average time/residue: 0.2526 time to fit residues: 333.9729 Evaluate side-chains 415 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 403 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.0770 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 50.0000 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN A 547 HIS A 654 ASN A 669 HIS A 698 HIS A 798 HIS A 832 HIS A 908 HIS ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1056 HIS A1162 GLN A1249 HIS A1253 GLN A1297 ASN ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 GLN A1423 HIS ** A1457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 547 HIS B 654 ASN B 669 HIS B 736 ASN B 798 HIS B 832 HIS ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 GLN B1056 HIS B1108 ASN B1162 GLN B1249 HIS B1253 GLN B1297 ASN B1423 HIS C 378 ASN C 398 ASN C 547 HIS C 553 HIS C 654 ASN C 669 HIS C 698 HIS C 736 ASN C 798 HIS C 832 HIS C 908 HIS ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1038 GLN C1056 HIS C1108 ASN C1162 GLN C1249 HIS C1297 ASN C1311 HIS C1423 HIS D 378 ASN D 547 HIS ** D 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 643 HIS D 654 ASN D 669 HIS D 698 HIS D 736 ASN D 798 HIS D 832 HIS D 908 HIS ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1038 GLN D1056 HIS D1162 GLN D1249 HIS D1297 ASN D1311 HIS D1423 HIS ** D1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.126896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.111006 restraints weight = 175152.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.107927 restraints weight = 150079.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106735 restraints weight = 107930.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106954 restraints weight = 90061.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.107055 restraints weight = 70153.908| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42654 Z= 0.153 Angle : 0.719 10.366 58284 Z= 0.372 Chirality : 0.042 0.255 7116 Planarity : 0.005 0.062 7384 Dihedral : 14.542 143.567 7364 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.54 % Favored : 92.32 % Rotamer: Outliers : 2.81 % Allowed : 11.09 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.09), residues: 5980 helix: -1.53 (0.07), residues: 3788 sheet: None (None), residues: 0 loop : -3.17 (0.11), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 463 TYR 0.034 0.002 TYR A1307 PHE 0.026 0.002 PHE A1386 TRP 0.026 0.002 TRP B1572 HIS 0.013 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (42652) covalent geometry : angle 0.71939 / 0.37 (58284) hydrogen bonds : bond 0.04554 / 3.30 ( 2352) hydrogen bonds : angle 5.82574 / 4.16 ( 7020) Misc. bond : bond 0.00298 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 487 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8323 (mmm) cc_final: 0.7114 (tmm) REVERT: A 463 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6306 (mmp-170) REVERT: A 530 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7562 (t80) REVERT: A 621 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8825 (tp) REVERT: A 1028 LEU cc_start: 0.9262 (mt) cc_final: 0.9035 (tp) REVERT: A 1173 ASP cc_start: 0.7317 (t0) cc_final: 0.5982 (t0) REVERT: A 1376 MET cc_start: 0.7762 (mtm) cc_final: 0.7358 (mtp) REVERT: B 386 MET cc_start: 0.8324 (mmm) cc_final: 0.7174 (tmm) REVERT: B 463 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6305 (mmp-170) REVERT: B 530 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7513 (t80) REVERT: B 621 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8567 (tm) REVERT: B 653 MET cc_start: 0.8032 (mtm) cc_final: 0.7484 (tmm) REVERT: B 676 VAL cc_start: 0.9221 (t) cc_final: 0.8870 (p) REVERT: B 1292 MET cc_start: 0.5692 (pp-130) cc_final: 0.4327 (ttt) REVERT: B 1376 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: B 1556 MET cc_start: 0.8015 (mtm) cc_final: 0.6383 (mtm) REVERT: C 386 MET cc_start: 0.8017 (mmm) cc_final: 0.7030 (ppp) REVERT: C 530 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 570 TYR cc_start: 0.8399 (t80) cc_final: 0.8049 (t80) REVERT: C 621 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8704 (tm) REVERT: C 625 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: C 653 MET cc_start: 0.7945 (mtm) cc_final: 0.7539 (tmm) REVERT: C 1028 LEU cc_start: 0.9287 (mt) cc_final: 0.9023 (tp) REVERT: C 1173 ASP cc_start: 0.7416 (t0) cc_final: 0.6207 (t0) REVERT: C 1292 MET cc_start: 0.4381 (pp-130) cc_final: 0.3156 (ttt) REVERT: C 1542 MET cc_start: 0.8058 (mmm) cc_final: 0.7856 (mmm) REVERT: C 1551 GLN cc_start: 0.7326 (mt0) cc_final: 0.6949 (mt0) REVERT: C 1592 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7526 (Cg_exo) REVERT: D 386 MET cc_start: 0.8326 (mmm) cc_final: 0.7015 (tmm) REVERT: D 530 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7589 (t80) REVERT: D 621 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8691 (tp) REVERT: D 1173 ASP cc_start: 0.7435 (t0) cc_final: 0.6206 (t0) REVERT: D 1274 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 1278 PHE cc_start: 0.7899 (m-80) cc_final: 0.7657 (m-80) REVERT: D 1292 MET cc_start: 0.4268 (pp-130) cc_final: 0.3137 (ttt) REVERT: D 1376 MET cc_start: 0.7805 (mtt) cc_final: 0.7584 (mtp) REVERT: D 1542 MET cc_start: 0.7696 (mmm) cc_final: 0.7437 (mmm) REVERT: D 1592 PRO cc_start: 0.8169 (Cg_endo) cc_final: 0.7632 (Cg_exo) outliers start: 94 outliers final: 25 residues processed: 562 average time/residue: 0.2492 time to fit residues: 237.5648 Evaluate side-chains 434 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1485 TYR Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 625 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1407 LEU Chi-restraints excluded: chain D residue 1485 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 483 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 565 optimal weight: 0.7980 chunk 475 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 313 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN A1257 GLN ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1565 GLN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 ASN D1565 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.126545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.110614 restraints weight = 174587.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.107251 restraints weight = 154263.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106794 restraints weight = 102363.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106719 restraints weight = 85674.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.106951 restraints weight = 69178.179| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42654 Z= 0.140 Angle : 0.659 9.652 58284 Z= 0.339 Chirality : 0.041 0.170 7116 Planarity : 0.004 0.082 7384 Dihedral : 13.458 140.661 7362 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.26 % Favored : 91.61 % Rotamer: Outliers : 2.57 % Allowed : 12.86 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.10), residues: 5980 helix: -0.41 (0.08), residues: 3840 sheet: None (None), residues: 0 loop : -3.03 (0.12), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 483 TYR 0.022 0.002 TYR B1337 PHE 0.021 0.001 PHE B1278 TRP 0.030 0.002 TRP C1429 HIS 0.010 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (42652) covalent geometry : angle 0.65855 / 0.34 (58284) hydrogen bonds : bond 0.03914 / 2.83 ( 2352) hydrogen bonds : angle 5.04997 / 3.62 ( 7020) Misc. bond : bond 0.00175 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 448 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8115 (mmm) cc_final: 0.6963 (tmm) REVERT: A 530 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 621 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 1367 ILE cc_start: 0.9009 (pt) cc_final: 0.8313 (pt) REVERT: A 1397 LEU cc_start: 0.9109 (tp) cc_final: 0.8865 (tt) REVERT: A 1415 GLN cc_start: 0.8463 (tp40) cc_final: 0.7801 (tp40) REVERT: B 386 MET cc_start: 0.8396 (mmm) cc_final: 0.7179 (tmm) REVERT: B 530 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 653 MET cc_start: 0.7842 (mtm) cc_final: 0.7503 (tmm) REVERT: B 1173 ASP cc_start: 0.7495 (t0) cc_final: 0.6542 (t0) REVERT: B 1272 LEU cc_start: 0.9089 (mm) cc_final: 0.8869 (mp) REVERT: B 1292 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.4227 (ttt) REVERT: B 1376 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7600 (mtp) REVERT: C 386 MET cc_start: 0.7891 (mmm) cc_final: 0.6761 (tmm) REVERT: C 530 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7333 (t80) REVERT: C 653 MET cc_start: 0.7773 (mtm) cc_final: 0.7538 (tmm) REVERT: C 1028 LEU cc_start: 0.9283 (mt) cc_final: 0.9075 (tp) REVERT: C 1292 MET cc_start: 0.4379 (OUTLIER) cc_final: 0.2953 (ttt) REVERT: C 1405 PHE cc_start: 0.8651 (m-10) cc_final: 0.8425 (m-80) REVERT: D 386 MET cc_start: 0.8302 (mmm) cc_final: 0.7398 (ttp) REVERT: D 530 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7588 (t80) REVERT: D 621 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8601 (tp) REVERT: D 1292 MET cc_start: 0.4228 (OUTLIER) cc_final: 0.2923 (ttt) REVERT: D 1415 GLN cc_start: 0.8593 (tp40) cc_final: 0.8220 (tp40) REVERT: D 1435 ASP cc_start: 0.7528 (t0) cc_final: 0.7081 (t0) REVERT: D 1437 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8446 (mm) REVERT: D 1542 MET cc_start: 0.7643 (mmm) cc_final: 0.7339 (mmm) REVERT: D 1564 ILE cc_start: 0.8946 (mp) cc_final: 0.8654 (mt) outliers start: 86 outliers final: 30 residues processed: 512 average time/residue: 0.2393 time to fit residues: 212.7541 Evaluate side-chains 431 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1547 VAL Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1276 VAL Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1276 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1547 VAL Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1551 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 412 optimal weight: 0.0270 chunk 411 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 GLN A 682 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1565 GLN ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1382 HIS ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 GLN D 682 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1382 HIS D1403 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.125567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104797 restraints weight = 173882.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.103681 restraints weight = 106665.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.103330 restraints weight = 100503.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.104039 restraints weight = 80372.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103993 restraints weight = 67023.406| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42654 Z= 0.157 Angle : 0.653 12.353 58284 Z= 0.334 Chirality : 0.041 0.206 7116 Planarity : 0.004 0.063 7384 Dihedral : 12.766 139.142 7358 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.03 % Favored : 91.86 % Rotamer: Outliers : 3.14 % Allowed : 13.58 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.11), residues: 5980 helix: 0.14 (0.08), residues: 3872 sheet: None (None), residues: 0 loop : -2.87 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1331 TYR 0.034 0.002 TYR B1528 PHE 0.017 0.001 PHE A1386 TRP 0.024 0.002 TRP B1338 HIS 0.011 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (42652) covalent geometry : angle 0.65260 / 0.33 (58284) hydrogen bonds : bond 0.03719 / 2.69 ( 2352) hydrogen bonds : angle 4.79061 / 3.43 ( 7020) Misc. bond : bond 0.00145 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 430 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8220 (mmm) cc_final: 0.7149 (ttp) REVERT: A 530 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7580 (t80) REVERT: A 541 MET cc_start: 0.9074 (ptp) cc_final: 0.8823 (ptp) REVERT: A 1292 MET cc_start: 0.4512 (ttt) cc_final: 0.4087 (ttm) REVERT: A 1397 LEU cc_start: 0.9072 (tp) cc_final: 0.8850 (tt) REVERT: A 1494 ILE cc_start: 0.8937 (tp) cc_final: 0.8669 (tp) REVERT: A 1551 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: B 386 MET cc_start: 0.8471 (mmm) cc_final: 0.7503 (ttp) REVERT: B 530 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7638 (t80) REVERT: B 653 MET cc_start: 0.7893 (mtm) cc_final: 0.7454 (tmm) REVERT: B 1053 MET cc_start: 0.8854 (ptt) cc_final: 0.8652 (ptp) REVERT: B 1272 LEU cc_start: 0.9194 (mm) cc_final: 0.8859 (mp) REVERT: B 1290 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6200 (m-10) REVERT: B 1292 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.4638 (ttt) REVERT: B 1331 ARG cc_start: 0.6314 (pmm-80) cc_final: 0.5674 (pmm-80) REVERT: B 1370 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9113 (tt) REVERT: B 1376 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7694 (ttp) REVERT: B 1551 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: C 386 MET cc_start: 0.8025 (mmm) cc_final: 0.6855 (tmm) REVERT: C 530 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7480 (t80) REVERT: C 653 MET cc_start: 0.8018 (mtm) cc_final: 0.7388 (tmm) REVERT: C 1292 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.3229 (ttm) REVERT: C 1415 GLN cc_start: 0.8401 (tp40) cc_final: 0.7787 (tp40) REVERT: C 1542 MET cc_start: 0.8181 (mmm) cc_final: 0.7935 (mmm) REVERT: C 1551 GLN cc_start: 0.7568 (mt0) cc_final: 0.7303 (mp10) REVERT: D 386 MET cc_start: 0.8322 (mmm) cc_final: 0.7330 (ttp) REVERT: D 530 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7678 (t80) REVERT: D 621 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 676 VAL cc_start: 0.9336 (t) cc_final: 0.9069 (p) REVERT: D 1292 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.3227 (ttm) REVERT: D 1435 ASP cc_start: 0.7363 (t0) cc_final: 0.7007 (t0) REVERT: D 1542 MET cc_start: 0.7856 (mmm) cc_final: 0.7636 (mmm) outliers start: 105 outliers final: 44 residues processed: 508 average time/residue: 0.2338 time to fit residues: 207.4319 Evaluate side-chains 446 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 389 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1141 GLU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1407 LEU Chi-restraints excluded: chain B residue 1433 ILE Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1540 ILE Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1276 VAL Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1276 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1549 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 197 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 303 optimal weight: 50.0000 chunk 382 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS A1382 HIS ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN ** B1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1317 HIS C1382 HIS ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.115716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096274 restraints weight = 163465.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094164 restraints weight = 117080.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094803 restraints weight = 121861.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094133 restraints weight = 97852.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094443 restraints weight = 99123.234| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 42654 Z= 0.207 Angle : 0.681 11.076 58284 Z= 0.349 Chirality : 0.041 0.221 7116 Planarity : 0.004 0.069 7384 Dihedral : 12.506 143.817 7356 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.41 % Favored : 90.45 % Rotamer: Outliers : 2.81 % Allowed : 14.77 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.11), residues: 5980 helix: 0.44 (0.08), residues: 3856 sheet: None (None), residues: 0 loop : -2.84 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1331 TYR 0.022 0.002 TYR A1327 PHE 0.035 0.002 PHE B1538 TRP 0.021 0.002 TRP B1266 HIS 0.010 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (42652) covalent geometry : angle 0.68066 / 0.35 (58284) hydrogen bonds : bond 0.03869 / 2.79 ( 2352) hydrogen bonds : angle 4.81686 / 3.44 ( 7020) Misc. bond : bond 0.00147 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 409 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8322 (mmm) cc_final: 0.7189 (ttp) REVERT: A 530 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7634 (t80) REVERT: A 1292 MET cc_start: 0.4566 (ttt) cc_final: 0.4136 (ttm) REVERT: A 1367 ILE cc_start: 0.9219 (pt) cc_final: 0.8611 (pt) REVERT: A 1415 GLN cc_start: 0.8454 (tp40) cc_final: 0.7809 (tp40) REVERT: A 1494 ILE cc_start: 0.8774 (tp) cc_final: 0.8462 (tp) REVERT: A 1542 MET cc_start: 0.8280 (mmm) cc_final: 0.7974 (mmm) REVERT: A 1551 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: B 386 MET cc_start: 0.8488 (mmm) cc_final: 0.7583 (ttp) REVERT: B 530 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 638 MET cc_start: 0.8444 (mmm) cc_final: 0.8141 (mmm) REVERT: B 653 MET cc_start: 0.7888 (mtm) cc_final: 0.7632 (tmm) REVERT: B 1272 LEU cc_start: 0.9219 (mm) cc_final: 0.8835 (mp) REVERT: B 1290 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5679 (m-10) REVERT: B 1292 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5796 (mpp) REVERT: B 1331 ARG cc_start: 0.6260 (pmm-80) cc_final: 0.5737 (pmm-80) REVERT: B 1376 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7611 (ttp) REVERT: B 1547 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.7642 (t) REVERT: B 1551 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: C 386 MET cc_start: 0.8160 (mmm) cc_final: 0.7229 (ttp) REVERT: C 463 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6113 (mmp-170) REVERT: C 530 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 653 MET cc_start: 0.8012 (mtm) cc_final: 0.7528 (tmm) REVERT: C 1290 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: C 1292 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4232 (ttt) REVERT: C 1435 ASP cc_start: 0.7415 (t0) cc_final: 0.7053 (t0) REVERT: C 1542 MET cc_start: 0.8267 (mmm) cc_final: 0.7817 (mmm) REVERT: D 386 MET cc_start: 0.8402 (mmm) cc_final: 0.7486 (ttp) REVERT: D 530 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 621 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8565 (tp) REVERT: D 1292 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.3673 (ttm) REVERT: D 1415 GLN cc_start: 0.8363 (tp40) cc_final: 0.7957 (tp40) outliers start: 94 outliers final: 49 residues processed: 473 average time/residue: 0.2306 time to fit residues: 191.4544 Evaluate side-chains 433 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 369 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1407 LEU Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1540 ILE Chi-restraints excluded: chain B residue 1547 VAL Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1276 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1440 LEU Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1276 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1416 ILE Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1550 ILE Chi-restraints excluded: chain D residue 1569 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 152 optimal weight: 30.0000 chunk 352 optimal weight: 0.8980 chunk 595 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 chunk 69 optimal weight: 0.0170 chunk 355 optimal weight: 0.7980 chunk 580 optimal weight: 0.6980 chunk 273 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 314 optimal weight: 0.2980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1482 ASN ** D 980 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 = 0.4174 r_free = 0.4174 target = 0.126066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104442 restraints weight = 174393.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.105002 restraints weight = 101051.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.104203 restraints weight = 76904.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.104657 restraints weight = 78643.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104681 restraints weight = 64856.820| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42654 Z= 0.121 Angle : 0.633 10.646 58284 Z= 0.321 Chirality : 0.040 0.212 7116 Planarity : 0.004 0.056 7384 Dihedral : 12.034 140.613 7356 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 2.60 % Allowed : 16.00 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.69 (0.11), residues: 5980 helix: 0.69 (0.08), residues: 3888 sheet: None (None), residues: 0 loop : -2.73 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1331 TYR 0.022 0.002 TYR A1307 PHE 0.024 0.001 PHE C1386 TRP 0.022 0.002 TRP B1266 HIS 0.011 0.001 HIS A1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (42652) covalent geometry : angle 0.63349 / 0.32 (58284) hydrogen bonds : bond 0.03466 / 2.50 ( 2352) hydrogen bonds : angle 4.55296 / 3.26 ( 7020) Misc. bond : bond 0.00127 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 427 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8298 (mmm) cc_final: 0.7177 (ttp) REVERT: A 530 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 638 MET cc_start: 0.8534 (mmm) cc_final: 0.8262 (mmm) REVERT: A 1292 MET cc_start: 0.4519 (ttt) cc_final: 0.4130 (ttm) REVERT: A 1367 ILE cc_start: 0.9062 (pt) cc_final: 0.8593 (pt) REVERT: A 1415 GLN cc_start: 0.8271 (tp40) cc_final: 0.7684 (tp40) REVERT: A 1547 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.7145 (t) REVERT: A 1551 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6647 (mt0) REVERT: A 1577 SER cc_start: 0.8902 (m) cc_final: 0.8694 (t) REVERT: B 386 MET cc_start: 0.8443 (mmm) cc_final: 0.7522 (ttp) REVERT: B 530 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 653 MET cc_start: 0.7914 (mtm) cc_final: 0.7536 (tmm) REVERT: B 1272 LEU cc_start: 0.9142 (mm) cc_final: 0.8735 (mp) REVERT: B 1292 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5848 (mpp) REVERT: B 1370 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9098 (tt) REVERT: B 1376 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7615 (ttp) REVERT: B 1399 TYR cc_start: 0.8361 (t80) cc_final: 0.7999 (t80) REVERT: B 1435 ASP cc_start: 0.7008 (t0) cc_final: 0.6768 (t0) REVERT: B 1551 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: C 386 MET cc_start: 0.8106 (mmm) cc_final: 0.6942 (tmm) REVERT: C 463 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5623 (mmm160) REVERT: C 530 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7456 (t80) REVERT: C 638 MET cc_start: 0.8548 (mmm) cc_final: 0.8314 (mmm) REVERT: C 653 MET cc_start: 0.7930 (mtm) cc_final: 0.7317 (tmm) REVERT: C 1272 LEU cc_start: 0.9253 (mm) cc_final: 0.8922 (mp) REVERT: C 1292 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.4322 (ttm) REVERT: C 1399 TYR cc_start: 0.8414 (t80) cc_final: 0.7957 (t80) REVERT: C 1500 LEU cc_start: 0.9484 (tt) cc_final: 0.9277 (tt) REVERT: D 386 MET cc_start: 0.8365 (mmm) cc_final: 0.7275 (ttp) REVERT: D 530 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7731 (t80) REVERT: D 621 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8605 (tp) REVERT: D 1272 LEU cc_start: 0.9244 (mm) cc_final: 0.8943 (mp) REVERT: D 1286 ILE cc_start: 0.9039 (mt) cc_final: 0.8500 (mt) REVERT: D 1290 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: D 1292 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.3397 (ttm) REVERT: D 1415 GLN cc_start: 0.8140 (tp40) cc_final: 0.7739 (tp40) outliers start: 87 outliers final: 39 residues processed: 488 average time/residue: 0.2104 time to fit residues: 180.1968 Evaluate side-chains 435 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1290 PHE Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1407 LEU Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1482 ASN Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1290 PHE Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1317 HIS Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1468 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 554 optimal weight: 0.8980 chunk 471 optimal weight: 10.0000 chunk 546 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 chunk 383 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1551 GLN ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1492 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 = 0.4140 r_free = 0.4140 target = 0.123965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107460 restraints weight = 171792.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.104069 restraints weight = 142682.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.103594 restraints weight = 96636.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.103314 restraints weight = 86455.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103591 restraints weight = 70861.318| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42654 Z= 0.177 Angle : 0.663 10.167 58284 Z= 0.337 Chirality : 0.041 0.209 7116 Planarity : 0.004 0.061 7384 Dihedral : 11.942 139.780 7356 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.05 % Favored : 90.87 % Rotamer: Outliers : 2.84 % Allowed : 16.72 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.11), residues: 5980 helix: 0.78 (0.08), residues: 3900 sheet: None (None), residues: 0 loop : -2.70 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1581 TYR 0.019 0.002 TYR A1339 PHE 0.037 0.001 PHE B1538 TRP 0.021 0.002 TRP C1266 HIS 0.010 0.001 HIS C1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (42652) covalent geometry : angle 0.66334 / 0.34 (58284) hydrogen bonds : bond 0.03656 / 2.63 ( 2352) hydrogen bonds : angle 4.62954 / 3.30 ( 7020) Misc. bond : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 385 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8391 (mmm) cc_final: 0.7361 (ttp) REVERT: A 530 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 1292 MET cc_start: 0.4580 (ttt) cc_final: 0.4157 (ttm) REVERT: B 386 MET cc_start: 0.8411 (mmm) cc_final: 0.7580 (ttp) REVERT: B 530 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 638 MET cc_start: 0.8387 (mmm) cc_final: 0.8099 (mmm) REVERT: B 653 MET cc_start: 0.7919 (mtm) cc_final: 0.7595 (tmm) REVERT: B 1272 LEU cc_start: 0.9066 (mm) cc_final: 0.8682 (mp) REVERT: B 1290 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6060 (m-10) REVERT: B 1292 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.4507 (tpp) REVERT: B 1376 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7588 (ttp) REVERT: B 1399 TYR cc_start: 0.8305 (t80) cc_final: 0.7836 (t80) REVERT: C 386 MET cc_start: 0.8155 (mmm) cc_final: 0.7252 (ttp) REVERT: C 463 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.5704 (mmm160) REVERT: C 530 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7475 (t80) REVERT: C 653 MET cc_start: 0.7973 (mtm) cc_final: 0.7436 (tmm) REVERT: C 1272 LEU cc_start: 0.9138 (mm) cc_final: 0.8758 (mp) REVERT: C 1290 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5380 (m-80) REVERT: C 1292 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.4139 (ttt) REVERT: C 1500 LEU cc_start: 0.9532 (tt) cc_final: 0.9311 (tt) REVERT: D 386 MET cc_start: 0.8348 (mmm) cc_final: 0.7504 (ttp) REVERT: D 530 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7643 (t80) REVERT: D 621 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8687 (tp) REVERT: D 1272 LEU cc_start: 0.9165 (mm) cc_final: 0.8831 (mp) REVERT: D 1286 ILE cc_start: 0.9094 (mt) cc_final: 0.8561 (mt) REVERT: D 1290 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: D 1292 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.4130 (ttm) REVERT: D 1415 GLN cc_start: 0.8267 (tp40) cc_final: 0.7749 (tp-100) outliers start: 95 outliers final: 60 residues processed: 446 average time/residue: 0.2266 time to fit residues: 178.9834 Evaluate side-chains 440 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1290 PHE Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1370 LEU Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1433 ILE Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1057 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1433 ILE Chi-restraints excluded: chain C residue 1440 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1547 VAL Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1290 PHE Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1547 VAL Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1550 ILE Chi-restraints excluded: chain D residue 1577 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 218 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 349 optimal weight: 0.0020 chunk 578 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 593 optimal weight: 3.9990 chunk 594 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 HIS ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1482 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1492 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 = 0.4182 r_free = 0.4182 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.105981 restraints weight = 173473.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.105128 restraints weight = 118161.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105117 restraints weight = 91976.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.105472 restraints weight = 84032.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.105621 restraints weight = 70903.588| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42654 Z= 0.112 Angle : 0.628 11.654 58284 Z= 0.315 Chirality : 0.040 0.202 7116 Planarity : 0.003 0.051 7384 Dihedral : 11.509 133.213 7356 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 2.33 % Allowed : 17.14 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.32 (0.11), residues: 5980 helix: 0.98 (0.09), residues: 3880 sheet: None (None), residues: 0 loop : -2.57 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1331 TYR 0.016 0.001 TYR B1528 PHE 0.024 0.001 PHE D1386 TRP 0.021 0.002 TRP D1572 HIS 0.011 0.001 HIS C1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (42652) covalent geometry : angle 0.62816 / 0.32 (58284) hydrogen bonds : bond 0.03305 / 2.38 ( 2352) hydrogen bonds : angle 4.43570 / 3.16 ( 7020) Misc. bond : bond 0.00120 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 416 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8354 (mmm) cc_final: 0.7264 (ttp) REVERT: A 530 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7586 (t80) REVERT: A 653 MET cc_start: 0.6707 (tmm) cc_final: 0.6249 (mtp) REVERT: A 1292 MET cc_start: 0.4512 (ttt) cc_final: 0.4283 (ttm) REVERT: A 1397 LEU cc_start: 0.9122 (tp) cc_final: 0.8910 (tt) REVERT: B 386 MET cc_start: 0.8438 (mmm) cc_final: 0.7554 (ttp) REVERT: B 530 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7634 (t80) REVERT: B 638 MET cc_start: 0.8418 (mmm) cc_final: 0.8127 (mmm) REVERT: B 653 MET cc_start: 0.7848 (mtm) cc_final: 0.7165 (tmm) REVERT: B 1272 LEU cc_start: 0.8985 (mm) cc_final: 0.8572 (mp) REVERT: B 1290 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: B 1292 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5723 (mpp) REVERT: B 1376 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7452 (ttp) REVERT: B 1399 TYR cc_start: 0.8187 (t80) cc_final: 0.7928 (t80) REVERT: B 1556 MET cc_start: 0.8057 (mtm) cc_final: 0.7802 (mtm) REVERT: C 386 MET cc_start: 0.8111 (mmm) cc_final: 0.7144 (ttp) REVERT: C 463 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5558 (mmm160) REVERT: C 530 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7512 (t80) REVERT: C 638 MET cc_start: 0.8454 (mmm) cc_final: 0.8211 (mmm) REVERT: C 653 MET cc_start: 0.7874 (mtm) cc_final: 0.7248 (tmm) REVERT: C 1272 LEU cc_start: 0.9088 (mm) cc_final: 0.8699 (mp) REVERT: C 1290 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: C 1292 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.4279 (ttm) REVERT: C 1376 MET cc_start: 0.8380 (ttp) cc_final: 0.8147 (ttm) REVERT: C 1415 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7990 (mm-40) REVERT: C 1500 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9267 (tt) REVERT: D 386 MET cc_start: 0.8332 (mmm) cc_final: 0.7257 (tmm) REVERT: D 463 ARG cc_start: 0.4931 (mmp-170) cc_final: 0.4484 (mmm160) REVERT: D 530 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7671 (t80) REVERT: D 1272 LEU cc_start: 0.9133 (mm) cc_final: 0.8798 (mp) REVERT: D 1286 ILE cc_start: 0.9019 (mt) cc_final: 0.8482 (mt) REVERT: D 1290 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5607 (m-80) REVERT: D 1292 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.4052 (ttm) outliers start: 78 outliers final: 48 residues processed: 467 average time/residue: 0.2283 time to fit residues: 187.8767 Evaluate side-chains 444 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 383 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1057 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1317 HIS Chi-restraints excluded: chain C residue 1440 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1482 ASN Chi-restraints excluded: chain C residue 1500 LEU Chi-restraints excluded: chain C residue 1547 VAL Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1290 PHE Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1317 HIS Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1550 ILE Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 248 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 565 optimal weight: 0.9980 chunk 154 optimal weight: 50.0000 chunk 425 optimal weight: 0.6980 chunk 573 optimal weight: 0.9990 chunk 550 optimal weight: 0.7980 chunk 584 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 444 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN B1317 HIS B1482 ASN ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1482 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.125374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.104294 restraints weight = 173770.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103348 restraints weight = 104794.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103153 restraints weight = 96547.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.103519 restraints weight = 76875.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.103544 restraints weight = 71173.757| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42654 Z= 0.138 Angle : 0.639 12.077 58284 Z= 0.321 Chirality : 0.040 0.230 7116 Planarity : 0.003 0.072 7384 Dihedral : 11.356 135.656 7354 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.39 % Favored : 91.54 % Rotamer: Outliers : 2.09 % Allowed : 17.76 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.29 (0.11), residues: 5980 helix: 1.00 (0.09), residues: 3908 sheet: None (None), residues: 0 loop : -2.62 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1581 TYR 0.019 0.001 TYR D1307 PHE 0.019 0.001 PHE A1386 TRP 0.021 0.002 TRP D1266 HIS 0.010 0.001 HIS B1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (42652) covalent geometry : angle 0.63924 / 0.32 (58284) hydrogen bonds : bond 0.03403 / 2.44 ( 2352) hydrogen bonds : angle 4.46583 / 3.18 ( 7020) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8392 (mmm) cc_final: 0.7295 (ttp) REVERT: A 530 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7590 (t80) REVERT: A 653 MET cc_start: 0.6703 (tmm) cc_final: 0.6194 (tmm) REVERT: A 1292 MET cc_start: 0.4558 (ttt) cc_final: 0.4331 (ttm) REVERT: A 1415 GLN cc_start: 0.8350 (tp40) cc_final: 0.8069 (mm-40) REVERT: B 386 MET cc_start: 0.8338 (mmm) cc_final: 0.7243 (tmm) REVERT: B 463 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5253 (mmm160) REVERT: B 530 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 653 MET cc_start: 0.7832 (mtm) cc_final: 0.7146 (tmm) REVERT: B 1272 LEU cc_start: 0.9061 (mm) cc_final: 0.8640 (mp) REVERT: B 1290 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5589 (m-10) REVERT: B 1292 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5667 (mpp) REVERT: B 1376 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7457 (ttp) REVERT: B 1399 TYR cc_start: 0.8272 (t80) cc_final: 0.8061 (t80) REVERT: C 386 MET cc_start: 0.8179 (mmm) cc_final: 0.7199 (ttp) REVERT: C 463 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5474 (mmm160) REVERT: C 530 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7519 (t80) REVERT: C 653 MET cc_start: 0.7955 (mtm) cc_final: 0.7313 (tmm) REVERT: C 1290 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5668 (m-80) REVERT: C 1292 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.4429 (ttt) REVERT: C 1399 TYR cc_start: 0.8297 (t80) cc_final: 0.8032 (t80) REVERT: C 1415 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8127 (mm-40) REVERT: C 1500 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9287 (tt) REVERT: D 386 MET cc_start: 0.8359 (mmm) cc_final: 0.7271 (tmm) REVERT: D 463 ARG cc_start: 0.5075 (mmp-170) cc_final: 0.4815 (mmm160) REVERT: D 530 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7641 (t80) REVERT: D 1272 LEU cc_start: 0.9129 (mm) cc_final: 0.8807 (mp) REVERT: D 1286 ILE cc_start: 0.9072 (mt) cc_final: 0.8582 (mt) REVERT: D 1290 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: D 1292 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.4255 (ttm) REVERT: D 1397 LEU cc_start: 0.9176 (tp) cc_final: 0.8955 (tt) outliers start: 70 outliers final: 48 residues processed: 436 average time/residue: 0.2217 time to fit residues: 171.9621 Evaluate side-chains 437 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1057 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1350 LEU Chi-restraints excluded: chain C residue 1440 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1482 ASN Chi-restraints excluded: chain C residue 1500 LEU Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1290 PHE Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1550 ILE Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 321 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 446 optimal weight: 2.9990 chunk 363 optimal weight: 0.9980 chunk 423 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 215 optimal weight: 9.9990 chunk 523 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 381 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1482 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1492 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 = 0.4137 r_free = 0.4137 target = 0.123713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.102031 restraints weight = 172410.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101266 restraints weight = 110021.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101166 restraints weight = 108986.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.101520 restraints weight = 80738.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101682 restraints weight = 72570.761| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 42654 Z= 0.188 Angle : 0.682 11.318 58284 Z= 0.343 Chirality : 0.042 0.237 7116 Planarity : 0.004 0.053 7384 Dihedral : 11.361 139.168 7354 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.26 % Favored : 90.67 % Rotamer: Outliers : 2.12 % Allowed : 18.06 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.26 (0.11), residues: 5980 helix: 1.01 (0.09), residues: 3880 sheet: None (None), residues: 0 loop : -2.53 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1581 TYR 0.020 0.002 TYR C1307 PHE 0.018 0.001 PHE D1386 TRP 0.021 0.002 TRP B1115 HIS 0.010 0.001 HIS B1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (42652) covalent geometry : angle 0.68185 / 0.34 (58284) hydrogen bonds : bond 0.03662 / 2.63 ( 2352) hydrogen bonds : angle 4.60035 / 3.28 ( 7020) Misc. bond : bond 0.00130 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 384 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8398 (mmm) cc_final: 0.7357 (ttp) REVERT: A 530 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 653 MET cc_start: 0.6702 (tmm) cc_final: 0.6165 (tmm) REVERT: A 1292 MET cc_start: 0.4532 (ttt) cc_final: 0.4300 (ttm) REVERT: A 1415 GLN cc_start: 0.8465 (tp40) cc_final: 0.8199 (mm-40) REVERT: B 386 MET cc_start: 0.8407 (mmm) cc_final: 0.7256 (tmm) REVERT: B 530 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7666 (t80) REVERT: B 653 MET cc_start: 0.7856 (mtm) cc_final: 0.7193 (tmm) REVERT: B 1272 LEU cc_start: 0.9077 (mm) cc_final: 0.8788 (mm) REVERT: B 1290 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6101 (m-10) REVERT: B 1292 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.4624 (tpp) REVERT: B 1376 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7570 (ttp) REVERT: B 1399 TYR cc_start: 0.8305 (t80) cc_final: 0.8068 (t80) REVERT: C 386 MET cc_start: 0.8259 (mmm) cc_final: 0.7266 (ttp) REVERT: C 463 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5552 (mmm160) REVERT: C 530 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7517 (t80) REVERT: C 653 MET cc_start: 0.8034 (mtm) cc_final: 0.7449 (tmm) REVERT: C 1290 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: C 1292 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5695 (mpp) REVERT: C 1399 TYR cc_start: 0.8341 (t80) cc_final: 0.8094 (t80) REVERT: C 1415 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8189 (mm-40) REVERT: C 1500 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9293 (tt) REVERT: C 1551 GLN cc_start: 0.7506 (mt0) cc_final: 0.6849 (mp10) REVERT: D 386 MET cc_start: 0.8404 (mmm) cc_final: 0.7449 (ttp) REVERT: D 653 MET cc_start: 0.6633 (tmm) cc_final: 0.6177 (tmm) REVERT: D 1272 LEU cc_start: 0.9117 (mm) cc_final: 0.8791 (mp) REVERT: D 1286 ILE cc_start: 0.9087 (mt) cc_final: 0.8693 (mt) REVERT: D 1290 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: D 1292 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5658 (mpp) REVERT: D 1397 LEU cc_start: 0.9206 (tp) cc_final: 0.8997 (tt) outliers start: 71 outliers final: 47 residues processed: 430 average time/residue: 0.2135 time to fit residues: 163.1032 Evaluate side-chains 433 residues out of total 4952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1290 PHE Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1057 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1440 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1482 ASN Chi-restraints excluded: chain C residue 1500 LEU Chi-restraints excluded: chain C residue 1547 VAL Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1290 PHE Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1433 ILE Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 209 optimal weight: 1.9990 chunk 578 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 189 optimal weight: 0.0970 chunk 379 optimal weight: 1.9990 chunk 580 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 444 optimal weight: 0.9980 chunk 560 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1482 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1492 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 = 0.4164 r_free = 0.4164 target = 0.125500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.104886 restraints weight = 173732.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.104231 restraints weight = 108524.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103954 restraints weight = 87649.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.104221 restraints weight = 82052.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104338 restraints weight = 72647.802| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42654 Z= 0.126 Angle : 0.653 11.473 58284 Z= 0.325 Chirality : 0.040 0.216 7116 Planarity : 0.003 0.052 7384 Dihedral : 11.024 133.362 7354 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.36 % Favored : 91.57 % Rotamer: Outliers : 1.88 % Allowed : 18.60 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.17 (0.11), residues: 5980 helix: 1.08 (0.09), residues: 3900 sheet: None (None), residues: 0 loop : -2.54 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C1483 TYR 0.047 0.002 TYR B1528 PHE 0.018 0.001 PHE C1386 TRP 0.021 0.002 TRP D1266 HIS 0.011 0.001 HIS C1294 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (42652) covalent geometry : angle 0.65258 / 0.32 (58284) hydrogen bonds : bond 0.03362 / 2.41 ( 2352) hydrogen bonds : angle 4.45329 / 3.18 ( 7020) Misc. bond : bond 0.00122 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8793.44 seconds wall clock time: 152 minutes 29.26 seconds (9149.26 seconds total)