Starting phenix.real_space_refine on Tue May 5 15:25:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pc6_71497/05_2026/9pc6_71497.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 2 5.49 5 S 78 5.16 5 C 18402 2.51 5 N 5235 2.21 5 O 5691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1576, 11580 Classifications: {'peptide': 1576} Link IDs: {'PTRANS': 91, 'TRANS': 1484} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1573, 11558 Classifications: {'peptide': 1573} Link IDs: {'PTRANS': 91, 'TRANS': 1481} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "K" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Time building chain proxies: 7.17, per 1000 atoms: 0.24 Number of scatterers: 29408 At special positions: 0 Unit cell: (134.32, 175.93, 189.07, 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 78 16.00 P 2 15.00 O 5691 8.00 N 5235 7.00 C 18402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 39 " - pdb=" SG CYS I 109 " distance=2.03 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS L 39 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 47 sheets defined 36.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.820A pdb=" N GLU A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.286A pdb=" N SER A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.724A pdb=" N GLN A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.709A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.026A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 4.000A pdb=" N GLY A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 522 through 533 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 566 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 600 through 622 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 634 through 643 removed outlier: 4.121A pdb=" N ALA A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 667 removed outlier: 4.237A pdb=" N SER A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 777 through 787 Processing helix chain 'A' and resid 791 through 801 removed outlier: 3.550A pdb=" N GLU A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 801 " --> pdb=" O ALA A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 836 through 851 removed outlier: 3.838A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 919 through 923 removed outlier: 4.000A pdb=" N GLY A 922 " --> pdb=" O ALA A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 941 removed outlier: 3.752A pdb=" N LEU A 929 " --> pdb=" O PRO A 925 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1024 through 1028 Processing helix chain 'A' and resid 1031 through 1044 removed outlier: 3.652A pdb=" N THR A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1144 Processing helix chain 'A' and resid 1159 through 1176 removed outlier: 3.538A pdb=" N ILE A1165 " --> pdb=" O GLY A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1189 No H-bonds generated for 'chain 'A' and resid 1187 through 1189' Processing helix chain 'A' and resid 1190 through 1198 Processing helix chain 'A' and resid 1239 through 1252 Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.528A pdb=" N LEU A1277 " --> pdb=" O GLU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1300 Processing helix chain 'A' and resid 1326 through 1348 Proline residue: A1336 - end of helix removed outlier: 3.861A pdb=" N ASP A1339 " --> pdb=" O ARG A1335 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA A1340 " --> pdb=" O PRO A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1367 Processing helix chain 'A' and resid 1371 through 1391 Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 5.957A pdb=" N MET A1409 " --> pdb=" O VAL A1406 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A1410 " --> pdb=" O SER A1407 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A1411 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A1412 " --> pdb=" O MET A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1424 Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1454 through 1464 Processing helix chain 'A' and resid 1469 through 1475 removed outlier: 4.237A pdb=" N GLY A1474 " --> pdb=" O LEU A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1496 Processing helix chain 'A' and resid 1503 through 1518 Processing helix chain 'A' and resid 1537 through 1553 removed outlier: 3.629A pdb=" N GLU A1543 " --> pdb=" O LEU A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1564 Processing helix chain 'A' and resid 1566 through 1576 Processing helix chain 'B' and resid 4 through 33 removed outlier: 3.576A pdb=" N LYS B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.504A pdb=" N LEU B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.506A pdb=" N VAL B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.771A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 180 through 191 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.563A pdb=" N VAL B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.535A pdb=" N GLN B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.589A pdb=" N ALA B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.531A pdb=" N GLY B 416 " --> pdb=" O TRP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'B' and resid 522 through 533 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 566 through 581 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 600 through 622 Proline residue: B 606 - end of helix Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.967A pdb=" N ILE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 638 " --> pdb=" O GLN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 706 through 721 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 741 through 749 Processing helix chain 'B' and resid 777 through 787 Processing helix chain 'B' and resid 791 through 801 Processing helix chain 'B' and resid 815 through 823 removed outlier: 4.114A pdb=" N LEU B 819 " --> pdb=" O THR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 850 Processing helix chain 'B' and resid 919 through 921 No H-bonds generated for 'chain 'B' and resid 919 through 921' Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.715A pdb=" N LEU B 929 " --> pdb=" O PRO B 925 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1024 through 1028 Processing helix chain 'B' and resid 1031 through 1041 removed outlier: 3.785A pdb=" N ALA B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1144 Processing helix chain 'B' and resid 1159 through 1176 Processing helix chain 'B' and resid 1187 through 1189 No H-bonds generated for 'chain 'B' and resid 1187 through 1189' Processing helix chain 'B' and resid 1190 through 1198 removed outlier: 3.660A pdb=" N GLY B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1253 Processing helix chain 'B' and resid 1267 through 1277 Processing helix chain 'B' and resid 1290 through 1301 Processing helix chain 'B' and resid 1326 through 1348 Proline residue: B1336 - end of helix removed outlier: 3.584A pdb=" N ASP B1339 " --> pdb=" O ARG B1335 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B1340 " --> pdb=" O PRO B1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing helix chain 'B' and resid 1371 through 1391 Processing helix chain 'B' and resid 1404 through 1408 Processing helix chain 'B' and resid 1414 through 1424 Processing helix chain 'B' and resid 1430 through 1445 Processing helix chain 'B' and resid 1454 through 1464 Processing helix chain 'B' and resid 1469 through 1473 Processing helix chain 'B' and resid 1488 through 1494 removed outlier: 3.999A pdb=" N ARG B1492 " --> pdb=" O SER B1488 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1518 Processing helix chain 'B' and resid 1530 through 1535 Processing helix chain 'B' and resid 1537 through 1553 removed outlier: 3.836A pdb=" N GLU B1543 " --> pdb=" O LEU B1539 " (cutoff:3.500A) Processing helix chain 'B' and resid 1559 through 1564 removed outlier: 3.558A pdb=" N ASP B1563 " --> pdb=" O ALA B1559 " (cutoff:3.500A) Processing helix chain 'B' and resid 1566 through 1576 removed outlier: 3.969A pdb=" N ALA B1576 " --> pdb=" O ASP B1572 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 34 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 163 through 165 No H-bonds generated for 'chain 'K' and resid 163 through 165' Processing helix chain 'I' and resid 100 through 104 removed outlier: 3.786A pdb=" N VAL I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 149 Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.942A pdb=" N HIS I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 104 removed outlier: 3.522A pdb=" N ASP L 103 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL L 104 " --> pdb=" O ALA L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 104' Processing helix chain 'L' and resid 143 through 150 removed outlier: 3.562A pdb=" N GLY L 150 " --> pdb=" O GLN L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 211 removed outlier: 3.738A pdb=" N HIS L 211 " --> pdb=" O ASP L 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.195A pdb=" N VAL A 335 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 334 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 447 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 297 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS A 449 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER A 295 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 451 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 290 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 274 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 40 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 272 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS A 42 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 270 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 228 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 230 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 151 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 199 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 153 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 198 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 198 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 151 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 199 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 153 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 228 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 230 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 39 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 276 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 37 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 290 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 292 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU B 453 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 294 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 334 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 368 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU B 365 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 475 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.404A pdb=" N VAL A 544 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A 630 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP A 546 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 543 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 724 through 727 removed outlier: 4.247A pdb=" N MET A 672 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 671 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 705 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 702 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 789 " --> pdb=" O ALA A 693 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 761 through 763 removed outlier: 4.342A pdb=" N PHE A 761 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 895 through 898 removed outlier: 3.774A pdb=" N ALA A 994 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 983 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 992 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N HIS A 993 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL A 950 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 995 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 948 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A 997 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 944 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER A1056 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLY A 946 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A1054 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A1050 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1076 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A1086 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A1074 " --> pdb=" O THR A1086 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 895 through 898 removed outlier: 3.774A pdb=" N ALA A 994 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 983 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 992 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N HIS A 993 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL A 950 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 995 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 948 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A 997 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 944 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER A1056 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLY A 946 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A1054 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A1050 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A1091 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP A1052 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A1089 " --> pdb=" O TRP A1052 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1059 through 1060 Processing sheet with id=AB1, first strand: chain 'A' and resid 1106 through 1109 Processing sheet with id=AB2, first strand: chain 'A' and resid 1112 through 1113 removed outlier: 4.428A pdb=" N ALA A1209 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 6.656A pdb=" N LEU A1258 " --> pdb=" O ALA A1282 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A1284 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A1260 " --> pdb=" O ALA A1284 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR A1231 " --> pdb=" O LEU A1307 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A1309 " --> pdb=" O THR A1231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1355 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A1356 " --> pdb=" O VAL A1396 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A1398 " --> pdb=" O PHE A1356 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A1358 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP A1400 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A1360 " --> pdb=" O TRP A1400 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1426 through 1427 removed outlier: 4.318A pdb=" N LYS A1452 " --> pdb=" O SER A1427 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1481 through 1482 removed outlier: 6.468A pdb=" N ARG A1481 " --> pdb=" O SER B1060 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB8, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB9, first strand: chain 'B' and resid 469 through 475 Processing sheet with id=AC1, first strand: chain 'B' and resid 628 through 631 removed outlier: 5.866A pdb=" N LYS B 543 " --> pdb=" O HIS B 803 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 724 through 726 removed outlier: 6.532A pdb=" N VAL B 702 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 789 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 762 through 763 Processing sheet with id=AC4, first strand: chain 'B' and resid 895 through 898 removed outlier: 3.854A pdb=" N ALA B 994 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER B 983 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG B 992 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS B 993 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 950 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS B 995 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 948 " --> pdb=" O HIS B 995 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 997 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 944 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER B1056 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 946 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B1054 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B1050 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 895 through 898 removed outlier: 3.854A pdb=" N ALA B 994 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER B 983 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG B 992 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS B 993 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 950 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS B 995 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 948 " --> pdb=" O HIS B 995 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 997 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 944 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER B1056 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 946 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B1054 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B1050 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B1091 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP B1052 " --> pdb=" O SER B1089 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER B1089 " --> pdb=" O TRP B1052 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 923 through 924 removed outlier: 4.470A pdb=" N VAL B 954 " --> pdb=" O VAL B 924 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1213 through 1216 removed outlier: 4.800A pdb=" N VAL B1108 " --> pdb=" O THR B1447 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR B1447 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER B1397 " --> pdb=" O LEU B1448 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B1450 " --> pdb=" O SER B1397 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA B1399 " --> pdb=" O ALA B1450 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE B1356 " --> pdb=" O VAL B1396 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B1398 " --> pdb=" O PHE B1356 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B1358 " --> pdb=" O ILE B1398 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TRP B1400 " --> pdb=" O LEU B1358 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER B1360 " --> pdb=" O TRP B1400 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B1231 " --> pdb=" O THR B1308 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL B1310 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B1233 " --> pdb=" O VAL B1310 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS B1312 " --> pdb=" O LEU B1233 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR B1235 " --> pdb=" O HIS B1312 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1112 through 1113 removed outlier: 4.001A pdb=" N ALA B1209 " --> pdb=" O ILE B1113 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N VAL B1202 " --> pdb=" O ILE B1180 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B1182 " --> pdb=" O VAL B1202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B1204 " --> pdb=" O LEU B1182 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B1184 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B1124 " --> pdb=" O ALA B1151 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1153 " --> pdb=" O LEU B1124 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR B1126 " --> pdb=" O VAL B1153 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1426 through 1427 removed outlier: 4.349A pdb=" N LYS B1452 " --> pdb=" O SER B1427 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.565A pdb=" N THR J 73 " --> pdb=" O GLN J 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 62 through 64 removed outlier: 6.669A pdb=" N TRP J 38 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE J 52 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET J 36 " --> pdb=" O PHE J 52 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG J 102 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR J 109 " --> pdb=" O ARG J 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 62 through 64 removed outlier: 6.669A pdb=" N TRP J 38 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE J 52 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET J 36 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.024A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 127 through 131 removed outlier: 6.024A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AD7, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD8, first strand: chain 'K' and resid 13 through 14 removed outlier: 7.134A pdb=" N MET K 36 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE K 52 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP K 38 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 13 through 14 removed outlier: 4.203A pdb=" N TYR K 109 " --> pdb=" O ARG K 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 127 through 131 removed outlier: 3.850A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR K 183 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 127 through 131 removed outlier: 3.850A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR K 183 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER K 184 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 158 through 161 Processing sheet with id=AE4, first strand: chain 'I' and resid 21 through 22 Processing sheet with id=AE5, first strand: chain 'I' and resid 74 through 75 removed outlier: 3.742A pdb=" N ASN I 74 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP I 56 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR I 70 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU I 54 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY I 105 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 136 through 140 removed outlier: 5.392A pdb=" N TYR I 195 " --> pdb=" O ASN I 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 167 through 170 Processing sheet with id=AE8, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AE9, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.659A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR L 70 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU L 54 " --> pdb=" O TYR L 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 138 through 140 removed outlier: 3.672A pdb=" N VAL L 155 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER L 153 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU L 203 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL L 155 " --> pdb=" O LEU L 201 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU L 201 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU L 157 " --> pdb=" O SER L 199 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER L 199 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN L 159 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU L 197 " --> pdb=" O ASN L 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 167 through 170 1476 hydrogen bonds defined for protein. 4023 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: 10.00 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10125 1.34 - 1.46: 6340 1.46 - 1.58: 13392 1.58 - 1.70: 4 1.70 - 1.82: 120 Bond restraints: 29981 Sorted by residual: bond pdb=" CT 4HH A1538 " pdb=" SU 4HH A1538 " ideal model delta sigma weight residual 1.825 1.771 0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" CL3 4HH B1538 " pdb=" NN 4HH B1538 " ideal model delta sigma weight residual 1.335 1.388 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" CT 4HH B1538 " pdb=" SU 4HH B1538 " ideal model delta sigma weight residual 1.825 1.772 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CL3 4HH A1538 " pdb=" NN 4HH A1538 " ideal model delta sigma weight residual 1.335 1.386 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" N GLU B1088 " pdb=" CA GLU B1088 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.28e+00 ... (remaining 29976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 40496 2.51 - 5.02: 367 5.02 - 7.53: 43 7.53 - 10.03: 10 10.03 - 12.54: 5 Bond angle restraints: 40921 Sorted by residual: angle pdb=" C SER B 843 " pdb=" N MET B 844 " pdb=" CA MET B 844 " ideal model delta sigma weight residual 121.14 113.12 8.02 1.75e+00 3.27e-01 2.10e+01 angle pdb=" N MET A 844 " pdb=" CA MET A 844 " pdb=" CB MET A 844 " ideal model delta sigma weight residual 110.40 117.45 -7.05 1.63e+00 3.76e-01 1.87e+01 angle pdb=" CA MET A 844 " pdb=" CB MET A 844 " pdb=" CG MET A 844 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA MET J 87 " pdb=" CB MET J 87 " pdb=" CG MET J 87 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LEU A 488 " pdb=" CB LEU A 488 " pdb=" CG LEU A 488 " ideal model delta sigma weight residual 116.30 128.84 -12.54 3.50e+00 8.16e-02 1.28e+01 ... (remaining 40916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 16886 25.68 - 51.35: 979 51.35 - 77.03: 86 77.03 - 102.70: 17 102.70 - 128.38: 1 Dihedral angle restraints: 17969 sinusoidal: 6743 harmonic: 11226 Sorted by residual: dihedral pdb=" CB CYS L 156 " pdb=" SG CYS L 156 " pdb=" SG CYS L 216 " pdb=" CB CYS L 216 " ideal model delta sinusoidal sigma weight residual -86.00 -172.83 86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" OG 4HH B1538 " pdb=" O3P 4HH B1538 " pdb=" P 4HH B1538 " pdb=" CJ 4HH B1538 " ideal model delta sinusoidal sigma weight residual 184.89 56.51 128.38 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" CB CYS I 156 " pdb=" SG CYS I 156 " pdb=" SG CYS I 216 " pdb=" CB CYS I 216 " ideal model delta sinusoidal sigma weight residual 93.00 59.89 33.11 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 17966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4344 0.080 - 0.160: 425 0.160 - 0.239: 5 0.239 - 0.319: 0 0.319 - 0.399: 1 Chirality restraints: 4775 Sorted by residual: chirality pdb=" CG LEU A 488 " pdb=" CB LEU A 488 " pdb=" CD1 LEU A 488 " pdb=" CD2 LEU A 488 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CG LEU A 20 " pdb=" CB LEU A 20 " pdb=" CD1 LEU A 20 " pdb=" CD2 LEU A 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA MET A 844 " pdb=" N MET A 844 " pdb=" C MET A 844 " pdb=" CB MET A 844 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 4772 not shown) Planarity restraints: 5382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 466 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 467 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 98 " 0.167 9.50e-02 1.11e+02 7.47e-02 3.48e+00 pdb=" NE ARG L 98 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG L 98 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG L 98 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 98 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1557 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A1558 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1558 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1558 " -0.024 5.00e-02 4.00e+02 ... (remaining 5379 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1097 2.70 - 3.25: 31096 3.25 - 3.80: 51788 3.80 - 4.35: 63111 4.35 - 4.90: 100885 Nonbonded interactions: 247977 Sorted by model distance: nonbonded pdb=" O ARG B 685 " pdb=" NH1 ARG B 685 " model vdw 2.148 3.120 nonbonded pdb=" OH TYR A 91 " pdb=" O LEU A 248 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP A 5 " pdb=" OH TYR I 53 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP A1382 " pdb=" OG SER A1397 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS B1337 " pdb=" O PHE B1359 " model vdw 2.217 3.120 ... (remaining 247972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 985 or resid 989 through 1576)) selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 21.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.670 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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: 59.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.003 0.054 29987 Z= 0.131 Angle : 0.589 12.543 40933 Z= 0.291 Chirality : 0.042 0.399 4775 Planarity : 0.004 0.075 5382 Dihedral : 15.287 128.379 10757 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.91 % Allowed : 21.93 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3941 helix: 1.42 (0.15), residues: 1216 sheet: 0.24 (0.18), residues: 895 loop : 0.03 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.017 0.001 TYR A 12 PHE 0.011 0.001 PHE I 140 TRP 0.017 0.001 TRP B 583 HIS 0.003 0.001 HIS B1573 Details of bonding type rmsd covalent geometry : bond 0.00269 (29981) covalent geometry : angle 0.58931 (40921) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.58496 ( 12) hydrogen bonds : bond 0.15822 ( 1377) hydrogen bonds : angle 6.56856 ( 4023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 1.064 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 322 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9258 (tp) REVERT: A 1435 MET cc_start: 0.0500 (mmp) cc_final: 0.0189 (mmp) REVERT: A 1545 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8242 (tmm-80) REVERT: B 77 ASP cc_start: 0.9687 (OUTLIER) cc_final: 0.9262 (p0) REVERT: B 119 MET cc_start: 0.8908 (pmm) cc_final: 0.8603 (pmm) REVERT: B 555 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.7905 (p-90) REVERT: B 1516 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9316 (m) REVERT: I 106 VAL cc_start: 0.9631 (OUTLIER) cc_final: 0.9415 (p) REVERT: L 100 GLU cc_start: 0.9023 (mp0) cc_final: 0.8719 (mp0) REVERT: L 110 MET cc_start: 0.8474 (tpp) cc_final: 0.8187 (ttm) outliers start: 58 outliers final: 48 residues processed: 144 average time/residue: 0.1921 time to fit residues: 45.7606 Evaluate side-chains 142 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1545 ARG Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 1240 THR Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1516 VAL Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 204 ASN Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN B 315 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.056113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034591 restraints weight = 251460.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035086 restraints weight = 160120.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035516 restraints weight = 117248.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035957 restraints weight = 95062.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036448 restraints weight = 78671.846| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29987 Z= 0.226 Angle : 0.619 12.354 40933 Z= 0.315 Chirality : 0.042 0.248 4775 Planarity : 0.005 0.083 5382 Dihedral : 7.147 119.426 4443 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.10 % Allowed : 18.87 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3941 helix: 1.24 (0.15), residues: 1258 sheet: 0.01 (0.18), residues: 866 loop : -0.01 (0.16), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 625 TYR 0.015 0.002 TYR B 782 PHE 0.017 0.002 PHE A 239 TRP 0.022 0.002 TRP B 583 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00460 (29981) covalent geometry : angle 0.61860 (40921) SS BOND : bond 0.00318 ( 6) SS BOND : angle 0.62934 ( 12) hydrogen bonds : bond 0.04280 ( 1377) hydrogen bonds : angle 5.47022 ( 4023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 87 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8912 (tpp) cc_final: 0.8629 (tpp) REVERT: A 314 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.9144 (mm-40) REVERT: A 852 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8761 (tp) REVERT: A 1168 LEU cc_start: -0.0166 (OUTLIER) cc_final: -0.0644 (mt) REVERT: A 1435 MET cc_start: -0.0599 (mmp) cc_final: -0.0995 (mmp) REVERT: B 119 MET cc_start: 0.8878 (pmm) cc_final: 0.8654 (pmm) REVERT: B 419 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: B 555 TRP cc_start: 0.8847 (OUTLIER) cc_final: 0.8021 (p-90) REVERT: B 1566 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9128 (tppt) REVERT: K 18 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7485 (ptp90) REVERT: K 157 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7283 (t) REVERT: L 100 GLU cc_start: 0.9141 (mp0) cc_final: 0.8647 (pm20) REVERT: L 102 GLU cc_start: 0.9052 (pm20) cc_final: 0.8351 (pm20) REVERT: L 110 MET cc_start: 0.8725 (tpp) cc_final: 0.8481 (ttm) outliers start: 155 outliers final: 81 residues processed: 237 average time/residue: 0.1879 time to fit residues: 74.0253 Evaluate side-chains 168 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 79 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1447 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1486 THR Chi-restraints excluded: chain B residue 1499 THR Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain B residue 1566 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 189 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 374 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 383 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.057365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034986 restraints weight = 246098.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.036002 restraints weight = 150089.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.036740 restraints weight = 107582.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036938 restraints weight = 86435.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.037488 restraints weight = 77089.229| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29987 Z= 0.124 Angle : 0.556 13.221 40933 Z= 0.274 Chirality : 0.042 0.213 4775 Planarity : 0.004 0.073 5382 Dihedral : 6.715 115.629 4402 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.68 % Allowed : 20.51 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3941 helix: 1.39 (0.15), residues: 1258 sheet: 0.06 (0.18), residues: 872 loop : -0.01 (0.16), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 21 TYR 0.016 0.001 TYR I 70 PHE 0.009 0.001 PHE K 173 TRP 0.015 0.001 TRP B 583 HIS 0.004 0.001 HIS B1573 Details of bonding type rmsd covalent geometry : bond 0.00263 (29981) covalent geometry : angle 0.55595 (40921) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.58131 ( 12) hydrogen bonds : bond 0.03491 ( 1377) hydrogen bonds : angle 5.09597 ( 4023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 90 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8887 (tpp) cc_final: 0.8636 (tpp) REVERT: A 744 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 852 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8774 (tp) REVERT: A 1435 MET cc_start: -0.0135 (mmp) cc_final: -0.0495 (mmp) REVERT: B 365 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8619 (tp) REVERT: B 419 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: J 48 GLU cc_start: 0.8905 (tt0) cc_final: 0.8659 (pt0) REVERT: K 18 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7514 (ptp90) REVERT: I 70 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8922 (p90) REVERT: L 82 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7026 (ptt90) REVERT: L 100 GLU cc_start: 0.9153 (mp0) cc_final: 0.8744 (mp0) outliers start: 112 outliers final: 64 residues processed: 195 average time/residue: 0.1807 time to fit residues: 59.4245 Evaluate side-chains 153 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 83 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 189 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 9.9990 chunk 304 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 0.0670 chunk 108 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 386 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.056595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034450 restraints weight = 247748.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035385 restraints weight = 152478.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036206 restraints weight = 111534.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036701 restraints weight = 89132.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036855 restraints weight = 77860.486| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29987 Z= 0.140 Angle : 0.560 13.735 40933 Z= 0.277 Chirality : 0.042 0.295 4775 Planarity : 0.004 0.064 5382 Dihedral : 6.563 112.675 4393 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.31 % Allowed : 19.72 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3941 helix: 1.39 (0.15), residues: 1256 sheet: 0.00 (0.18), residues: 853 loop : -0.01 (0.16), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.018 0.001 TYR B 782 PHE 0.010 0.001 PHE A 441 TRP 0.017 0.001 TRP B 583 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00297 (29981) covalent geometry : angle 0.55998 (40921) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.58157 ( 12) hydrogen bonds : bond 0.03293 ( 1377) hydrogen bonds : angle 4.98038 ( 4023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 85 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8893 (tpp) cc_final: 0.8630 (tpp) REVERT: A 852 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 1168 LEU cc_start: 0.0069 (OUTLIER) cc_final: -0.0407 (mt) REVERT: A 1435 MET cc_start: 0.0544 (mmp) cc_final: 0.0181 (mmp) REVERT: B 365 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8610 (tp) REVERT: B 419 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: B 555 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.7969 (p-90) REVERT: J 48 GLU cc_start: 0.8897 (tt0) cc_final: 0.8675 (pt0) REVERT: K 18 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: I 70 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8969 (p90) REVERT: L 82 ARG cc_start: 0.8072 (ptt90) cc_final: 0.7055 (ptt90) REVERT: L 100 GLU cc_start: 0.9127 (mp0) cc_final: 0.8646 (mp0) outliers start: 131 outliers final: 86 residues processed: 210 average time/residue: 0.1705 time to fit residues: 61.3050 Evaluate side-chains 173 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 80 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1499 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 199 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 132 optimal weight: 0.0970 chunk 232 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 350 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 318 optimal weight: 0.6980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.056297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034604 restraints weight = 248024.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035431 restraints weight = 153319.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036083 restraints weight = 111192.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036587 restraints weight = 89552.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036830 restraints weight = 76919.358| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29987 Z= 0.143 Angle : 0.565 14.494 40933 Z= 0.277 Chirality : 0.042 0.272 4775 Planarity : 0.004 0.057 5382 Dihedral : 6.520 111.995 4392 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.37 % Allowed : 20.05 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3941 helix: 1.40 (0.15), residues: 1258 sheet: 0.01 (0.18), residues: 865 loop : -0.02 (0.16), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 98 TYR 0.015 0.001 TYR B 782 PHE 0.009 0.001 PHE A 569 TRP 0.018 0.001 TRP B 583 HIS 0.004 0.001 HIS B1526 Details of bonding type rmsd covalent geometry : bond 0.00300 (29981) covalent geometry : angle 0.56528 (40921) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.54049 ( 12) hydrogen bonds : bond 0.03201 ( 1377) hydrogen bonds : angle 4.88952 ( 4023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 83 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8880 (tpp) cc_final: 0.8579 (tpp) REVERT: A 852 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8783 (tp) REVERT: A 1168 LEU cc_start: 0.0434 (OUTLIER) cc_final: -0.0046 (mt) REVERT: A 1435 MET cc_start: 0.0702 (mmp) cc_final: 0.0326 (mmp) REVERT: B 119 MET cc_start: 0.8681 (pmm) cc_final: 0.8430 (pmm) REVERT: B 365 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8633 (tp) REVERT: B 419 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: B 555 TRP cc_start: 0.8805 (OUTLIER) cc_final: 0.7959 (p-90) REVERT: K 18 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7366 (ptp90) REVERT: I 70 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8999 (p90) REVERT: I 106 VAL cc_start: 0.9662 (OUTLIER) cc_final: 0.9437 (p) REVERT: L 82 ARG cc_start: 0.8134 (ptt90) cc_final: 0.7273 (ptt90) REVERT: L 100 GLU cc_start: 0.9129 (mp0) cc_final: 0.8879 (mp0) outliers start: 133 outliers final: 96 residues processed: 213 average time/residue: 0.1803 time to fit residues: 64.8676 Evaluate side-chains 181 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 77 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1529 ARG Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 160 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 21 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 chunk 359 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.058310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.040856 restraints weight = 298683.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041273 restraints weight = 162571.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.041933 restraints weight = 104980.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042165 restraints weight = 79246.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042604 restraints weight = 68259.375| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29987 Z= 0.211 Angle : 0.619 14.166 40933 Z= 0.310 Chirality : 0.042 0.220 4775 Planarity : 0.005 0.062 5382 Dihedral : 6.641 111.968 4389 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.90 % Allowed : 20.02 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3941 helix: 1.31 (0.15), residues: 1250 sheet: -0.14 (0.18), residues: 846 loop : -0.07 (0.16), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 790 TYR 0.021 0.002 TYR B 782 PHE 0.014 0.002 PHE K 107 TRP 0.024 0.002 TRP B 583 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00434 (29981) covalent geometry : angle 0.61886 (40921) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.64305 ( 12) hydrogen bonds : bond 0.03504 ( 1377) hydrogen bonds : angle 5.10395 ( 4023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 83 time to evaluate : 1.036 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 119 MET cc_start: 0.8837 (tpp) cc_final: 0.8521 (tpp) REVERT: A 852 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 1435 MET cc_start: 0.0771 (mmp) cc_final: 0.0332 (mmp) REVERT: B 365 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8658 (tp) REVERT: B 419 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: B 555 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8029 (p-90) REVERT: B 612 MET cc_start: 0.9304 (mmm) cc_final: 0.9071 (mmm) REVERT: K 18 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7263 (ptp90) REVERT: I 70 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.9060 (p90) REVERT: I 106 VAL cc_start: 0.9655 (OUTLIER) cc_final: 0.9428 (p) REVERT: I 128 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.8011 (tp) REVERT: L 70 TYR cc_start: 0.9627 (p90) cc_final: 0.9290 (p90) outliers start: 149 outliers final: 118 residues processed: 229 average time/residue: 0.1785 time to fit residues: 68.3821 Evaluate side-chains 203 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 77 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1447 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1499 THR Chi-restraints excluded: chain B residue 1529 ARG Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 189 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 108 optimal weight: 3.9990 chunk 242 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 346 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 269 optimal weight: 0.2980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A1422 GLN ** B 338 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 = 0.3573 r_free = 0.3573 target = 0.055997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034289 restraints weight = 247717.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035284 restraints weight = 153134.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035907 restraints weight = 109953.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.036084 restraints weight = 88130.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036321 restraints weight = 79332.371| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29987 Z= 0.121 Angle : 0.577 13.449 40933 Z= 0.280 Chirality : 0.042 0.356 4775 Planarity : 0.004 0.055 5382 Dihedral : 6.475 113.411 4389 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.98 % Allowed : 21.56 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3941 helix: 1.41 (0.15), residues: 1256 sheet: -0.05 (0.18), residues: 867 loop : -0.03 (0.16), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 98 TYR 0.014 0.001 TYR B 731 PHE 0.009 0.001 PHE K 173 TRP 0.019 0.001 TRP B 583 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00261 (29981) covalent geometry : angle 0.57731 (40921) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.59068 ( 12) hydrogen bonds : bond 0.03136 ( 1377) hydrogen bonds : angle 4.87535 ( 4023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 85 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8829 (tpp) cc_final: 0.8501 (tpp) REVERT: A 852 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 1435 MET cc_start: 0.0865 (mmp) cc_final: 0.0504 (mmp) REVERT: B 365 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8622 (tp) REVERT: B 419 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: B 555 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.7927 (p-90) REVERT: B 612 MET cc_start: 0.9333 (mmm) cc_final: 0.9078 (mmm) REVERT: B 929 LEU cc_start: 0.9797 (OUTLIER) cc_final: 0.9521 (pp) REVERT: B 1013 ASP cc_start: 0.8899 (m-30) cc_final: 0.8485 (p0) REVERT: K 18 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7416 (ptp90) REVERT: I 106 VAL cc_start: 0.9648 (OUTLIER) cc_final: 0.9431 (p) REVERT: I 128 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7803 (tp) REVERT: L 82 ARG cc_start: 0.7960 (ptt90) cc_final: 0.7445 (ptt90) REVERT: L 98 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7950 (mtt-85) outliers start: 121 outliers final: 94 residues processed: 203 average time/residue: 0.1693 time to fit residues: 58.0258 Evaluate side-chains 186 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 83 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1447 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 98 ARG Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 160 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 363 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 378 optimal weight: 0.8980 chunk 269 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN B 158 GLN ** B 338 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 = 0.3585 r_free = 0.3585 target = 0.056447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.034595 restraints weight = 249418.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035538 restraints weight = 152087.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036026 restraints weight = 109039.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036731 restraints weight = 90074.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036970 restraints weight = 77083.425| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29987 Z= 0.102 Angle : 0.586 18.603 40933 Z= 0.280 Chirality : 0.043 0.298 4775 Planarity : 0.004 0.055 5382 Dihedral : 6.348 112.440 4389 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.48 % Allowed : 22.06 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3941 helix: 1.48 (0.15), residues: 1253 sheet: 0.01 (0.18), residues: 867 loop : 0.00 (0.16), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 114 TYR 0.018 0.001 TYR B 12 PHE 0.007 0.001 PHE K 129 TRP 0.016 0.001 TRP B 583 HIS 0.003 0.001 HIS A 875 Details of bonding type rmsd covalent geometry : bond 0.00227 (29981) covalent geometry : angle 0.58626 (40921) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.61836 ( 12) hydrogen bonds : bond 0.02936 ( 1377) hydrogen bonds : angle 4.70614 ( 4023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 81 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9422 (tp) REVERT: A 852 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8847 (tp) REVERT: A 1435 MET cc_start: 0.0920 (mmp) cc_final: 0.0543 (mmp) REVERT: B 98 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9245 (mm) REVERT: B 365 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 419 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: B 555 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.7908 (p-90) REVERT: B 612 MET cc_start: 0.9371 (mmm) cc_final: 0.9093 (mmm) REVERT: B 929 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9528 (pp) REVERT: K 18 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7443 (ptp90) REVERT: I 106 VAL cc_start: 0.9660 (OUTLIER) cc_final: 0.9442 (p) REVERT: L 70 TYR cc_start: 0.9354 (p90) cc_final: 0.9150 (p90) outliers start: 106 outliers final: 77 residues processed: 184 average time/residue: 0.1867 time to fit residues: 57.1262 Evaluate side-chains 167 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 81 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1525 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain B residue 1561 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 113 optimal weight: 0.0980 chunk 342 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 383 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN ** B 338 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 = 0.3583 r_free = 0.3583 target = 0.056348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.034569 restraints weight = 248698.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035318 restraints weight = 152755.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036278 restraints weight = 110120.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036466 restraints weight = 88870.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.037053 restraints weight = 79352.167| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29987 Z= 0.108 Angle : 0.588 16.368 40933 Z= 0.281 Chirality : 0.042 0.290 4775 Planarity : 0.004 0.082 5382 Dihedral : 6.246 111.332 4385 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 22.49 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3941 helix: 1.53 (0.15), residues: 1255 sheet: 0.00 (0.18), residues: 871 loop : 0.00 (0.16), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG L 98 TYR 0.016 0.001 TYR A 12 PHE 0.008 0.001 PHE A1106 TRP 0.014 0.001 TRP B 583 HIS 0.009 0.001 HIS B1526 Details of bonding type rmsd covalent geometry : bond 0.00240 (29981) covalent geometry : angle 0.58796 (40921) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.61857 ( 12) hydrogen bonds : bond 0.02905 ( 1377) hydrogen bonds : angle 4.65665 ( 4023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 84 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9451 (tp) REVERT: A 852 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 1435 MET cc_start: 0.1353 (mmp) cc_final: 0.0982 (mmp) REVERT: B 98 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9269 (mm) REVERT: B 365 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8694 (tp) REVERT: B 419 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: B 555 TRP cc_start: 0.8678 (OUTLIER) cc_final: 0.7838 (p-90) REVERT: B 612 MET cc_start: 0.9341 (mmm) cc_final: 0.9076 (mmm) REVERT: B 929 LEU cc_start: 0.9807 (OUTLIER) cc_final: 0.9537 (pp) REVERT: K 18 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7422 (ptp90) REVERT: I 70 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8565 (p90) REVERT: I 106 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9432 (p) outliers start: 99 outliers final: 82 residues processed: 181 average time/residue: 0.1766 time to fit residues: 54.4084 Evaluate side-chains 173 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 81 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 326 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A1422 GLN ** B 338 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 = 0.3569 r_free = 0.3569 target = 0.055758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.034906 restraints weight = 248502.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035733 restraints weight = 160886.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035565 restraints weight = 126830.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.035908 restraints weight = 92633.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036261 restraints weight = 80411.805| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29987 Z= 0.130 Angle : 0.590 15.778 40933 Z= 0.284 Chirality : 0.042 0.275 4775 Planarity : 0.004 0.074 5382 Dihedral : 6.227 110.296 4382 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.22 % Allowed : 22.58 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3941 helix: 1.49 (0.15), residues: 1257 sheet: -0.04 (0.17), residues: 875 loop : 0.01 (0.16), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG L 98 TYR 0.022 0.001 TYR K 183 PHE 0.014 0.001 PHE K 29 TRP 0.016 0.001 TRP B 583 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00282 (29981) covalent geometry : angle 0.58975 (40921) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.56159 ( 12) hydrogen bonds : bond 0.02965 ( 1377) hydrogen bonds : angle 4.68606 ( 4023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7882 Ramachandran restraints generated. 3941 Oldfield, 0 Emsley, 3941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 81 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9462 (tp) REVERT: A 852 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8830 (tp) REVERT: A 1435 MET cc_start: 0.0274 (mmp) cc_final: -0.0114 (mmp) REVERT: B 365 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8758 (tp) REVERT: B 419 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: B 555 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.7905 (p-90) REVERT: B 612 MET cc_start: 0.9396 (mmm) cc_final: 0.9127 (mmm) REVERT: B 929 LEU cc_start: 0.9798 (OUTLIER) cc_final: 0.9519 (pp) REVERT: B 1013 ASP cc_start: 0.8941 (m-30) cc_final: 0.8523 (p0) REVERT: K 18 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7503 (ptp90) REVERT: I 70 TYR cc_start: 0.9483 (OUTLIER) cc_final: 0.8668 (p90) REVERT: I 106 VAL cc_start: 0.9650 (OUTLIER) cc_final: 0.9424 (p) outliers start: 98 outliers final: 85 residues processed: 177 average time/residue: 0.1685 time to fit residues: 51.2586 Evaluate side-chains 174 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 80 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 222 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1176 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1313 THR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1499 THR Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1570 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1405 THR Chi-restraints excluded: chain B residue 1454 ASP Chi-restraints excluded: chain B residue 1555 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 10 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 326 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.055744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.034997 restraints weight = 249589.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035770 restraints weight = 161796.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035573 restraints weight = 121551.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.035996 restraints weight = 93452.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.036268 restraints weight = 78944.497| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 29987 Z= 0.138 Angle : 0.693 59.200 40933 Z= 0.363 Chirality : 0.043 0.705 4775 Planarity : 0.004 0.076 5382 Dihedral : 6.224 110.289 4382 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.35 % Allowed : 22.49 % Favored : 74.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3941 helix: 1.50 (0.15), residues: 1257 sheet: -0.04 (0.17), residues: 875 loop : 0.02 (0.16), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 98 TYR 0.019 0.001 TYR K 183 PHE 0.011 0.001 PHE K 29 TRP 0.015 0.001 TRP B 583 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00297 (29981) covalent geometry : angle 0.69258 (40921) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.55636 ( 12) hydrogen bonds : bond 0.02961 ( 1377) hydrogen bonds : angle 4.68371 ( 4023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7006.34 seconds wall clock time: 121 minutes 28.61 seconds (7288.61 seconds total)