Starting phenix.real_space_refine on Tue Jul 29 01:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.map" model { file = "/net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hw4_35050/07_2025/8hw4_35050.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6997 2.51 5 N 1791 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10746 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10696 Classifications: {'peptide': 1364} Link IDs: {'PTRANS': 59, 'TRANS': 1304} Chain breaks: 2 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'ZWY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.69 Number of scatterers: 10746 At special positions: 0 Unit cell: (74.9, 109.14, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1899 8.00 N 1791 7.00 C 6997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 6 sheets defined 64.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 4.451A pdb=" N CYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.527A pdb=" N ARG A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.646A pdb=" N MET A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 93 removed outlier: 4.239A pdb=" N ALA A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 102 through 128 removed outlier: 3.925A pdb=" N THR A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 4.577A pdb=" N MET A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.632A pdb=" N ILE A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 190 removed outlier: 3.502A pdb=" N ALA A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.845A pdb=" N PHE A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.959A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.651A pdb=" N LEU A 240 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.096A pdb=" N ALA A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.905A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.917A pdb=" N LYS A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.210A pdb=" N GLN A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.882A pdb=" N VAL A 352 " --> pdb=" O TRP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 377 through 395 removed outlier: 3.811A pdb=" N MET A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.547A pdb=" N LYS A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.141A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 423 through 428 removed outlier: 4.273A pdb=" N ASN A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.523A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.299A pdb=" N ALA A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 504 removed outlier: 3.512A pdb=" N LEU A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 527 removed outlier: 3.510A pdb=" N LEU A 524 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 5.209A pdb=" N LEU A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 removed outlier: 4.408A pdb=" N ASP A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 580 removed outlier: 4.160A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 597 through 607 Processing helix chain 'A' and resid 667 through 676 removed outlier: 4.114A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 716 through 727 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 744 through 748 removed outlier: 3.803A pdb=" N LYS A 747 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.606A pdb=" N ARG A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 4.439A pdb=" N ALA A 780 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 843 through 850 removed outlier: 3.629A pdb=" N ASN A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 849 " --> pdb=" O PHE A 845 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 965 removed outlier: 4.402A pdb=" N PHE A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 997 removed outlier: 3.988A pdb=" N LEU A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1025 removed outlier: 3.647A pdb=" N ARG A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 4.064A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A1051 " --> pdb=" O ALA A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.777A pdb=" N PHE A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 4.078A pdb=" N VAL A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1108 removed outlier: 3.769A pdb=" N VAL A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.714A pdb=" N THR A1112 " --> pdb=" O PRO A1109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1113 " --> pdb=" O LEU A1110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1109 through 1113' Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 3.957A pdb=" N ARG A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1151 removed outlier: 3.986A pdb=" N TYR A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1162 removed outlier: 5.360A pdb=" N SER A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL A1160 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1202 removed outlier: 4.071A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A1174 " --> pdb=" O PHE A1170 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Proline residue: A1187 - end of helix removed outlier: 3.823A pdb=" N VAL A1202 " --> pdb=" O GLY A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1216 Processing helix chain 'A' and resid 1222 through 1234 removed outlier: 4.234A pdb=" N VAL A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A1228 " --> pdb=" O GLY A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1248 Processing helix chain 'A' and resid 1254 through 1263 removed outlier: 3.637A pdb=" N GLU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1287 removed outlier: 3.606A pdb=" N ARG A1286 " --> pdb=" O TRP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1337 removed outlier: 4.266A pdb=" N THR A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1337 " --> pdb=" O THR A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1357 No H-bonds generated for 'chain 'A' and resid 1355 through 1357' Processing helix chain 'A' and resid 1358 through 1366 removed outlier: 3.821A pdb=" N SER A1364 " --> pdb=" O HIS A1360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1366 " --> pdb=" O LEU A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1404 through 1410 Processing helix chain 'A' and resid 1413 through 1417 Processing helix chain 'A' and resid 1427 through 1443 removed outlier: 4.202A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A1443 " --> pdb=" O ALA A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1472 removed outlier: 3.619A pdb=" N GLN A1471 " --> pdb=" O THR A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1514 Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 4.137A pdb=" N MET A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 616 through 617 removed outlier: 3.828A pdb=" N ILE A 627 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 649 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 647 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 633 " --> pdb=" O HIS A 645 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N HIS A 645 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 693 removed outlier: 6.056A pdb=" N ALA A 692 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 772 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL A 808 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL A 657 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 658 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 824 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 660 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 821 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 832 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 823 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1306 through 1309 removed outlier: 5.627A pdb=" N ARG A1307 " --> pdb=" O VAL A1296 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A1296 " --> pdb=" O ARG A1307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1306 through 1309 removed outlier: 5.627A pdb=" N ARG A1307 " --> pdb=" O VAL A1296 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A1296 " --> pdb=" O ARG A1307 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A1291 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A1348 " --> pdb=" O PHE A1291 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASN A1293 " --> pdb=" O GLU A1346 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU A1346 " --> pdb=" O ASN A1293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1319 through 1323 removed outlier: 6.253A pdb=" N GLY A1320 " --> pdb=" O LEU A1494 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A1496 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A1322 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1503 " --> pdb=" O VAL A1495 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP A1497 " --> pdb=" O VAL A1501 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1368 through 1369 removed outlier: 3.518A pdb=" N ILE A1369 " --> pdb=" O VAL A1448 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1458 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: 7.05 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2066 1.33 - 1.45: 2630 1.45 - 1.57: 6205 1.57 - 1.69: 7 1.69 - 1.81: 93 Bond restraints: 11001 Sorted by residual: bond pdb=" C15 ZWY A1602 " pdb=" C16 ZWY A1602 " ideal model delta sigma weight residual 1.549 1.277 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C04 ZWY A1602 " pdb=" C05 ZWY A1602 " ideal model delta sigma weight residual 1.541 1.686 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C05 ZWY A1602 " pdb=" C06 ZWY A1602 " ideal model delta sigma weight residual 1.545 1.418 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" O20 ZWY A1602 " pdb=" S21 ZWY A1602 " ideal model delta sigma weight residual 1.628 1.740 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O20 ZWY A1601 " pdb=" S21 ZWY A1601 " ideal model delta sigma weight residual 1.628 1.740 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 10996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 14769 3.15 - 6.29: 185 6.29 - 9.44: 19 9.44 - 12.58: 3 12.58 - 15.73: 2 Bond angle restraints: 14978 Sorted by residual: angle pdb=" N LEU A 365 " pdb=" CA LEU A 365 " pdb=" C LEU A 365 " ideal model delta sigma weight residual 114.56 106.76 7.80 1.27e+00 6.20e-01 3.77e+01 angle pdb=" N ILE A 366 " pdb=" CA ILE A 366 " pdb=" C ILE A 366 " ideal model delta sigma weight residual 112.29 106.54 5.75 9.40e-01 1.13e+00 3.74e+01 angle pdb=" N VAL A 75 " pdb=" CA VAL A 75 " pdb=" C VAL A 75 " ideal model delta sigma weight residual 112.96 107.67 5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" C06 ZWY A1602 " pdb=" C07 ZWY A1602 " pdb=" C08 ZWY A1602 " ideal model delta sigma weight residual 120.63 104.90 15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C13 ZWY A1602 " pdb=" C14 ZWY A1602 " pdb=" C15 ZWY A1602 " ideal model delta sigma weight residual 122.95 108.50 14.45 3.00e+00 1.11e-01 2.32e+01 ... (remaining 14973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 6057 21.79 - 43.58: 494 43.58 - 65.36: 39 65.36 - 87.15: 17 87.15 - 108.94: 5 Dihedral angle restraints: 6612 sinusoidal: 2650 harmonic: 3962 Sorted by residual: dihedral pdb=" CD ARG A1245 " pdb=" NE ARG A1245 " pdb=" CZ ARG A1245 " pdb=" NH1 ARG A1245 " ideal model delta sinusoidal sigma weight residual 0.00 -83.40 83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 6609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 1736 0.188 - 0.377: 8 0.377 - 0.565: 2 0.565 - 0.753: 2 0.753 - 0.941: 1 Chirality restraints: 1749 Sorted by residual: chirality pdb=" C15 ZWY A1602 " pdb=" C05 ZWY A1602 " pdb=" C14 ZWY A1602 " pdb=" C16 ZWY A1602 " both_signs ideal model delta sigma weight residual False 2.89 1.95 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" C15 ZWY A1601 " pdb=" C05 ZWY A1601 " pdb=" C14 ZWY A1601 " pdb=" C16 ZWY A1601 " both_signs ideal model delta sigma weight residual False 2.89 2.17 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C05 ZWY A1602 " pdb=" C04 ZWY A1602 " pdb=" C06 ZWY A1602 " pdb=" C15 ZWY A1602 " both_signs ideal model delta sigma weight residual False -2.46 -1.86 -0.60 2.00e-01 2.50e+01 8.92e+00 ... (remaining 1746 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A1601 " 0.194 2.00e-02 2.50e+03 1.73e-01 3.76e+02 pdb=" C13 ZWY A1601 " -0.196 2.00e-02 2.50e+03 pdb=" C14 ZWY A1601 " -0.192 2.00e-02 2.50e+03 pdb=" C15 ZWY A1601 " 0.001 2.00e-02 2.50e+03 pdb=" C19 ZWY A1601 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1245 " -1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A1245 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A1245 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A1245 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A1245 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A1602 " -0.052 2.00e-02 2.50e+03 9.40e-02 1.10e+02 pdb=" C13 ZWY A1602 " 0.127 2.00e-02 2.50e+03 pdb=" C14 ZWY A1602 " -0.148 2.00e-02 2.50e+03 pdb=" C15 ZWY A1602 " 0.057 2.00e-02 2.50e+03 pdb=" C19 ZWY A1602 " 0.016 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 357 2.69 - 3.25: 11828 3.25 - 3.80: 17221 3.80 - 4.35: 22133 4.35 - 4.90: 35657 Nonbonded interactions: 87196 Sorted by model distance: nonbonded pdb=" OG1 THR A1479 " pdb=" OH TYR A1490 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU A 617 " pdb=" ND1 HIS A 686 " model vdw 2.191 3.120 nonbonded pdb=" O GLY A1282 " pdb=" NH1 ARG A1286 " model vdw 2.236 3.120 nonbonded pdb=" O ILE A 396 " pdb=" OG1 THR A 397 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP A 247 " pdb=" OH TYR A1186 " model vdw 2.247 3.040 ... (remaining 87191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 169.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.011 0.752 11002 Z= 0.804 Angle : 0.891 15.729 14978 Z= 0.461 Chirality : 0.063 0.941 1749 Planarity : 0.013 0.489 1864 Dihedral : 15.423 108.938 4052 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1358 helix: -1.57 (0.17), residues: 826 sheet: -0.76 (0.61), residues: 65 loop : -1.36 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1194 HIS 0.007 0.001 HIS A 369 PHE 0.030 0.002 PHE A1151 TYR 0.019 0.002 TYR A 207 ARG 0.003 0.000 ARG A1278 Details of bonding type rmsd hydrogen bonds : bond 0.19163 ( 497) hydrogen bonds : angle 8.13435 ( 1458) covalent geometry : bond 0.00814 (11001) covalent geometry : angle 0.89101 (14978) Misc. bond : bond 0.75206 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.852 Fit side-chains REVERT: A 361 MET cc_start: 0.7775 (tpt) cc_final: 0.7573 (tpt) REVERT: A 499 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8624 (ttmt) REVERT: A 1115 ILE cc_start: 0.8961 (tp) cc_final: 0.8737 (tp) REVERT: A 1245 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6802 (tpp-160) REVERT: A 1272 TRP cc_start: 0.7668 (m-10) cc_final: 0.7427 (m-10) REVERT: A 1432 GLN cc_start: 0.8535 (mp10) cc_final: 0.8328 (mp10) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2794 time to fit residues: 67.3131 Evaluate side-chains 134 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 64 optimal weight: 0.0000 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136714 restraints weight = 13996.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132298 restraints weight = 10113.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133994 restraints weight = 11335.971| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11002 Z= 0.141 Angle : 0.714 12.221 14978 Z= 0.355 Chirality : 0.044 0.194 1749 Planarity : 0.005 0.053 1864 Dihedral : 8.492 90.540 1593 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.94 % Allowed : 9.43 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.22), residues: 1358 helix: -1.06 (0.17), residues: 861 sheet: -0.24 (0.64), residues: 65 loop : -1.38 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 222 HIS 0.006 0.001 HIS A1403 PHE 0.022 0.002 PHE A1059 TYR 0.022 0.001 TYR A 720 ARG 0.003 0.000 ARG A1286 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 497) hydrogen bonds : angle 5.25234 ( 1458) covalent geometry : bond 0.00313 (11001) covalent geometry : angle 0.71426 (14978) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 LEU cc_start: 0.8717 (tp) cc_final: 0.8340 (tp) REVERT: A 1031 MET cc_start: 0.7314 (mmt) cc_final: 0.7019 (mmt) REVERT: A 1052 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7764 (mmmm) outliers start: 11 outliers final: 8 residues processed: 160 average time/residue: 0.2238 time to fit residues: 52.9357 Evaluate side-chains 137 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1215 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.189211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135346 restraints weight = 14682.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132256 restraints weight = 11170.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133581 restraints weight = 12123.667| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11002 Z= 0.155 Angle : 0.686 9.576 14978 Z= 0.340 Chirality : 0.044 0.180 1749 Planarity : 0.004 0.058 1864 Dihedral : 7.958 88.472 1589 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.23 % Allowed : 13.97 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.23), residues: 1358 helix: -0.84 (0.17), residues: 869 sheet: -0.27 (0.59), residues: 77 loop : -1.41 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 991 HIS 0.004 0.001 HIS A1403 PHE 0.020 0.001 PHE A 544 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 497) hydrogen bonds : angle 4.81856 ( 1458) covalent geometry : bond 0.00371 (11001) covalent geometry : angle 0.68589 (14978) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8832 (tt) cc_final: 0.8609 (mt) REVERT: A 566 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: A 580 LEU cc_start: 0.8766 (tp) cc_final: 0.8284 (tp) REVERT: A 649 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 740 ASP cc_start: 0.7300 (p0) cc_final: 0.7062 (p0) REVERT: A 1245 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6923 (tpp-160) outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 0.2008 time to fit residues: 49.3296 Evaluate side-chains 150 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1482 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** 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 = 0.4448 r_free = 0.4448 target = 0.203137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149605 restraints weight = 14264.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145202 restraints weight = 9586.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147021 restraints weight = 10221.635| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11002 Z= 0.138 Angle : 0.655 9.499 14978 Z= 0.325 Chirality : 0.043 0.176 1749 Planarity : 0.004 0.061 1864 Dihedral : 7.595 84.760 1589 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.74 % Allowed : 15.77 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1358 helix: -0.66 (0.18), residues: 867 sheet: -0.14 (0.61), residues: 77 loop : -1.44 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1272 HIS 0.004 0.001 HIS A1360 PHE 0.020 0.001 PHE A1170 TYR 0.011 0.001 TYR A 207 ARG 0.006 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 497) hydrogen bonds : angle 4.50226 ( 1458) covalent geometry : bond 0.00321 (11001) covalent geometry : angle 0.65467 (14978) Misc. bond : bond 0.00197 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8811 (tt) cc_final: 0.8525 (mt) REVERT: A 507 GLU cc_start: 0.8205 (pp20) cc_final: 0.7508 (pp20) REVERT: A 566 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: A 580 LEU cc_start: 0.8709 (tp) cc_final: 0.8108 (tp) REVERT: A 706 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7371 (mm-40) REVERT: A 788 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7596 (m-70) REVERT: A 1263 TYR cc_start: 0.7881 (m-10) cc_final: 0.7222 (m-10) outliers start: 32 outliers final: 17 residues processed: 175 average time/residue: 0.1962 time to fit residues: 53.1519 Evaluate side-chains 157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 ASN A1360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.203302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150020 restraints weight = 14340.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145404 restraints weight = 9495.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147560 restraints weight = 9901.091| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11002 Z= 0.142 Angle : 0.663 9.397 14978 Z= 0.327 Chirality : 0.044 0.240 1749 Planarity : 0.004 0.065 1864 Dihedral : 7.324 82.462 1589 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.00 % Allowed : 17.40 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1358 helix: -0.53 (0.18), residues: 868 sheet: 0.03 (0.61), residues: 77 loop : -1.38 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 991 HIS 0.007 0.001 HIS A 686 PHE 0.030 0.001 PHE A1170 TYR 0.012 0.001 TYR A 766 ARG 0.006 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 497) hydrogen bonds : angle 4.44039 ( 1458) covalent geometry : bond 0.00334 (11001) covalent geometry : angle 0.66301 (14978) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8742 (tt) cc_final: 0.8481 (mt) REVERT: A 491 MET cc_start: 0.8610 (tpp) cc_final: 0.8352 (tpp) REVERT: A 501 LEU cc_start: 0.8582 (tp) cc_final: 0.8300 (tp) REVERT: A 507 GLU cc_start: 0.8112 (pp20) cc_final: 0.7578 (pp20) REVERT: A 580 LEU cc_start: 0.8699 (tp) cc_final: 0.8059 (tp) REVERT: A 788 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7579 (m-70) REVERT: A 1170 PHE cc_start: 0.8648 (t80) cc_final: 0.8418 (t80) REVERT: A 1245 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7135 (tpp-160) REVERT: A 1263 TYR cc_start: 0.8057 (m-10) cc_final: 0.7447 (m-10) outliers start: 35 outliers final: 21 residues processed: 172 average time/residue: 0.1914 time to fit residues: 49.9320 Evaluate side-chains 160 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.202147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148682 restraints weight = 14476.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143880 restraints weight = 9983.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145683 restraints weight = 9933.547| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11002 Z= 0.157 Angle : 0.667 10.147 14978 Z= 0.328 Chirality : 0.044 0.189 1749 Planarity : 0.004 0.070 1864 Dihedral : 7.107 80.353 1589 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.66 % Allowed : 18.51 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1358 helix: -0.45 (0.18), residues: 870 sheet: 0.07 (0.61), residues: 77 loop : -1.39 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 991 HIS 0.006 0.001 HIS A 686 PHE 0.020 0.001 PHE A1059 TYR 0.012 0.001 TYR A 207 ARG 0.008 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 497) hydrogen bonds : angle 4.40072 ( 1458) covalent geometry : bond 0.00377 (11001) covalent geometry : angle 0.66735 (14978) Misc. bond : bond 0.00145 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 491 MET cc_start: 0.8638 (tpp) cc_final: 0.8409 (tpp) REVERT: A 507 GLU cc_start: 0.8193 (pp20) cc_final: 0.7830 (pp20) REVERT: A 580 LEU cc_start: 0.8739 (tp) cc_final: 0.8097 (tp) REVERT: A 788 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7611 (m-70) REVERT: A 1170 PHE cc_start: 0.8808 (t80) cc_final: 0.8560 (t80) REVERT: A 1245 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7143 (tpp-160) REVERT: A 1263 TYR cc_start: 0.8016 (m-10) cc_final: 0.7463 (m-10) outliers start: 31 outliers final: 24 residues processed: 161 average time/residue: 0.2093 time to fit residues: 50.2386 Evaluate side-chains 164 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** 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 = 0.4461 r_free = 0.4461 target = 0.204278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150196 restraints weight = 14609.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147316 restraints weight = 9655.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149048 restraints weight = 10025.183| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11002 Z= 0.131 Angle : 0.655 11.845 14978 Z= 0.319 Chirality : 0.043 0.175 1749 Planarity : 0.004 0.072 1864 Dihedral : 6.809 76.269 1589 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.83 % Allowed : 18.94 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1358 helix: -0.23 (0.18), residues: 854 sheet: 0.18 (0.62), residues: 77 loop : -1.30 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 991 HIS 0.006 0.001 HIS A 686 PHE 0.021 0.001 PHE A 544 TYR 0.010 0.001 TYR A 207 ARG 0.008 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 497) hydrogen bonds : angle 4.26735 ( 1458) covalent geometry : bond 0.00308 (11001) covalent geometry : angle 0.65479 (14978) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: 0.8611 (tpp) cc_final: 0.8375 (tpp) REVERT: A 507 GLU cc_start: 0.8167 (pp20) cc_final: 0.7958 (pp20) REVERT: A 580 LEU cc_start: 0.8734 (tp) cc_final: 0.8079 (tp) REVERT: A 706 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 788 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7525 (m-70) REVERT: A 1170 PHE cc_start: 0.8714 (t80) cc_final: 0.8472 (t80) REVERT: A 1245 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7172 (tpp-160) REVERT: A 1246 MET cc_start: 0.8123 (mmp) cc_final: 0.7862 (mmt) REVERT: A 1263 TYR cc_start: 0.7992 (m-10) cc_final: 0.7481 (m-10) outliers start: 33 outliers final: 22 residues processed: 176 average time/residue: 0.2509 time to fit residues: 67.2111 Evaluate side-chains 167 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** 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 = 0.4451 r_free = 0.4451 target = 0.203623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.151490 restraints weight = 14435.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147425 restraints weight = 10572.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149672 restraints weight = 10679.586| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11002 Z= 0.137 Angle : 0.666 12.043 14978 Z= 0.325 Chirality : 0.044 0.174 1749 Planarity : 0.004 0.076 1864 Dihedral : 6.646 72.171 1589 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.57 % Allowed : 19.37 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1358 helix: -0.23 (0.18), residues: 863 sheet: 0.18 (0.62), residues: 77 loop : -1.29 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1283 HIS 0.006 0.001 HIS A 686 PHE 0.029 0.001 PHE A 32 TYR 0.010 0.001 TYR A 207 ARG 0.005 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 497) hydrogen bonds : angle 4.26017 ( 1458) covalent geometry : bond 0.00325 (11001) covalent geometry : angle 0.66568 (14978) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 398 ASN cc_start: 0.7495 (p0) cc_final: 0.7258 (p0) REVERT: A 501 LEU cc_start: 0.8554 (tp) cc_final: 0.8278 (tp) REVERT: A 507 GLU cc_start: 0.8174 (pp20) cc_final: 0.7891 (pp20) REVERT: A 580 LEU cc_start: 0.8735 (tp) cc_final: 0.8068 (tp) REVERT: A 706 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7559 (mm-40) REVERT: A 788 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7484 (m-70) REVERT: A 1245 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7085 (tpp-160) REVERT: A 1246 MET cc_start: 0.8195 (mmp) cc_final: 0.7934 (mmt) REVERT: A 1263 TYR cc_start: 0.7973 (m-10) cc_final: 0.7452 (m-10) REVERT: A 1488 MET cc_start: 0.8258 (pmm) cc_final: 0.7679 (pmm) outliers start: 30 outliers final: 22 residues processed: 169 average time/residue: 0.1943 time to fit residues: 50.8354 Evaluate side-chains 167 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 23 optimal weight: 0.0870 chunk 117 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.206199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152748 restraints weight = 14600.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149372 restraints weight = 10085.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151668 restraints weight = 9825.847| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11002 Z= 0.118 Angle : 0.660 11.948 14978 Z= 0.320 Chirality : 0.043 0.176 1749 Planarity : 0.004 0.079 1864 Dihedral : 6.334 66.235 1589 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.71 % Allowed : 20.22 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1358 helix: -0.03 (0.18), residues: 859 sheet: 0.28 (0.63), residues: 77 loop : -1.15 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1283 HIS 0.006 0.001 HIS A 686 PHE 0.020 0.001 PHE A 32 TYR 0.010 0.001 TYR A1232 ARG 0.011 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 497) hydrogen bonds : angle 4.15676 ( 1458) covalent geometry : bond 0.00267 (11001) covalent geometry : angle 0.66016 (14978) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7751 (tt) REVERT: A 180 LEU cc_start: 0.8656 (mm) cc_final: 0.8297 (mm) REVERT: A 215 LEU cc_start: 0.8776 (tt) cc_final: 0.8549 (mt) REVERT: A 369 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7872 (m-70) REVERT: A 491 MET cc_start: 0.8501 (tpp) cc_final: 0.8212 (tpp) REVERT: A 501 LEU cc_start: 0.8549 (tp) cc_final: 0.8245 (tp) REVERT: A 507 GLU cc_start: 0.8150 (pp20) cc_final: 0.7935 (pm20) REVERT: A 580 LEU cc_start: 0.8667 (tp) cc_final: 0.8000 (tp) REVERT: A 788 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7438 (m-70) REVERT: A 976 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7614 (mt) REVERT: A 1191 SER cc_start: 0.8110 (t) cc_final: 0.7635 (p) REVERT: A 1245 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7090 (tpp-160) REVERT: A 1246 MET cc_start: 0.8198 (mmp) cc_final: 0.7928 (mmt) REVERT: A 1488 MET cc_start: 0.8203 (pmm) cc_final: 0.7809 (pmm) outliers start: 20 outliers final: 15 residues processed: 165 average time/residue: 0.1818 time to fit residues: 46.3972 Evaluate side-chains 158 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 56 optimal weight: 9.9990 chunk 52 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.0370 chunk 129 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.207184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152915 restraints weight = 14416.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151209 restraints weight = 8927.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152869 restraints weight = 8451.897| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11002 Z= 0.117 Angle : 0.670 11.916 14978 Z= 0.322 Chirality : 0.042 0.171 1749 Planarity : 0.004 0.078 1864 Dihedral : 6.015 59.540 1589 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.71 % Allowed : 21.08 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1358 helix: 0.09 (0.18), residues: 863 sheet: 0.44 (0.63), residues: 77 loop : -1.12 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1283 HIS 0.006 0.001 HIS A 686 PHE 0.033 0.001 PHE A1170 TYR 0.012 0.001 TYR A 766 ARG 0.010 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 497) hydrogen bonds : angle 4.11636 ( 1458) covalent geometry : bond 0.00262 (11001) covalent geometry : angle 0.66960 (14978) Misc. bond : bond 0.00091 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7720 (tt) REVERT: A 140 PHE cc_start: 0.8743 (t80) cc_final: 0.8366 (t80) REVERT: A 180 LEU cc_start: 0.8676 (mm) cc_final: 0.8296 (mm) REVERT: A 369 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7875 (m-70) REVERT: A 491 MET cc_start: 0.8524 (tpp) cc_final: 0.8162 (tpp) REVERT: A 501 LEU cc_start: 0.8546 (tp) cc_final: 0.8291 (tp) REVERT: A 507 GLU cc_start: 0.8165 (pp20) cc_final: 0.7932 (pm20) REVERT: A 544 PHE cc_start: 0.8432 (t80) cc_final: 0.8088 (t80) REVERT: A 580 LEU cc_start: 0.8609 (tp) cc_final: 0.7981 (tp) REVERT: A 706 GLN cc_start: 0.7528 (mm-40) cc_final: 0.6778 (mm-40) REVERT: A 788 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7502 (m-70) REVERT: A 976 LEU cc_start: 0.8329 (tt) cc_final: 0.7584 (mt) REVERT: A 1191 SER cc_start: 0.8073 (t) cc_final: 0.7622 (p) REVERT: A 1246 MET cc_start: 0.8179 (mmp) cc_final: 0.7950 (mmt) REVERT: A 1263 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: A 1488 MET cc_start: 0.8209 (pmm) cc_final: 0.7904 (pmm) outliers start: 20 outliers final: 14 residues processed: 169 average time/residue: 0.1837 time to fit residues: 48.5395 Evaluate side-chains 161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 788 HIS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1482 HIS Chi-restraints excluded: chain A residue 1501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 86 optimal weight: 0.1980 chunk 60 optimal weight: 20.0000 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 HIS A1360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.208408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154151 restraints weight = 14505.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151118 restraints weight = 9249.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153078 restraints weight = 9034.847| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11002 Z= 0.120 Angle : 0.677 11.712 14978 Z= 0.326 Chirality : 0.043 0.179 1749 Planarity : 0.004 0.079 1864 Dihedral : 5.789 59.342 1589 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.80 % Allowed : 21.59 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1358 helix: 0.20 (0.18), residues: 858 sheet: 0.48 (0.63), residues: 77 loop : -1.04 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1283 HIS 0.005 0.001 HIS A 686 PHE 0.029 0.001 PHE A1170 TYR 0.013 0.001 TYR A1232 ARG 0.010 0.000 ARG A 756 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 497) hydrogen bonds : angle 4.05462 ( 1458) covalent geometry : bond 0.00271 (11001) covalent geometry : angle 0.67696 (14978) Misc. bond : bond 0.00093 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.65 seconds wall clock time: 72 minutes 33.86 seconds (4353.86 seconds total)