Starting phenix.real_space_refine on Tue Jul 29 00:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvh_35043/07_2025/8hvh_35043.cif" } resolution = 3.07 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= 0.001 sd= 0.082 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 56 5.16 5 C 6963 2.51 5 N 1794 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10704 Classifications: {'peptide': 1364} Link IDs: {'PTRANS': 59, 'TRANS': 1304} Chain breaks: 2 Time building chain proxies: 6.73, per 1000 atoms: 0.63 Number of scatterers: 10704 At special positions: 0 Unit cell: (72.76, 113.42, 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 56 16.00 O 1891 8.00 N 1794 7.00 C 6963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.6 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: 75 helices and 6 sheets defined 62.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.573A pdb=" N TRP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Proline residue: A 41 - end of helix removed outlier: 4.139A pdb=" N TRP A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.938A pdb=" N LEU A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.605A pdb=" N LEU A 72 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 93 removed outlier: 4.070A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.992A pdb=" N PHE A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.935A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.629A pdb=" N ILE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 154 through 159 removed outlier: 5.428A pdb=" N LEU A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.550A pdb=" N LEU A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.814A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.048A pdb=" N GLN A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 4.069A pdb=" N GLY A 349 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.636A pdb=" N HIS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.817A pdb=" N LEU A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.381A pdb=" N PHE A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.994A pdb=" N ALA A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.921A pdb=" N MET A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 474 through 497 removed outlier: 3.832A pdb=" N LYS A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.566A pdb=" N ILE A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.771A pdb=" N THR A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 583 removed outlier: 3.642A pdb=" N SER A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.668A pdb=" N LEU A 588 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.504A pdb=" N LYS A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 removed outlier: 3.697A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 716 through 727 removed outlier: 3.662A pdb=" N GLN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 removed outlier: 4.297A pdb=" N MET A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 736' Processing helix chain 'A' and resid 752 through 768 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 843 through 849 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.868A pdb=" N PHE A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 996 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 3.659A pdb=" N TYR A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A1018 " --> pdb=" O VAL A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 3.878A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.692A pdb=" N PHE A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1072 removed outlier: 3.538A pdb=" N ILE A1068 " --> pdb=" O PRO A1064 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1069 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1072' Processing helix chain 'A' and resid 1073 through 1082 removed outlier: 3.639A pdb=" N TYR A1077 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.615A pdb=" N ILE A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1107 " --> pdb=" O VAL A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1116 through 1153 removed outlier: 3.775A pdb=" N TYR A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1132 " --> pdb=" O PHE A1128 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN A1135 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Proline residue: A1146 - end of helix removed outlier: 3.982A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1164 Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 3.625A pdb=" N PHE A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1200 removed outlier: 3.702A pdb=" N GLY A1198 " --> pdb=" O TRP A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 4.006A pdb=" N VAL A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1211 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1232 Processing helix chain 'A' and resid 1233 through 1236 Processing helix chain 'A' and resid 1237 through 1254 removed outlier: 3.524A pdb=" N ASN A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP A1242 " --> pdb=" O PHE A1238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A1251 " --> pdb=" O MET A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1264 removed outlier: 3.711A pdb=" N GLU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1334 removed outlier: 3.559A pdb=" N THR A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1357 removed outlier: 3.531A pdb=" N ILE A1357 " --> pdb=" O VAL A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1413 through 1417 Processing helix chain 'A' and resid 1427 through 1443 Processing helix chain 'A' and resid 1457 through 1472 Processing helix chain 'A' and resid 1483 through 1488 removed outlier: 4.037A pdb=" N ILE A1487 " --> pdb=" O ARG A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1513 Processing helix chain 'A' and resid 1515 through 1523 Processing sheet with id=AA1, first strand: chain 'A' and resid 616 through 617 removed outlier: 4.336A pdb=" N ALA A 626 " --> pdb=" O PRO A 652 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 628 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN A 650 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS A 630 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP A 648 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY A 632 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 removed outlier: 3.740A pdb=" N GLU A 682 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR A 635 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS A 680 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 691 through 694 removed outlier: 6.255A pdb=" N PHE A 772 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 808 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 657 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A 656 " --> pdb=" O PHE A 820 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 822 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 658 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 824 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 660 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 821 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A 832 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 823 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.631A pdb=" N CYS A 703 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1306 through 1313 removed outlier: 6.063A pdb=" N ARG A1307 " --> pdb=" O VAL A1296 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL A1296 " --> pdb=" O ARG A1307 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A1311 " --> pdb=" O ARG A1292 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG A1292 " --> pdb=" O LEU A1311 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A1313 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A1290 " --> pdb=" O VAL A1313 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A1294 " --> pdb=" O LYS A1344 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A1344 " --> pdb=" O TYR A1294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1366 through 1369 removed outlier: 6.802A pdb=" N THR A1367 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP A1450 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A1369 " --> pdb=" O ASP A1450 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A1447 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A1480 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1449 " --> pdb=" O ILE A1480 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS A1318 " --> pdb=" O ARG A1492 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A1494 " --> pdb=" O LYS A1318 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY A1320 " --> pdb=" O LEU A1494 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1496 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A1322 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A1503 " --> pdb=" O VAL A1495 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP A1497 " --> pdb=" O VAL A1501 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1416 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: 3.90 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3295 1.34 - 1.45: 1733 1.45 - 1.57: 5835 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10953 Sorted by residual: bond pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 1.524 1.464 0.059 2.25e-02 1.98e+03 6.92e+00 bond pdb=" CG LEU A 243 " pdb=" CD2 LEU A 243 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CG1 ILE A1190 " pdb=" CD1 ILE A1190 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" C SER A 216 " pdb=" O SER A 216 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.62e-02 3.81e+03 1.64e+00 bond pdb=" CG LEU A1250 " pdb=" CD1 LEU A1250 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 10948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 14437 1.91 - 3.83: 387 3.83 - 5.74: 53 5.74 - 7.66: 15 7.66 - 9.57: 4 Bond angle restraints: 14896 Sorted by residual: angle pdb=" N ILE A 498 " pdb=" CA ILE A 498 " pdb=" C ILE A 498 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" N VAL A 111 " pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 113.53 109.08 4.45 9.80e-01 1.04e+00 2.07e+01 angle pdb=" C ILE A 385 " pdb=" N MET A 386 " pdb=" CA MET A 386 " ideal model delta sigma weight residual 122.31 115.30 7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N VAL A1014 " pdb=" CA VAL A1014 " pdb=" C VAL A1014 " ideal model delta sigma weight residual 112.98 108.91 4.07 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N PRO A 103 " pdb=" CD PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 103.20 98.48 4.72 1.50e+00 4.44e-01 9.91e+00 ... (remaining 14891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5833 17.85 - 35.70: 554 35.70 - 53.55: 81 53.55 - 71.40: 20 71.40 - 89.25: 8 Dihedral angle restraints: 6496 sinusoidal: 2534 harmonic: 3962 Sorted by residual: dihedral pdb=" CA TYR A1186 " pdb=" C TYR A1186 " pdb=" N PRO A1187 " pdb=" CA PRO A1187 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLN A 436 " pdb=" C GLN A 436 " pdb=" N ILE A 437 " pdb=" CA ILE A 437 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLU A 209 " pdb=" C GLU A 209 " pdb=" N THR A 210 " pdb=" CA THR A 210 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 6493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1119 0.041 - 0.082: 479 0.082 - 0.123: 119 0.123 - 0.164: 18 0.164 - 0.204: 2 Chirality restraints: 1737 Sorted by residual: chirality pdb=" CG LEU A 137 " pdb=" CB LEU A 137 " pdb=" CD1 LEU A 137 " pdb=" CD2 LEU A 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 196 " pdb=" N PHE A 196 " pdb=" C PHE A 196 " pdb=" CB PHE A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA ASN A1165 " pdb=" N ASN A1165 " pdb=" C ASN A1165 " pdb=" CB ASN A1165 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1734 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 328 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 329 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1116 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A1117 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1117 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 542 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 543 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.025 5.00e-02 4.00e+02 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 167 2.67 - 3.22: 10778 3.22 - 3.78: 16458 3.78 - 4.34: 23189 4.34 - 4.90: 37230 Nonbonded interactions: 87822 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU A 126 " model vdw 2.107 3.040 nonbonded pdb=" O SER A 216 " pdb=" OG SER A 216 " model vdw 2.243 3.040 nonbonded pdb=" O ALA A 764 " pdb=" OG SER A 767 " model vdw 2.247 3.040 nonbonded pdb=" O ASP A1461 " pdb=" NE2 GLN A1465 " model vdw 2.274 3.120 nonbonded pdb=" O THR A1108 " pdb=" OG1 THR A1108 " model vdw 2.279 3.040 ... (remaining 87817 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.005 0.059 10953 Z= 0.232 Angle : 0.761 9.572 14896 Z= 0.416 Chirality : 0.046 0.204 1737 Planarity : 0.005 0.066 1862 Dihedral : 14.435 89.249 3936 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -3.04 (0.21), residues: 1358 helix: -2.01 (0.17), residues: 841 sheet: -0.22 (0.63), residues: 74 loop : -1.97 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 347 HIS 0.006 0.001 HIS A 372 PHE 0.029 0.002 PHE A 311 TYR 0.018 0.002 TYR A 504 ARG 0.010 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.20583 ( 488) hydrogen bonds : angle 8.02541 ( 1416) covalent geometry : bond 0.00548 (10953) covalent geometry : angle 0.76081 (14896) *********************** 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 281 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 SER cc_start: 0.7858 (t) cc_final: 0.7404 (m) REVERT: A 821 ILE cc_start: 0.6691 (mt) cc_final: 0.6355 (mt) REVERT: A 1115 ILE cc_start: 0.8788 (tp) cc_final: 0.8575 (tp) REVERT: A 1122 TYR cc_start: 0.7441 (t80) cc_final: 0.7032 (t80) REVERT: A 1294 TYR cc_start: 0.8157 (t80) cc_final: 0.7907 (t80) REVERT: A 1321 ILE cc_start: 0.8582 (mm) cc_final: 0.8369 (mm) REVERT: A 1344 LYS cc_start: 0.7062 (mmtt) cc_final: 0.6636 (mmmt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2496 time to fit residues: 100.0289 Evaluate side-chains 156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1057 GLN A1092 ASN A1181 ASN A1182 GLN A1465 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111339 restraints weight = 15616.255| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.51 r_work: 0.3412 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10953 Z= 0.155 Angle : 0.711 10.201 14896 Z= 0.360 Chirality : 0.044 0.171 1737 Planarity : 0.005 0.063 1862 Dihedral : 5.537 23.343 1468 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.71 % Allowed : 11.39 % Favored : 86.90 % 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: -2.14 (0.22), residues: 1358 helix: -1.23 (0.17), residues: 865 sheet: -0.02 (0.60), residues: 74 loop : -1.74 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 347 HIS 0.003 0.001 HIS A 59 PHE 0.025 0.001 PHE A 196 TYR 0.019 0.001 TYR A 720 ARG 0.005 0.001 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 488) hydrogen bonds : angle 5.16877 ( 1416) covalent geometry : bond 0.00330 (10953) covalent geometry : angle 0.71137 (14896) *********************** 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 211 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LYS cc_start: 0.8569 (pttt) cc_final: 0.8184 (pttp) REVERT: A 251 MET cc_start: 0.8988 (mmm) cc_final: 0.8719 (mmp) REVERT: A 415 VAL cc_start: 0.8598 (t) cc_final: 0.8231 (m) REVERT: A 721 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 768 ASP cc_start: 0.8867 (m-30) cc_final: 0.8503 (m-30) REVERT: A 775 ASP cc_start: 0.7829 (m-30) cc_final: 0.7546 (m-30) REVERT: A 821 ILE cc_start: 0.7080 (mt) cc_final: 0.6840 (mt) REVERT: A 839 LEU cc_start: 0.6858 (tp) cc_final: 0.6623 (mt) REVERT: A 1338 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: A 1344 LYS cc_start: 0.6928 (mmtt) cc_final: 0.6617 (mmmt) REVERT: A 1432 GLN cc_start: 0.8297 (mp10) cc_final: 0.7680 (mp10) REVERT: A 1488 MET cc_start: 0.8227 (mmm) cc_final: 0.7671 (tmm) outliers start: 20 outliers final: 13 residues processed: 202 average time/residue: 0.2190 time to fit residues: 65.7190 Evaluate side-chains 173 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN A 702 ASN A 706 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111640 restraints weight = 15798.575| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.52 r_work: 0.3410 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10953 Z= 0.124 Angle : 0.621 9.085 14896 Z= 0.311 Chirality : 0.042 0.162 1737 Planarity : 0.004 0.039 1862 Dihedral : 5.066 22.440 1468 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.23 % Allowed : 14.55 % Favored : 83.22 % 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: -1.61 (0.22), residues: 1358 helix: -0.77 (0.18), residues: 859 sheet: -0.47 (0.61), residues: 68 loop : -1.47 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 222 HIS 0.002 0.001 HIS A 630 PHE 0.024 0.001 PHE A 196 TYR 0.011 0.001 TYR A 720 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 488) hydrogen bonds : angle 4.64160 ( 1416) covalent geometry : bond 0.00274 (10953) covalent geometry : angle 0.62060 (14896) *********************** 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 203 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6542 (ttp80) cc_final: 0.6130 (ptm-80) REVERT: A 180 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7200 (mp) REVERT: A 251 MET cc_start: 0.8999 (mmm) cc_final: 0.8761 (mmp) REVERT: A 415 VAL cc_start: 0.8640 (t) cc_final: 0.8313 (m) REVERT: A 545 LEU cc_start: 0.8683 (tp) cc_final: 0.8468 (tp) REVERT: A 768 ASP cc_start: 0.8920 (m-30) cc_final: 0.8540 (m-30) REVERT: A 832 MET cc_start: 0.6703 (ttt) cc_final: 0.6436 (ttt) REVERT: A 839 LEU cc_start: 0.7134 (tp) cc_final: 0.6900 (mt) REVERT: A 1027 MET cc_start: 0.7747 (mmp) cc_final: 0.6478 (ttt) REVERT: A 1063 THR cc_start: 0.8092 (m) cc_final: 0.7661 (p) REVERT: A 1122 TYR cc_start: 0.8288 (t80) cc_final: 0.7680 (t80) REVERT: A 1247 MET cc_start: 0.8142 (ttm) cc_final: 0.7899 (ttm) REVERT: A 1338 ARG cc_start: 0.8771 (mmm-85) cc_final: 0.8318 (mmm-85) REVERT: A 1353 ASN cc_start: 0.7741 (t0) cc_final: 0.7492 (t0) REVERT: A 1488 MET cc_start: 0.8405 (mmm) cc_final: 0.7778 (tmm) REVERT: A 1505 ASP cc_start: 0.7469 (t70) cc_final: 0.7154 (t70) outliers start: 26 outliers final: 19 residues processed: 196 average time/residue: 0.2594 time to fit residues: 77.5684 Evaluate side-chains 177 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 ASN A1418 GLN A1465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106254 restraints weight = 15616.164| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.46 r_work: 0.3325 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10953 Z= 0.180 Angle : 0.660 8.734 14896 Z= 0.327 Chirality : 0.044 0.141 1737 Planarity : 0.004 0.037 1862 Dihedral : 5.022 25.046 1468 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.20 % Allowed : 15.33 % Favored : 80.48 % 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: -1.52 (0.22), residues: 1358 helix: -0.73 (0.17), residues: 869 sheet: -0.37 (0.61), residues: 68 loop : -1.38 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 995 HIS 0.005 0.001 HIS A 372 PHE 0.031 0.002 PHE A1059 TYR 0.012 0.001 TYR A1122 ARG 0.006 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 488) hydrogen bonds : angle 4.58749 ( 1416) covalent geometry : bond 0.00420 (10953) covalent geometry : angle 0.66024 (14896) *********************** 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 222 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7201 (mp) REVERT: A 348 TRP cc_start: 0.7671 (m-10) cc_final: 0.7450 (m-10) REVERT: A 415 VAL cc_start: 0.8623 (t) cc_final: 0.8347 (m) REVERT: A 630 HIS cc_start: 0.6947 (m-70) cc_final: 0.6736 (m-70) REVERT: A 672 SER cc_start: 0.8264 (m) cc_final: 0.7799 (t) REVERT: A 678 MET cc_start: 0.8167 (mtp) cc_final: 0.7669 (mtp) REVERT: A 687 MET cc_start: 0.7467 (ttp) cc_final: 0.7130 (ptm) REVERT: A 766 TYR cc_start: 0.8599 (t80) cc_final: 0.8319 (t80) REVERT: A 768 ASP cc_start: 0.8961 (m-30) cc_final: 0.8696 (m-30) REVERT: A 1024 PHE cc_start: 0.7567 (m-10) cc_final: 0.6930 (t80) REVERT: A 1027 MET cc_start: 0.7838 (mmp) cc_final: 0.6817 (ttt) REVERT: A 1063 THR cc_start: 0.8240 (m) cc_final: 0.7845 (p) REVERT: A 1290 GLU cc_start: 0.7459 (pt0) cc_final: 0.7191 (pm20) REVERT: A 1338 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: A 1353 ASN cc_start: 0.7964 (t0) cc_final: 0.7701 (t0) REVERT: A 1488 MET cc_start: 0.8278 (mmm) cc_final: 0.7787 (tmm) REVERT: A 1505 ASP cc_start: 0.7413 (t70) cc_final: 0.7039 (t70) outliers start: 49 outliers final: 36 residues processed: 209 average time/residue: 0.2315 time to fit residues: 73.8732 Evaluate side-chains 195 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1500 VAL 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 119 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 706 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108277 restraints weight = 15642.008| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.52 r_work: 0.3354 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10953 Z= 0.125 Angle : 0.612 10.920 14896 Z= 0.298 Chirality : 0.042 0.140 1737 Planarity : 0.004 0.035 1862 Dihedral : 4.835 23.383 1468 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.34 % Allowed : 17.89 % Favored : 78.77 % 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: -1.12 (0.23), residues: 1358 helix: -0.39 (0.18), residues: 857 sheet: -0.14 (0.59), residues: 76 loop : -1.31 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1194 HIS 0.002 0.001 HIS A1360 PHE 0.023 0.001 PHE A 196 TYR 0.010 0.001 TYR A1518 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 488) hydrogen bonds : angle 4.34755 ( 1416) covalent geometry : bond 0.00291 (10953) covalent geometry : angle 0.61170 (14896) *********************** 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 204 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6441 (ttp80) cc_final: 0.6030 (ptm-80) REVERT: A 180 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 348 TRP cc_start: 0.7663 (m-10) cc_final: 0.7206 (m-10) REVERT: A 415 VAL cc_start: 0.8571 (t) cc_final: 0.8292 (m) REVERT: A 515 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 630 HIS cc_start: 0.6959 (m-70) cc_final: 0.6528 (m-70) REVERT: A 687 MET cc_start: 0.7442 (ttp) cc_final: 0.7087 (ptm) REVERT: A 706 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 766 TYR cc_start: 0.8688 (t80) cc_final: 0.8336 (t80) REVERT: A 1024 PHE cc_start: 0.7447 (m-10) cc_final: 0.6877 (t80) REVERT: A 1027 MET cc_start: 0.7763 (mmp) cc_final: 0.6861 (ttt) REVERT: A 1063 THR cc_start: 0.8249 (m) cc_final: 0.7831 (p) REVERT: A 1290 GLU cc_start: 0.7475 (pt0) cc_final: 0.7075 (pm20) REVERT: A 1338 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8301 (mmm-85) REVERT: A 1353 ASN cc_start: 0.7994 (t0) cc_final: 0.7735 (t0) REVERT: A 1488 MET cc_start: 0.8426 (mmm) cc_final: 0.7865 (tmm) REVERT: A 1505 ASP cc_start: 0.7644 (t70) cc_final: 0.7327 (t0) outliers start: 39 outliers final: 33 residues processed: 192 average time/residue: 0.2828 time to fit residues: 84.3637 Evaluate side-chains 192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.154177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108871 restraints weight = 15603.909| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.48 r_work: 0.3362 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10953 Z= 0.115 Angle : 0.604 9.600 14896 Z= 0.292 Chirality : 0.042 0.136 1737 Planarity : 0.004 0.033 1862 Dihedral : 4.705 24.049 1468 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.60 % Allowed : 18.66 % Favored : 77.74 % 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: -0.88 (0.23), residues: 1358 helix: -0.20 (0.18), residues: 857 sheet: -0.20 (0.59), residues: 76 loop : -1.18 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 991 HIS 0.002 0.001 HIS A 372 PHE 0.021 0.001 PHE A 196 TYR 0.010 0.001 TYR A1518 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 488) hydrogen bonds : angle 4.25108 ( 1416) covalent geometry : bond 0.00267 (10953) covalent geometry : angle 0.60436 (14896) *********************** 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 211 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6505 (ttp80) cc_final: 0.6110 (ptm-80) REVERT: A 180 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 348 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.7298 (m-10) REVERT: A 415 VAL cc_start: 0.8587 (t) cc_final: 0.8332 (m) REVERT: A 499 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8032 (tptm) REVERT: A 515 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 630 HIS cc_start: 0.6944 (m-70) cc_final: 0.6619 (m-70) REVERT: A 678 MET cc_start: 0.8211 (mtp) cc_final: 0.7607 (mtp) REVERT: A 687 MET cc_start: 0.7323 (ttp) cc_final: 0.6918 (ptm) REVERT: A 1024 PHE cc_start: 0.7408 (m-10) cc_final: 0.6906 (t80) REVERT: A 1063 THR cc_start: 0.8226 (m) cc_final: 0.7793 (p) REVERT: A 1275 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: A 1290 GLU cc_start: 0.7480 (pt0) cc_final: 0.7089 (pm20) REVERT: A 1338 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8340 (mmm-85) REVERT: A 1353 ASN cc_start: 0.8029 (t0) cc_final: 0.7786 (t0) REVERT: A 1357 ILE cc_start: 0.7474 (mp) cc_final: 0.7264 (mm) REVERT: A 1488 MET cc_start: 0.8315 (mmm) cc_final: 0.7851 (tmm) REVERT: A 1505 ASP cc_start: 0.7707 (t70) cc_final: 0.7372 (t0) outliers start: 42 outliers final: 35 residues processed: 193 average time/residue: 0.2009 time to fit residues: 59.8385 Evaluate side-chains 197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 46 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109122 restraints weight = 15750.637| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.56 r_work: 0.3364 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10953 Z= 0.112 Angle : 0.600 9.502 14896 Z= 0.288 Chirality : 0.041 0.137 1737 Planarity : 0.004 0.031 1862 Dihedral : 4.608 23.422 1468 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.77 % Allowed : 19.09 % Favored : 77.14 % 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: -0.68 (0.23), residues: 1358 helix: -0.04 (0.18), residues: 854 sheet: -0.23 (0.58), residues: 76 loop : -1.10 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.002 0.001 HIS A1360 PHE 0.020 0.001 PHE A 196 TYR 0.009 0.001 TYR A1518 ARG 0.007 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 488) hydrogen bonds : angle 4.18406 ( 1416) covalent geometry : bond 0.00258 (10953) covalent geometry : angle 0.60015 (14896) *********************** 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 208 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6488 (ttp80) cc_final: 0.6095 (ptm-80) REVERT: A 180 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7181 (mp) REVERT: A 348 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: A 415 VAL cc_start: 0.8600 (t) cc_final: 0.8333 (m) REVERT: A 499 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7988 (tptm) REVERT: A 515 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 630 HIS cc_start: 0.6921 (m-70) cc_final: 0.6587 (m-70) REVERT: A 675 LEU cc_start: 0.9131 (mt) cc_final: 0.8927 (mt) REVERT: A 678 MET cc_start: 0.8201 (mtp) cc_final: 0.7632 (mtp) REVERT: A 687 MET cc_start: 0.7355 (ttp) cc_final: 0.6935 (ptm) REVERT: A 1024 PHE cc_start: 0.7336 (m-10) cc_final: 0.6974 (t80) REVERT: A 1027 MET cc_start: 0.7740 (mmp) cc_final: 0.6929 (ttp) REVERT: A 1063 THR cc_start: 0.8242 (m) cc_final: 0.7807 (p) REVERT: A 1247 MET cc_start: 0.8357 (mtp) cc_final: 0.7477 (tpt) REVERT: A 1290 GLU cc_start: 0.7469 (pt0) cc_final: 0.7143 (pm20) REVERT: A 1338 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8332 (mmm-85) REVERT: A 1353 ASN cc_start: 0.8036 (t0) cc_final: 0.7772 (t0) REVERT: A 1488 MET cc_start: 0.8422 (mmm) cc_final: 0.7855 (tmm) REVERT: A 1505 ASP cc_start: 0.7707 (t70) cc_final: 0.7390 (t0) outliers start: 44 outliers final: 35 residues processed: 191 average time/residue: 0.3330 time to fit residues: 102.7341 Evaluate side-chains 190 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109332 restraints weight = 15478.496| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.53 r_work: 0.3367 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10953 Z= 0.109 Angle : 0.592 9.569 14896 Z= 0.286 Chirality : 0.041 0.134 1737 Planarity : 0.004 0.031 1862 Dihedral : 4.537 23.198 1468 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.42 % Allowed : 19.61 % Favored : 76.97 % 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: -0.55 (0.23), residues: 1358 helix: 0.05 (0.18), residues: 859 sheet: -0.19 (0.58), residues: 76 loop : -1.04 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.003 0.001 HIS A1360 PHE 0.019 0.001 PHE A 196 TYR 0.009 0.001 TYR A1518 ARG 0.006 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 488) hydrogen bonds : angle 4.14162 ( 1416) covalent geometry : bond 0.00250 (10953) covalent geometry : angle 0.59213 (14896) *********************** 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 206 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6469 (ttp80) cc_final: 0.6091 (ptm-80) REVERT: A 251 MET cc_start: 0.9110 (mmm) cc_final: 0.8757 (tpt) REVERT: A 348 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: A 415 VAL cc_start: 0.8613 (t) cc_final: 0.8358 (m) REVERT: A 499 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8034 (tptm) REVERT: A 515 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 630 HIS cc_start: 0.6755 (m-70) cc_final: 0.6421 (m-70) REVERT: A 675 LEU cc_start: 0.9117 (mt) cc_final: 0.8903 (mt) REVERT: A 678 MET cc_start: 0.8198 (mtp) cc_final: 0.7653 (mtp) REVERT: A 687 MET cc_start: 0.7352 (ttp) cc_final: 0.6900 (ptm) REVERT: A 818 THR cc_start: 0.9000 (p) cc_final: 0.8797 (t) REVERT: A 820 PHE cc_start: 0.6826 (t80) cc_final: 0.6431 (t80) REVERT: A 1024 PHE cc_start: 0.7366 (m-10) cc_final: 0.7008 (t80) REVERT: A 1027 MET cc_start: 0.7786 (mmp) cc_final: 0.6937 (ttp) REVERT: A 1063 THR cc_start: 0.8248 (m) cc_final: 0.7814 (p) REVERT: A 1247 MET cc_start: 0.8313 (mtp) cc_final: 0.7455 (tpt) REVERT: A 1258 GLU cc_start: 0.8256 (pp20) cc_final: 0.7995 (pp20) REVERT: A 1290 GLU cc_start: 0.7409 (pt0) cc_final: 0.7118 (pm20) REVERT: A 1338 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8363 (mmm-85) REVERT: A 1353 ASN cc_start: 0.8031 (t0) cc_final: 0.7653 (t0) REVERT: A 1488 MET cc_start: 0.8411 (mmm) cc_final: 0.7849 (tmm) REVERT: A 1505 ASP cc_start: 0.7731 (t70) cc_final: 0.7404 (t0) outliers start: 40 outliers final: 37 residues processed: 189 average time/residue: 0.2016 time to fit residues: 58.9836 Evaluate side-chains 200 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 1 optimal weight: 0.0010 chunk 119 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.157038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110450 restraints weight = 15650.378| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.56 r_work: 0.3381 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10953 Z= 0.100 Angle : 0.584 9.592 14896 Z= 0.279 Chirality : 0.041 0.136 1737 Planarity : 0.003 0.031 1862 Dihedral : 4.431 22.888 1468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.08 % Allowed : 20.03 % Favored : 76.88 % 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: -0.36 (0.23), residues: 1358 helix: 0.20 (0.18), residues: 855 sheet: -0.16 (0.58), residues: 76 loop : -0.94 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.003 0.000 HIS A1360 PHE 0.018 0.001 PHE A 196 TYR 0.009 0.001 TYR A1122 ARG 0.006 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 488) hydrogen bonds : angle 4.06989 ( 1416) covalent geometry : bond 0.00227 (10953) covalent geometry : angle 0.58378 (14896) *********************** 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 201 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6547 (ttp80) cc_final: 0.6128 (ptm-80) REVERT: A 251 MET cc_start: 0.9074 (mmm) cc_final: 0.8751 (tpt) REVERT: A 348 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: A 415 VAL cc_start: 0.8622 (t) cc_final: 0.8390 (m) REVERT: A 499 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8048 (tptm) REVERT: A 515 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 630 HIS cc_start: 0.6754 (m-70) cc_final: 0.6386 (m-70) REVERT: A 678 MET cc_start: 0.8146 (mtp) cc_final: 0.7630 (mtp) REVERT: A 687 MET cc_start: 0.7285 (ttp) cc_final: 0.6916 (ptm) REVERT: A 814 PHE cc_start: 0.8412 (m-80) cc_final: 0.8108 (m-10) REVERT: A 1024 PHE cc_start: 0.7368 (m-10) cc_final: 0.6983 (t80) REVERT: A 1027 MET cc_start: 0.7804 (mmp) cc_final: 0.6937 (ttp) REVERT: A 1063 THR cc_start: 0.8247 (m) cc_final: 0.7821 (p) REVERT: A 1247 MET cc_start: 0.8290 (mtp) cc_final: 0.7433 (tpt) REVERT: A 1275 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: A 1290 GLU cc_start: 0.7457 (pt0) cc_final: 0.7135 (pm20) REVERT: A 1353 ASN cc_start: 0.8001 (t0) cc_final: 0.7608 (t0) REVERT: A 1488 MET cc_start: 0.8455 (mmm) cc_final: 0.7852 (tmm) REVERT: A 1505 ASP cc_start: 0.7721 (t70) cc_final: 0.7386 (t0) outliers start: 36 outliers final: 32 residues processed: 187 average time/residue: 0.1828 time to fit residues: 53.9596 Evaluate side-chains 193 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109816 restraints weight = 15649.867| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.53 r_work: 0.3365 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10953 Z= 0.117 Angle : 0.593 9.815 14896 Z= 0.285 Chirality : 0.042 0.161 1737 Planarity : 0.003 0.031 1862 Dihedral : 4.418 22.985 1468 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.17 % Allowed : 20.38 % Favored : 76.46 % 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: -0.33 (0.23), residues: 1358 helix: 0.21 (0.18), residues: 858 sheet: -0.08 (0.58), residues: 75 loop : -0.92 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 991 HIS 0.004 0.001 HIS A1360 PHE 0.017 0.001 PHE A 196 TYR 0.009 0.001 TYR A1518 ARG 0.006 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 488) hydrogen bonds : angle 4.07536 ( 1416) covalent geometry : bond 0.00272 (10953) covalent geometry : angle 0.59299 (14896) ********************** 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 199 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6519 (ttp80) cc_final: 0.6160 (ptm-80) REVERT: A 251 MET cc_start: 0.9094 (mmm) cc_final: 0.8773 (tpt) REVERT: A 348 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: A 415 VAL cc_start: 0.8660 (t) cc_final: 0.8400 (m) REVERT: A 499 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8065 (tptm) REVERT: A 515 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 630 HIS cc_start: 0.6710 (m-70) cc_final: 0.6342 (m-70) REVERT: A 672 SER cc_start: 0.8274 (m) cc_final: 0.7814 (t) REVERT: A 675 LEU cc_start: 0.9097 (mt) cc_final: 0.8875 (mt) REVERT: A 678 MET cc_start: 0.8170 (mtp) cc_final: 0.7889 (mmm) REVERT: A 687 MET cc_start: 0.7377 (ttp) cc_final: 0.7018 (ptm) REVERT: A 814 PHE cc_start: 0.8256 (m-80) cc_final: 0.7944 (m-10) REVERT: A 1024 PHE cc_start: 0.7433 (m-10) cc_final: 0.7013 (t80) REVERT: A 1027 MET cc_start: 0.7691 (mmp) cc_final: 0.6860 (ttp) REVERT: A 1063 THR cc_start: 0.8248 (m) cc_final: 0.7821 (p) REVERT: A 1247 MET cc_start: 0.8372 (mtp) cc_final: 0.7529 (tpt) REVERT: A 1258 GLU cc_start: 0.8299 (pp20) cc_final: 0.8042 (pp20) REVERT: A 1290 GLU cc_start: 0.7497 (pt0) cc_final: 0.7166 (pm20) REVERT: A 1353 ASN cc_start: 0.8009 (t0) cc_final: 0.7607 (t0) REVERT: A 1488 MET cc_start: 0.8416 (mmm) cc_final: 0.7764 (tmm) REVERT: A 1505 ASP cc_start: 0.7818 (t70) cc_final: 0.7479 (t0) outliers start: 37 outliers final: 33 residues processed: 185 average time/residue: 0.2012 time to fit residues: 58.2858 Evaluate side-chains 194 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 TRP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1432 GLN Chi-restraints excluded: chain A residue 1448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110073 restraints weight = 15590.982| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.54 r_work: 0.3368 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10953 Z= 0.112 Angle : 0.591 10.043 14896 Z= 0.284 Chirality : 0.042 0.161 1737 Planarity : 0.003 0.030 1862 Dihedral : 4.378 22.919 1468 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.68 % Allowed : 19.95 % Favored : 76.37 % 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: -0.29 (0.23), residues: 1358 helix: 0.24 (0.18), residues: 858 sheet: -0.10 (0.58), residues: 75 loop : -0.88 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 991 HIS 0.004 0.001 HIS A1360 PHE 0.018 0.001 PHE A 196 TYR 0.008 0.001 TYR A1122 ARG 0.006 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 488) hydrogen bonds : angle 4.05223 ( 1416) covalent geometry : bond 0.00259 (10953) covalent geometry : angle 0.59123 (14896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8018.39 seconds wall clock time: 147 minutes 44.91 seconds (8864.91 seconds total)