Starting phenix.real_space_refine on Fri Mar 6 08:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otv_13067/03_2026/7otv_13067.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 191 5.16 5 C 18632 2.51 5 N 4903 2.21 5 O 5315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 28910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3636, 28910 Classifications: {'peptide': 3636} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 158, 'TRANS': 3477} Chain breaks: 16 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 131 Unusual residues: {'KWT': 1} Classifications: {'peptide': 20, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19, None: 1} Not linked: pdbres="UNK A6020 " pdbres="KWT A6101 " Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.87, per 1000 atoms: 0.20 Number of scatterers: 29041 At special positions: 0 Unit cell: (122.576, 156.48, 183.864, 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 191 16.00 O 5315 8.00 N 4903 7.00 C 18632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 5 sheets defined 70.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.988A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.128A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 4.099A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.648A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.544A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.812A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.934A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.613A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.895A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.940A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.811A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 4.258A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.185A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.641A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.069A pdb=" N VAL A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.697A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.859A pdb=" N SER A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.856A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 450 through 469 removed outlier: 4.242A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.238A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.906A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.682A pdb=" N PHE A 641 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 643 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Proline residue: A 644 - end of helix Processing helix chain 'A' and resid 645 through 660 removed outlier: 4.155A pdb=" N GLN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.518A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 3.653A pdb=" N THR A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.925A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 760 removed outlier: 3.943A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 3.934A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.654A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 797 through 802 removed outlier: 3.676A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.836A pdb=" N SER A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 921 removed outlier: 4.027A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 945 Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.823A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.634A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 removed outlier: 3.575A pdb=" N ARG A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1023 through 1044 removed outlier: 3.635A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1051 removed outlier: 4.155A pdb=" N GLU A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.690A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.645A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N LEU A1145 " --> pdb=" O LYS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.548A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1272 removed outlier: 3.573A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.787A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 3.516A pdb=" N ALA A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.704A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1361 removed outlier: 3.991A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.180A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.770A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1433 removed outlier: 3.589A pdb=" N CYS A1432 " --> pdb=" O ILE A1428 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1433 " --> pdb=" O GLU A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'A' and resid 1481 through 1486 Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.620A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.716A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 4.402A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 removed outlier: 3.813A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 3.669A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1630 removed outlier: 3.501A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.796A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.615A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.852A pdb=" N PHE A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.808A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1813 through 1822 removed outlier: 3.719A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 3.650A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1882 Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 3.727A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 3.679A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A1923 " --> pdb=" O CYS A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 removed outlier: 3.578A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1975 removed outlier: 3.894A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1975 " --> pdb=" O PRO A1971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1970 through 1975' Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.882A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.625A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.605A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.811A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2153 through 2158' Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 5.040A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 removed outlier: 3.580A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 4.009A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 removed outlier: 3.515A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2267 through 2269 No H-bonds generated for 'chain 'A' and resid 2267 through 2269' Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.532A pdb=" N MET A2281 " --> pdb=" O LEU A2277 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 removed outlier: 4.266A pdb=" N TYR A2299 " --> pdb=" O GLN A2295 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.008A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 4.188A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2370 removed outlier: 3.720A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2375 removed outlier: 3.938A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.941A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2418 Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.711A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2424' Processing helix chain 'A' and resid 2429 through 2443 removed outlier: 3.597A pdb=" N CYS A2435 " --> pdb=" O ARG A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.925A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.731A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.775A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2543 through 2546 Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2864 removed outlier: 3.659A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2871 removed outlier: 4.236A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2900 removed outlier: 3.678A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A2898 " --> pdb=" O GLU A2894 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A2900 " --> pdb=" O ALA A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2933 removed outlier: 3.579A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.524A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2954 through 2962 removed outlier: 3.546A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.650A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 4.424A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.595A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3054 removed outlier: 3.504A pdb=" N SER A3047 " --> pdb=" O TYR A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3071 removed outlier: 4.270A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3081 removed outlier: 3.689A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.705A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.547A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.568A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 3.953A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A3140 " --> pdb=" O THR A3136 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3167 removed outlier: 4.240A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A3167 " --> pdb=" O THR A3163 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.787A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A3196 " --> pdb=" O LYS A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.744A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3262 Processing helix chain 'A' and resid 3271 through 3287 removed outlier: 3.765A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A3283 " --> pdb=" O SER A3279 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3307 removed outlier: 4.577A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 3.721A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3353 removed outlier: 4.037A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU A3353 " --> pdb=" O GLU A3350 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3364 removed outlier: 3.982A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3392 Processing helix chain 'A' and resid 3406 through 3430 removed outlier: 3.630A pdb=" N ILE A3410 " --> pdb=" O ALA A3406 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A3430 " --> pdb=" O LYS A3426 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.811A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3464 removed outlier: 3.604A pdb=" N LYS A3464 " --> pdb=" O GLU A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3472 removed outlier: 3.824A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3480 removed outlier: 3.734A pdb=" N GLU A3478 " --> pdb=" O TYR A3475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A3480 " --> pdb=" O GLU A3477 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3488 removed outlier: 3.544A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3504 through 3506 No H-bonds generated for 'chain 'A' and resid 3504 through 3506' Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.537A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.912A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3563 removed outlier: 4.094A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 removed outlier: 3.647A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3605 through 3607 No H-bonds generated for 'chain 'A' and resid 3605 through 3607' Processing helix chain 'A' and resid 3608 through 3617 removed outlier: 3.526A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.688A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3649 through 3653 Processing helix chain 'A' and resid 3657 through 3671 removed outlier: 3.622A pdb=" N ASP A3661 " --> pdb=" O SER A3657 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3672 through 3674 No H-bonds generated for 'chain 'A' and resid 3672 through 3674' Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3777 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.740A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3819 removed outlier: 3.585A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3846 removed outlier: 4.063A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 4.015A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3876 removed outlier: 3.654A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 removed outlier: 3.751A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.995A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.608A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A3986 " --> pdb=" O SER A3982 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.613A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.681A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4043 through 4050 removed outlier: 3.855A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 removed outlier: 3.593A pdb=" N CYS A4061 " --> pdb=" O ALA A4057 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4082 Processing helix chain 'A' and resid 4101 through 4112 removed outlier: 3.663A pdb=" N LEU A4107 " --> pdb=" O GLN A4103 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 6002 through 6010 removed outlier: 3.646A pdb=" N UNK A6007 " --> pdb=" O UNK A6003 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK A6009 " --> pdb=" O UNK A6005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.796A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.796A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3809 through 3811 1481 hydrogen bonds defined for protein. 4359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.93 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.57: 29329 1.57 - 1.95: 306 1.95 - 2.33: 0 2.33 - 2.71: 0 2.71 - 3.09: 1 Bond restraints: 29636 Sorted by residual: bond pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " ideal model delta sigma weight residual 1.335 3.092 -1.757 2.00e-02 2.50e+03 7.72e+03 bond pdb=" C4 KWT A6101 " pdb=" C9 KWT A6101 " ideal model delta sigma weight residual 1.468 1.640 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C2 KWT A6101 " pdb=" C3 KWT A6101 " ideal model delta sigma weight residual 1.457 1.584 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C8 KWT A6101 " pdb=" C9 KWT A6101 " ideal model delta sigma weight residual 1.531 1.629 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C5 KWT A6101 " pdb=" C6 KWT A6101 " ideal model delta sigma weight residual 1.439 1.537 -0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 29631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 40071 7.50 - 14.99: 11 14.99 - 22.49: 1 22.49 - 29.99: 3 29.99 - 37.48: 1 Bond angle restraints: 40087 Sorted by residual: angle pdb=" C3 KWT A6101 " pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " ideal model delta sigma weight residual 110.21 72.73 37.48 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C19 KWT A6101 " pdb=" C3 KWT A6101 " pdb=" C4 KWT A6101 " ideal model delta sigma weight residual 105.57 132.11 -26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " pdb=" C5 KWT A6101 " ideal model delta sigma weight residual 107.35 81.37 25.98 3.00e+00 1.11e-01 7.50e+01 angle pdb=" N MET A3483 " pdb=" CA MET A3483 " pdb=" C MET A3483 " ideal model delta sigma weight residual 111.11 121.23 -10.12 1.20e+00 6.94e-01 7.11e+01 angle pdb=" C19 KWT A6101 " pdb=" C3 KWT A6101 " pdb=" C2 KWT A6101 " ideal model delta sigma weight residual 134.33 110.62 23.71 3.00e+00 1.11e-01 6.25e+01 ... (remaining 40082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 16202 17.62 - 35.24: 1591 35.24 - 52.87: 277 52.87 - 70.49: 52 70.49 - 88.11: 21 Dihedral angle restraints: 18143 sinusoidal: 7386 harmonic: 10757 Sorted by residual: dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA LEU A3480 " pdb=" C LEU A3480 " pdb=" N SER A3481 " pdb=" CA SER A3481 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR A3315 " pdb=" C TYR A3315 " pdb=" N LEU A3316 " pdb=" CA LEU A3316 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4367 0.095 - 0.189: 194 0.189 - 0.284: 4 0.284 - 0.379: 1 0.379 - 0.473: 3 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C13 KWT A6101 " pdb=" C12 KWT A6101 " pdb=" C15 KWT A6101 " pdb=" C18 KWT A6101 " both_signs ideal model delta sigma weight residual False -2.69 -3.16 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA MET A3483 " pdb=" N MET A3483 " pdb=" C MET A3483 " pdb=" CB MET A3483 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C9 KWT A6101 " pdb=" C1 KWT A6101 " pdb=" C4 KWT A6101 " pdb=" C8 KWT A6101 " both_signs ideal model delta sigma weight residual False -2.55 -2.96 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 4566 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 KWT A6101 " 0.418 2.00e-02 2.50e+03 2.69e-01 1.45e+03 pdb=" C2 KWT A6101 " -0.512 2.00e-02 2.50e+03 pdb=" C3 KWT A6101 " 0.070 2.00e-02 2.50e+03 pdb=" C4 KWT A6101 " 0.091 2.00e-02 2.50e+03 pdb=" C5 KWT A6101 " -0.056 2.00e-02 2.50e+03 pdb=" C6 KWT A6101 " -0.045 2.00e-02 2.50e+03 pdb=" C9 KWT A6101 " 0.264 2.00e-02 2.50e+03 pdb=" O5 KWT A6101 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A3727 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C THR A3727 " 0.075 2.00e-02 2.50e+03 pdb=" O THR A3727 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A3728 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1409 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A1410 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1410 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1410 " 0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 415 2.65 - 3.21: 29220 3.21 - 3.78: 44257 3.78 - 4.34: 60171 4.34 - 4.90: 97999 Nonbonded interactions: 232062 Sorted by model distance: nonbonded pdb=" OG1 THR A3809 " pdb=" CE MET A3929 " model vdw 2.090 3.460 nonbonded pdb=" CB THR A3809 " pdb=" CE MET A3929 " model vdw 2.161 3.890 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.198 3.120 nonbonded pdb=" O GLU A 203 " pdb=" OG1 THR A 206 " model vdw 2.198 3.040 nonbonded pdb=" O ALA A2796 " pdb=" NH1 ARG A2800 " model vdw 2.209 3.120 ... (remaining 232057 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=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 : 0.012 1.757 29637 Z= 0.601 Angle : 0.785 37.482 40087 Z= 0.399 Chirality : 0.047 0.473 4569 Planarity : 0.005 0.269 5088 Dihedral : 14.389 88.111 11131 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 0.34 % Allowed : 0.31 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3602 helix: -0.04 (0.11), residues: 2316 sheet: -1.08 (0.70), residues: 47 loop : -2.13 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3696 TYR 0.025 0.002 TYR A2412 PHE 0.019 0.001 PHE A 147 TRP 0.023 0.001 TRP A3686 HIS 0.011 0.001 HIS A2105 Details of bonding type rmsd covalent geometry : bond 0.01190 (29636) covalent geometry : angle 0.78476 (40087) hydrogen bonds : bond 0.16220 ( 1480) hydrogen bonds : angle 6.18571 ( 4359) Misc. bond : bond 0.26539 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 742 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.2576 (mpp) cc_final: 0.1799 (mtp) REVERT: A 294 PHE cc_start: 0.6950 (t80) cc_final: 0.6673 (t80) REVERT: A 326 MET cc_start: 0.6174 (ptp) cc_final: 0.4497 (ptt) REVERT: A 338 LEU cc_start: 0.7679 (pp) cc_final: 0.7458 (pp) REVERT: A 413 PHE cc_start: 0.6588 (m-80) cc_final: 0.6092 (m-80) REVERT: A 441 MET cc_start: 0.6320 (tmm) cc_final: 0.5561 (tpp) REVERT: A 718 MET cc_start: 0.7735 (ptm) cc_final: 0.7170 (ppp) REVERT: A 785 MET cc_start: 0.7801 (mmm) cc_final: 0.7296 (tpt) REVERT: A 884 VAL cc_start: 0.7423 (t) cc_final: 0.7177 (p) REVERT: A 1009 LEU cc_start: 0.8892 (mm) cc_final: 0.8532 (mt) REVERT: A 1209 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8414 (tptt) REVERT: A 1258 ASP cc_start: 0.8431 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1332 TYR cc_start: 0.7558 (t80) cc_final: 0.7217 (t80) REVERT: A 1567 ILE cc_start: 0.7588 (mt) cc_final: 0.7279 (tt) REVERT: A 1606 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7391 (ttp-110) REVERT: A 1672 PHE cc_start: 0.7698 (t80) cc_final: 0.7448 (t80) REVERT: A 1673 THR cc_start: 0.8626 (p) cc_final: 0.8423 (t) REVERT: A 1940 TYR cc_start: 0.6757 (t80) cc_final: 0.6271 (t80) REVERT: A 2097 LEU cc_start: 0.8094 (mt) cc_final: 0.7839 (mt) REVERT: A 2251 ILE cc_start: 0.7518 (mp) cc_final: 0.7257 (mp) REVERT: A 2253 TYR cc_start: 0.6804 (m-80) cc_final: 0.6599 (m-80) REVERT: A 2437 ASP cc_start: 0.7591 (t0) cc_final: 0.7310 (m-30) REVERT: A 2877 SER cc_start: 0.8223 (m) cc_final: 0.7978 (p) REVERT: A 2935 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 3089 LEU cc_start: 0.8666 (tp) cc_final: 0.8087 (tp) REVERT: A 3173 MET cc_start: 0.7751 (tpt) cc_final: 0.7529 (tpp) REVERT: A 3183 ILE cc_start: 0.7837 (mm) cc_final: 0.7486 (mm) REVERT: A 3244 ASP cc_start: 0.7776 (m-30) cc_final: 0.7324 (m-30) REVERT: A 3414 MET cc_start: 0.6985 (mmm) cc_final: 0.6703 (mmm) REVERT: A 3761 ASP cc_start: 0.7450 (t0) cc_final: 0.7101 (m-30) REVERT: A 3932 MET cc_start: 0.7890 (mtm) cc_final: 0.7538 (mmm) REVERT: A 3940 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.6333 (pt) outliers start: 11 outliers final: 2 residues processed: 748 average time/residue: 0.2053 time to fit residues: 236.5296 Evaluate side-chains 393 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3753 LYS Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3940 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 533 HIS A 753 GLN A 857 GLN A1374 GLN A1477 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1613 HIS A1946 ASN A2305 ASN A2456 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3390 GLN ** A3501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 GLN A3580 ASN A3766 GLN A4088 ASN A4110 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.173488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.145922 restraints weight = 60222.110| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 3.76 r_work: 0.3861 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29637 Z= 0.146 Angle : 0.701 13.547 40087 Z= 0.351 Chirality : 0.043 0.398 4569 Planarity : 0.005 0.053 5088 Dihedral : 5.216 54.636 4001 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.80 % Favored : 93.06 % Rotamer: Outliers : 1.88 % Allowed : 10.51 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3602 helix: 0.25 (0.11), residues: 2331 sheet: -0.71 (0.70), residues: 52 loop : -1.99 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2158 TYR 0.021 0.002 TYR A3540 PHE 0.019 0.002 PHE A3952 TRP 0.021 0.001 TRP A4124 HIS 0.008 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00319 (29636) covalent geometry : angle 0.70103 (40087) hydrogen bonds : bond 0.04216 ( 1480) hydrogen bonds : angle 4.43687 ( 4359) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 414 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.7594 (mp0) cc_final: 0.6933 (pm20) REVERT: A 343 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 441 MET cc_start: 0.7254 (tmm) cc_final: 0.6271 (tpp) REVERT: A 453 MET cc_start: 0.7861 (tpp) cc_final: 0.7515 (tpp) REVERT: A 551 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.4215 (m-80) REVERT: A 1209 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8305 (tptt) REVERT: A 1213 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7614 (ptpp) REVERT: A 1258 ASP cc_start: 0.8434 (m-30) cc_final: 0.8176 (m-30) REVERT: A 1332 TYR cc_start: 0.7719 (t80) cc_final: 0.7400 (t80) REVERT: A 1408 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7282 (ptp) REVERT: A 1567 ILE cc_start: 0.7718 (mt) cc_final: 0.7290 (tt) REVERT: A 1743 MET cc_start: 0.6795 (mmm) cc_final: 0.6588 (tpp) REVERT: A 1758 LEU cc_start: 0.8010 (tp) cc_final: 0.7708 (tp) REVERT: A 1774 MET cc_start: 0.6148 (tpp) cc_final: 0.5471 (mmm) REVERT: A 2126 MET cc_start: 0.5912 (ppp) cc_final: 0.5499 (ppp) REVERT: A 2185 MET cc_start: 0.7925 (tpt) cc_final: 0.7454 (mtt) REVERT: A 2251 ILE cc_start: 0.8091 (mp) cc_final: 0.7823 (mp) REVERT: A 2253 TYR cc_start: 0.7813 (m-80) cc_final: 0.7038 (m-80) REVERT: A 2301 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8227 (tp-100) REVERT: A 2321 GLU cc_start: 0.8837 (tp30) cc_final: 0.8493 (mm-30) REVERT: A 2437 ASP cc_start: 0.8258 (t0) cc_final: 0.7818 (m-30) REVERT: A 2459 VAL cc_start: 0.6696 (t) cc_final: 0.6422 (m) REVERT: A 2473 MET cc_start: 0.7979 (tmm) cc_final: 0.7714 (tmm) REVERT: A 2493 ASN cc_start: 0.8254 (m-40) cc_final: 0.7943 (p0) REVERT: A 3145 ILE cc_start: 0.8600 (tp) cc_final: 0.8331 (tp) REVERT: A 3244 ASP cc_start: 0.7839 (m-30) cc_final: 0.7396 (m-30) REVERT: A 3669 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5919 (pptt) REVERT: A 3670 MET cc_start: 0.6825 (mtp) cc_final: 0.6194 (tpt) REVERT: A 3820 MET cc_start: 0.6896 (mtt) cc_final: 0.6579 (mtt) outliers start: 60 outliers final: 29 residues processed: 456 average time/residue: 0.1804 time to fit residues: 132.5717 Evaluate side-chains 363 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 330 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2163 HIS Chi-restraints excluded: chain A residue 2385 LEU Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2477 LEU Chi-restraints excluded: chain A residue 3669 LYS Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 3940 ILE Chi-restraints excluded: chain A residue 4058 VAL Chi-restraints excluded: chain A residue 4110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 361 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 159 optimal weight: 0.0070 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 HIS A1146 ASN A1175 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2807 GLN A2865 HIS A3390 GLN A3422 GLN ** A3501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3766 GLN A4110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.167571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.134407 restraints weight = 58887.169| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.42 r_work: 0.3742 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29637 Z= 0.166 Angle : 0.674 12.097 40087 Z= 0.339 Chirality : 0.042 0.308 4569 Planarity : 0.005 0.055 5088 Dihedral : 4.959 51.582 3997 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 2.07 % Allowed : 13.64 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3602 helix: 0.33 (0.11), residues: 2332 sheet: -0.39 (0.73), residues: 52 loop : -1.93 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2452 TYR 0.029 0.002 TYR A1802 PHE 0.038 0.002 PHE A 341 TRP 0.023 0.002 TRP A3842 HIS 0.008 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00373 (29636) covalent geometry : angle 0.67384 (40087) hydrogen bonds : bond 0.03882 ( 1480) hydrogen bonds : angle 4.27256 ( 4359) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 368 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 PHE cc_start: 0.7863 (m-80) cc_final: 0.7241 (m-80) REVERT: A 343 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 441 MET cc_start: 0.7751 (tmm) cc_final: 0.6909 (tpp) REVERT: A 453 MET cc_start: 0.7969 (tpp) cc_final: 0.7661 (tpp) REVERT: A 567 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 1258 ASP cc_start: 0.8391 (m-30) cc_final: 0.8044 (m-30) REVERT: A 1332 TYR cc_start: 0.7817 (t80) cc_final: 0.7452 (t80) REVERT: A 1408 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7272 (ptp) REVERT: A 1592 MET cc_start: 0.7935 (tpp) cc_final: 0.7631 (tpp) REVERT: A 1643 MET cc_start: 0.7763 (mtp) cc_final: 0.7518 (mtp) REVERT: A 1758 LEU cc_start: 0.8045 (tp) cc_final: 0.7743 (tp) REVERT: A 1774 MET cc_start: 0.6661 (tpp) cc_final: 0.6230 (mmm) REVERT: A 1804 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.3998 (ptt) REVERT: A 1940 TYR cc_start: 0.7514 (t80) cc_final: 0.6490 (t80) REVERT: A 2185 MET cc_start: 0.7892 (tpt) cc_final: 0.7301 (mtt) REVERT: A 2188 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8369 (pt0) REVERT: A 2253 TYR cc_start: 0.7965 (m-80) cc_final: 0.7398 (m-80) REVERT: A 2301 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8133 (tp-100) REVERT: A 2321 GLU cc_start: 0.8851 (tp30) cc_final: 0.8623 (tp30) REVERT: A 2437 ASP cc_start: 0.8205 (t0) cc_final: 0.7688 (m-30) REVERT: A 3089 LEU cc_start: 0.8599 (tp) cc_final: 0.8343 (mt) REVERT: A 3145 ILE cc_start: 0.8691 (tp) cc_final: 0.8372 (tp) REVERT: A 3820 MET cc_start: 0.7060 (mtt) cc_final: 0.6743 (mtt) REVERT: A 3924 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7259 (p90) REVERT: A 4020 MET cc_start: 0.5975 (mmm) cc_final: 0.5654 (mmm) outliers start: 66 outliers final: 40 residues processed: 409 average time/residue: 0.1875 time to fit residues: 124.7820 Evaluate side-chains 353 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1489 LYS Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1804 MET Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2163 HIS Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2385 LEU Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2492 ASP Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2992 ASP Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3180 ASP Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3530 VAL Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3924 HIS Chi-restraints excluded: chain A residue 3985 VAL Chi-restraints excluded: chain A residue 3998 LEU Chi-restraints excluded: chain A residue 4058 VAL Chi-restraints excluded: chain A residue 4061 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 256 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 334 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 246 optimal weight: 0.0870 chunk 192 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 293 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 GLN A1238 GLN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3470 GLN A3501 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.168296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.135587 restraints weight = 58220.876| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.60 r_work: 0.3752 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29637 Z= 0.121 Angle : 0.631 15.389 40087 Z= 0.316 Chirality : 0.041 0.246 4569 Planarity : 0.004 0.049 5088 Dihedral : 4.786 53.882 3995 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 2.03 % Allowed : 15.11 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3602 helix: 0.42 (0.11), residues: 2347 sheet: -0.27 (0.72), residues: 52 loop : -1.87 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4082 TYR 0.029 0.001 TYR A 340 PHE 0.028 0.001 PHE A 341 TRP 0.023 0.001 TRP A3842 HIS 0.006 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00267 (29636) covalent geometry : angle 0.63113 (40087) hydrogen bonds : bond 0.03467 ( 1480) hydrogen bonds : angle 4.07618 ( 4359) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 342 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.7337 (ppp) cc_final: 0.6807 (ppp) REVERT: A 343 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 441 MET cc_start: 0.7706 (tmm) cc_final: 0.7081 (tpt) REVERT: A 567 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 779 TYR cc_start: 0.8083 (m-10) cc_final: 0.7853 (m-10) REVERT: A 788 TYR cc_start: 0.8199 (m-80) cc_final: 0.7826 (m-80) REVERT: A 1332 TYR cc_start: 0.7754 (t80) cc_final: 0.7401 (t80) REVERT: A 1408 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7270 (ptp) REVERT: A 1758 LEU cc_start: 0.7925 (tp) cc_final: 0.7670 (tp) REVERT: A 1774 MET cc_start: 0.6498 (tpp) cc_final: 0.5667 (mmm) REVERT: A 1940 TYR cc_start: 0.7465 (t80) cc_final: 0.6566 (t80) REVERT: A 2126 MET cc_start: 0.5933 (ppp) cc_final: 0.5450 (ppp) REVERT: A 2185 MET cc_start: 0.7923 (tpt) cc_final: 0.7217 (mtt) REVERT: A 2188 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8526 (pt0) REVERT: A 2253 TYR cc_start: 0.8022 (m-80) cc_final: 0.7433 (m-80) REVERT: A 2301 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8150 (tp-100) REVERT: A 2321 GLU cc_start: 0.8771 (tp30) cc_final: 0.8504 (tp30) REVERT: A 2437 ASP cc_start: 0.8164 (t0) cc_final: 0.7767 (m-30) REVERT: A 2568 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7008 (ptp) REVERT: A 2935 GLU cc_start: 0.7860 (mp0) cc_final: 0.7489 (mm-30) REVERT: A 3145 ILE cc_start: 0.8596 (tp) cc_final: 0.8262 (tp) REVERT: A 3242 MET cc_start: 0.8594 (mtp) cc_final: 0.8378 (mtp) REVERT: A 3244 ASP cc_start: 0.7899 (m-30) cc_final: 0.7545 (m-30) REVERT: A 3924 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7181 (p90) outliers start: 65 outliers final: 37 residues processed: 383 average time/residue: 0.1758 time to fit residues: 110.6343 Evaluate side-chains 343 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1303 MET Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1489 LYS Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 2163 HIS Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2385 LEU Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2477 LEU Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3636 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 3924 HIS Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 4061 CYS Chi-restraints excluded: chain A residue 4065 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 298 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 231 optimal weight: 0.0970 chunk 266 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 328 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 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 394 GLN A1477 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.167449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.135236 restraints weight = 58469.867| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.33 r_work: 0.3743 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29637 Z= 0.119 Angle : 0.620 14.813 40087 Z= 0.307 Chirality : 0.041 0.175 4569 Planarity : 0.004 0.048 5088 Dihedral : 4.630 47.846 3995 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.19 % Favored : 93.70 % Rotamer: Outliers : 2.57 % Allowed : 15.99 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3602 helix: 0.51 (0.11), residues: 2354 sheet: -0.19 (0.73), residues: 52 loop : -1.88 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 888 TYR 0.019 0.001 TYR A1558 PHE 0.020 0.001 PHE A 341 TRP 0.054 0.001 TRP A2196 HIS 0.006 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00266 (29636) covalent geometry : angle 0.61988 (40087) hydrogen bonds : bond 0.03325 ( 1480) hydrogen bonds : angle 4.01006 ( 4359) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 324 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7960 (mm-30) REVERT: A 441 MET cc_start: 0.7784 (tmm) cc_final: 0.7212 (tpt) REVERT: A 534 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 567 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 779 TYR cc_start: 0.8117 (m-10) cc_final: 0.7887 (m-10) REVERT: A 1332 TYR cc_start: 0.7755 (t80) cc_final: 0.7411 (t80) REVERT: A 1408 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7146 (ptp) REVERT: A 1668 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: A 1774 MET cc_start: 0.6762 (tpp) cc_final: 0.5976 (mmm) REVERT: A 1778 PHE cc_start: 0.7478 (m-10) cc_final: 0.6721 (m-10) REVERT: A 1878 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8134 (t70) REVERT: A 1940 TYR cc_start: 0.7436 (t80) cc_final: 0.6486 (t80) REVERT: A 1946 ASN cc_start: 0.8376 (m110) cc_final: 0.7925 (m110) REVERT: A 2126 MET cc_start: 0.6180 (ppp) cc_final: 0.5610 (ppp) REVERT: A 2185 MET cc_start: 0.7653 (tpt) cc_final: 0.6872 (mtt) REVERT: A 2188 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8217 (pt0) REVERT: A 2196 TRP cc_start: 0.7840 (m-90) cc_final: 0.7304 (m-90) REVERT: A 2253 TYR cc_start: 0.7971 (m-80) cc_final: 0.7520 (m-80) REVERT: A 2301 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8187 (tp-100) REVERT: A 2307 MET cc_start: 0.6604 (mtm) cc_final: 0.6353 (mpp) REVERT: A 2321 GLU cc_start: 0.8756 (tp30) cc_final: 0.8491 (tp30) REVERT: A 2437 ASP cc_start: 0.8113 (t0) cc_final: 0.7776 (m-30) REVERT: A 2459 VAL cc_start: 0.6973 (t) cc_final: 0.6645 (m) REVERT: A 2568 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7095 (ptp) REVERT: A 2935 GLU cc_start: 0.7982 (mp0) cc_final: 0.7616 (mm-30) REVERT: A 3182 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7711 (pt) REVERT: A 3924 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.7236 (p90) outliers start: 82 outliers final: 44 residues processed: 376 average time/residue: 0.1758 time to fit residues: 108.8288 Evaluate side-chains 347 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1477 HIS Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2163 HIS Chi-restraints excluded: chain A residue 2186 VAL Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2379 MET Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2992 ASP Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3924 HIS Chi-restraints excluded: chain A residue 3929 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 19 optimal weight: 30.0000 chunk 354 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.166881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.133967 restraints weight = 58197.967| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.34 r_work: 0.3732 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29637 Z= 0.121 Angle : 0.637 15.452 40087 Z= 0.311 Chirality : 0.041 0.277 4569 Planarity : 0.004 0.043 5088 Dihedral : 4.534 41.537 3995 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 2.10 % Allowed : 17.30 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3602 helix: 0.61 (0.11), residues: 2349 sheet: -0.19 (0.73), residues: 52 loop : -1.86 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4082 TYR 0.019 0.001 TYR A 340 PHE 0.019 0.001 PHE A 341 TRP 0.029 0.001 TRP A2196 HIS 0.008 0.001 HIS A1477 Details of bonding type rmsd covalent geometry : bond 0.00274 (29636) covalent geometry : angle 0.63716 (40087) hydrogen bonds : bond 0.03230 ( 1480) hydrogen bonds : angle 3.94625 ( 4359) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 441 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7402 (tpt) REVERT: A 567 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 984 TYR cc_start: 0.8063 (m-80) cc_final: 0.7631 (m-80) REVERT: A 1213 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7875 (ptpt) REVERT: A 1332 TYR cc_start: 0.7746 (t80) cc_final: 0.7407 (t80) REVERT: A 1408 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7130 (ptp) REVERT: A 1774 MET cc_start: 0.6748 (tpp) cc_final: 0.5998 (mmm) REVERT: A 1778 PHE cc_start: 0.7531 (m-10) cc_final: 0.6842 (m-10) REVERT: A 1804 MET cc_start: 0.5218 (ptt) cc_final: 0.4755 (ptt) REVERT: A 1878 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8226 (t70) REVERT: A 1938 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8756 (ttp-170) REVERT: A 1940 TYR cc_start: 0.7549 (t80) cc_final: 0.6761 (t80) REVERT: A 1946 ASN cc_start: 0.8509 (m110) cc_final: 0.8074 (m110) REVERT: A 2168 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7991 (pp) REVERT: A 2185 MET cc_start: 0.7817 (tpt) cc_final: 0.7116 (mtt) REVERT: A 2188 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8287 (pt0) REVERT: A 2254 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7011 (mmt180) REVERT: A 2301 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8166 (tp-100) REVERT: A 2321 GLU cc_start: 0.8713 (tp30) cc_final: 0.8390 (mm-30) REVERT: A 2459 VAL cc_start: 0.6966 (t) cc_final: 0.6625 (m) REVERT: A 2564 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 2568 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7073 (ptp) REVERT: A 2935 GLU cc_start: 0.8062 (mp0) cc_final: 0.7719 (mm-30) REVERT: A 3176 MET cc_start: 0.8312 (mmt) cc_final: 0.8110 (mmt) REVERT: A 3242 MET cc_start: 0.8525 (mtp) cc_final: 0.8088 (mtp) REVERT: A 3613 MET cc_start: 0.6009 (tmm) cc_final: 0.5611 (tmm) REVERT: A 3694 PHE cc_start: 0.4007 (OUTLIER) cc_final: 0.3532 (t80) REVERT: A 3883 LEU cc_start: 0.8899 (tp) cc_final: 0.8678 (mt) REVERT: A 3924 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.7130 (p90) outliers start: 67 outliers final: 44 residues processed: 357 average time/residue: 0.1710 time to fit residues: 101.1333 Evaluate side-chains 340 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1725 GLN Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 ARG Chi-restraints excluded: chain A residue 2168 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2379 MET Chi-restraints excluded: chain A residue 2395 THR Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2477 LEU Chi-restraints excluded: chain A residue 2493 ASN Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2992 ASP Chi-restraints excluded: chain A residue 3052 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3924 HIS Chi-restraints excluded: chain A residue 3929 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN A2954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.161921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121291 restraints weight = 57974.399| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.80 r_work: 0.3653 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29637 Z= 0.202 Angle : 0.706 13.960 40087 Z= 0.348 Chirality : 0.044 0.205 4569 Planarity : 0.005 0.056 5088 Dihedral : 4.763 36.750 3995 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.25 % Rotamer: Outliers : 2.47 % Allowed : 17.68 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3602 helix: 0.40 (0.11), residues: 2349 sheet: -0.64 (0.69), residues: 54 loop : -2.01 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2538 TYR 0.025 0.002 TYR A 984 PHE 0.037 0.002 PHE A2231 TRP 0.088 0.002 TRP A2196 HIS 0.008 0.001 HIS A1830 Details of bonding type rmsd covalent geometry : bond 0.00480 (29636) covalent geometry : angle 0.70585 (40087) hydrogen bonds : bond 0.03713 ( 1480) hydrogen bonds : angle 4.15686 ( 4359) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8415 (mm-30) REVERT: A 441 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7626 (tpt) REVERT: A 534 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 567 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 1108 MET cc_start: 0.8365 (mmm) cc_final: 0.8045 (mmm) REVERT: A 1408 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7183 (ptp) REVERT: A 1668 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: A 1774 MET cc_start: 0.7023 (tpp) cc_final: 0.6271 (mtp) REVERT: A 1778 PHE cc_start: 0.7809 (m-10) cc_final: 0.7332 (m-80) REVERT: A 1878 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 1940 TYR cc_start: 0.7732 (t80) cc_final: 0.7042 (t80) REVERT: A 1946 ASN cc_start: 0.8712 (m110) cc_final: 0.8458 (m-40) REVERT: A 2126 MET cc_start: 0.5867 (ppp) cc_final: 0.5501 (ppp) REVERT: A 2185 MET cc_start: 0.7801 (tpt) cc_final: 0.7154 (mtt) REVERT: A 2196 TRP cc_start: 0.8115 (m-90) cc_final: 0.7826 (m-90) REVERT: A 2236 GLU cc_start: 0.8045 (tp30) cc_final: 0.7840 (tt0) REVERT: A 2301 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8196 (tp-100) REVERT: A 2307 MET cc_start: 0.6718 (mtm) cc_final: 0.6296 (mpp) REVERT: A 2321 GLU cc_start: 0.8710 (tp30) cc_final: 0.8193 (mm-30) REVERT: A 2564 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 2935 GLU cc_start: 0.8092 (mp0) cc_final: 0.7824 (mm-30) REVERT: A 3145 ILE cc_start: 0.8660 (tp) cc_final: 0.8412 (tp) REVERT: A 3613 MET cc_start: 0.6045 (tmm) cc_final: 0.5761 (tmm) REVERT: A 3694 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.4036 (t80) outliers start: 79 outliers final: 51 residues processed: 360 average time/residue: 0.1749 time to fit residues: 103.8516 Evaluate side-chains 344 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1537 VAL Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1564 SER Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1725 GLN Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2379 MET Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2493 ASN Chi-restraints excluded: chain A residue 2564 GLU Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3052 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3177 ASN Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3193 ILE Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3929 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 217 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 246 optimal weight: 0.0370 chunk 248 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 318 optimal weight: 0.0470 chunk 120 optimal weight: 8.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1426 GLN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2152 ASN A3527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.164869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.125645 restraints weight = 57723.384| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.02 r_work: 0.3701 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29637 Z= 0.116 Angle : 0.657 14.873 40087 Z= 0.319 Chirality : 0.041 0.166 4569 Planarity : 0.004 0.040 5088 Dihedral : 4.550 28.939 3995 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 1.88 % Allowed : 19.12 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3602 helix: 0.65 (0.11), residues: 2333 sheet: -0.46 (0.70), residues: 54 loop : -1.93 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2538 TYR 0.031 0.001 TYR A2253 PHE 0.039 0.001 PHE A 345 TRP 0.045 0.001 TRP A2196 HIS 0.006 0.001 HIS A1830 Details of bonding type rmsd covalent geometry : bond 0.00256 (29636) covalent geometry : angle 0.65722 (40087) hydrogen bonds : bond 0.03231 ( 1480) hydrogen bonds : angle 3.99136 ( 4359) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 330 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7867 (pp) REVERT: A 343 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 441 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7535 (tpt) REVERT: A 534 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8489 (mt) REVERT: A 567 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 779 TYR cc_start: 0.8070 (m-10) cc_final: 0.7867 (m-10) REVERT: A 1213 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7266 (mmpt) REVERT: A 1270 PHE cc_start: 0.8348 (m-80) cc_final: 0.7683 (m-80) REVERT: A 1274 ARG cc_start: 0.7220 (mmt-90) cc_final: 0.6879 (tpp-160) REVERT: A 1408 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7120 (ptp) REVERT: A 1607 GLU cc_start: 0.7959 (tp30) cc_final: 0.7744 (tp30) REVERT: A 1668 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: A 1738 ASN cc_start: 0.8589 (m110) cc_final: 0.8384 (m-40) REVERT: A 1774 MET cc_start: 0.6969 (tpp) cc_final: 0.6383 (mmm) REVERT: A 1778 PHE cc_start: 0.7838 (m-10) cc_final: 0.7500 (m-80) REVERT: A 1804 MET cc_start: 0.4834 (ptt) cc_final: 0.4510 (ptt) REVERT: A 1878 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8092 (t70) REVERT: A 1938 ARG cc_start: 0.8842 (ttp-170) cc_final: 0.8546 (ttp-170) REVERT: A 1940 TYR cc_start: 0.7964 (t80) cc_final: 0.7233 (t80) REVERT: A 1946 ASN cc_start: 0.8637 (m110) cc_final: 0.8420 (m-40) REVERT: A 2126 MET cc_start: 0.5731 (ppp) cc_final: 0.5246 (ppp) REVERT: A 2185 MET cc_start: 0.8043 (tpt) cc_final: 0.7239 (mtt) REVERT: A 2254 ARG cc_start: 0.7614 (mmt180) cc_final: 0.7192 (mmt180) REVERT: A 2301 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8141 (tp-100) REVERT: A 2307 MET cc_start: 0.6726 (mtm) cc_final: 0.6513 (mpp) REVERT: A 2321 GLU cc_start: 0.8753 (tp30) cc_final: 0.8225 (mm-30) REVERT: A 2459 VAL cc_start: 0.7019 (t) cc_final: 0.6659 (m) REVERT: A 2564 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 2568 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7387 (ptp) REVERT: A 2935 GLU cc_start: 0.8061 (mp0) cc_final: 0.7789 (mm-30) REVERT: A 3145 ILE cc_start: 0.8622 (tp) cc_final: 0.8362 (tp) REVERT: A 3244 ASP cc_start: 0.7944 (m-30) cc_final: 0.7594 (m-30) REVERT: A 3694 PHE cc_start: 0.4082 (OUTLIER) cc_final: 0.3657 (t80) outliers start: 60 outliers final: 37 residues processed: 368 average time/residue: 0.1852 time to fit residues: 111.0253 Evaluate side-chains 347 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1725 GLN Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2379 MET Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2493 ASN Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3052 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3850 HIS Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 4108 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 285 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 254 optimal weight: 0.9990 chunk 190 optimal weight: 0.0670 chunk 196 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 GLN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.161250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.121622 restraints weight = 57621.970| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.11 r_work: 0.3608 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29637 Z= 0.187 Angle : 0.717 15.152 40087 Z= 0.349 Chirality : 0.043 0.223 4569 Planarity : 0.004 0.050 5088 Dihedral : 4.650 29.444 3995 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 1.78 % Allowed : 19.40 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3602 helix: 0.46 (0.11), residues: 2363 sheet: -0.74 (0.70), residues: 54 loop : -1.93 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4082 TYR 0.033 0.002 TYR A2253 PHE 0.027 0.002 PHE A 345 TRP 0.043 0.002 TRP A3842 HIS 0.006 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00442 (29636) covalent geometry : angle 0.71736 (40087) hydrogen bonds : bond 0.03548 ( 1480) hydrogen bonds : angle 4.11784 ( 4359) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 303 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 343 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 441 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7655 (tpt) REVERT: A 534 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 567 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 779 TYR cc_start: 0.8231 (m-10) cc_final: 0.7994 (m-10) REVERT: A 1108 MET cc_start: 0.8405 (mmm) cc_final: 0.8058 (mmm) REVERT: A 1213 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7281 (mmpt) REVERT: A 1270 PHE cc_start: 0.8366 (m-80) cc_final: 0.7792 (m-80) REVERT: A 1408 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7182 (ptp) REVERT: A 1668 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: A 1738 ASN cc_start: 0.8489 (m110) cc_final: 0.8271 (m-40) REVERT: A 1774 MET cc_start: 0.6917 (tpp) cc_final: 0.6579 (mtp) REVERT: A 1804 MET cc_start: 0.4867 (ptt) cc_final: 0.4510 (ptt) REVERT: A 1878 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8143 (t70) REVERT: A 1938 ARG cc_start: 0.8850 (ttp-170) cc_final: 0.8539 (ttp-170) REVERT: A 1940 TYR cc_start: 0.7998 (t80) cc_final: 0.7612 (t80) REVERT: A 1946 ASN cc_start: 0.8757 (m110) cc_final: 0.8547 (m-40) REVERT: A 2126 MET cc_start: 0.5993 (ppp) cc_final: 0.5550 (ppp) REVERT: A 2149 LEU cc_start: 0.8660 (tp) cc_final: 0.8120 (mp) REVERT: A 2196 TRP cc_start: 0.7654 (m-90) cc_final: 0.7406 (m-90) REVERT: A 2254 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7237 (mmt180) REVERT: A 2321 GLU cc_start: 0.8764 (tp30) cc_final: 0.8249 (mm-30) REVERT: A 2379 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5778 (mpp) REVERT: A 2564 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: A 2576 MET cc_start: 0.3835 (ptt) cc_final: 0.3536 (ptt) REVERT: A 2935 GLU cc_start: 0.8066 (mp0) cc_final: 0.7796 (mm-30) REVERT: A 3145 ILE cc_start: 0.8741 (tp) cc_final: 0.8481 (tp) REVERT: A 3244 ASP cc_start: 0.8145 (m-30) cc_final: 0.7825 (m-30) REVERT: A 3613 MET cc_start: 0.6117 (tmm) cc_final: 0.5847 (tmm) REVERT: A 3694 PHE cc_start: 0.4547 (OUTLIER) cc_final: 0.4055 (t80) REVERT: A 4041 ARG cc_start: 0.6948 (tmt170) cc_final: 0.6408 (ptm160) outliers start: 57 outliers final: 38 residues processed: 339 average time/residue: 0.1824 time to fit residues: 101.8957 Evaluate side-chains 333 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1668 PHE Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2379 MET Chi-restraints excluded: chain A residue 2493 ASN Chi-restraints excluded: chain A residue 2564 GLU Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3052 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3230 LEU Chi-restraints excluded: chain A residue 3231 ILE Chi-restraints excluded: chain A residue 3300 VAL Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3692 VAL Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3806 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 4108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 332 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 228 optimal weight: 0.2980 chunk 339 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.163431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.129919 restraints weight = 57689.733| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.54 r_work: 0.3668 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29637 Z= 0.122 Angle : 0.678 16.017 40087 Z= 0.327 Chirality : 0.041 0.181 4569 Planarity : 0.004 0.040 5088 Dihedral : 4.523 29.568 3995 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 1.50 % Allowed : 19.96 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3602 helix: 0.62 (0.11), residues: 2351 sheet: -0.73 (0.70), residues: 54 loop : -1.85 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4082 TYR 0.033 0.001 TYR A2253 PHE 0.029 0.001 PHE A 345 TRP 0.042 0.002 TRP A3842 HIS 0.005 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00277 (29636) covalent geometry : angle 0.67767 (40087) hydrogen bonds : bond 0.03248 ( 1480) hydrogen bonds : angle 4.02006 ( 4359) Misc. bond : bond 0.00066 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7912 (pp) REVERT: A 343 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8388 (mm-30) REVERT: A 534 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 567 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 779 TYR cc_start: 0.8171 (m-10) cc_final: 0.7921 (m-10) REVERT: A 984 TYR cc_start: 0.8182 (m-80) cc_final: 0.7768 (m-80) REVERT: A 1108 MET cc_start: 0.8210 (mmm) cc_final: 0.7653 (mmm) REVERT: A 1213 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7371 (mmpt) REVERT: A 1270 PHE cc_start: 0.8268 (m-80) cc_final: 0.7659 (m-80) REVERT: A 1274 ARG cc_start: 0.7404 (mmt-90) cc_final: 0.7102 (tpp-160) REVERT: A 1369 MET cc_start: 0.8803 (mmm) cc_final: 0.8170 (mpp) REVERT: A 1408 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7130 (ptp) REVERT: A 1484 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7128 (mm) REVERT: A 1774 MET cc_start: 0.6779 (tpp) cc_final: 0.6451 (mtp) REVERT: A 1804 MET cc_start: 0.4966 (ptt) cc_final: 0.4639 (ptt) REVERT: A 1878 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8232 (t70) REVERT: A 1938 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8583 (ttp-170) REVERT: A 1940 TYR cc_start: 0.7978 (t80) cc_final: 0.7613 (t80) REVERT: A 1946 ASN cc_start: 0.8655 (m110) cc_final: 0.8416 (m-40) REVERT: A 2126 MET cc_start: 0.5940 (ppp) cc_final: 0.5539 (ppp) REVERT: A 2149 LEU cc_start: 0.8645 (tp) cc_final: 0.8206 (mp) REVERT: A 2185 MET cc_start: 0.7944 (tpt) cc_final: 0.7302 (mtt) REVERT: A 2321 GLU cc_start: 0.8702 (tp30) cc_final: 0.8174 (mm-30) REVERT: A 2576 MET cc_start: 0.3700 (ptt) cc_final: 0.3439 (ptt) REVERT: A 2935 GLU cc_start: 0.8163 (mp0) cc_final: 0.7889 (mm-30) REVERT: A 3145 ILE cc_start: 0.8683 (tp) cc_final: 0.8421 (tp) REVERT: A 3240 MET cc_start: 0.8918 (mmm) cc_final: 0.8631 (mmp) REVERT: A 3244 ASP cc_start: 0.8085 (m-30) cc_final: 0.7725 (m-30) REVERT: A 3694 PHE cc_start: 0.4187 (OUTLIER) cc_final: 0.3713 (t80) REVERT: A 4041 ARG cc_start: 0.6869 (tmt170) cc_final: 0.6294 (ptm160) outliers start: 48 outliers final: 30 residues processed: 331 average time/residue: 0.1791 time to fit residues: 98.1172 Evaluate side-chains 325 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1213 LYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1423 ILE Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1721 HIS Chi-restraints excluded: chain A residue 1742 CYS Chi-restraints excluded: chain A residue 1793 THR Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2351 GLN Chi-restraints excluded: chain A residue 2442 MET Chi-restraints excluded: chain A residue 2493 ASN Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3424 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3692 VAL Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3700 GLU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 4108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 241 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 325 optimal weight: 1.9990 chunk 165 optimal weight: 0.0770 chunk 264 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 255 optimal weight: 0.5980 chunk 283 optimal weight: 7.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 HIS ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.130561 restraints weight = 58087.236| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.38 r_work: 0.3682 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29637 Z= 0.117 Angle : 0.676 16.020 40087 Z= 0.326 Chirality : 0.041 0.246 4569 Planarity : 0.004 0.040 5088 Dihedral : 4.411 26.948 3993 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 1.22 % Allowed : 20.09 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3602 helix: 0.67 (0.11), residues: 2353 sheet: -0.66 (0.69), residues: 54 loop : -1.87 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4082 TYR 0.043 0.001 TYR A1881 PHE 0.028 0.001 PHE A 345 TRP 0.047 0.002 TRP A3842 HIS 0.005 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00261 (29636) covalent geometry : angle 0.67598 (40087) hydrogen bonds : bond 0.03201 ( 1480) hydrogen bonds : angle 3.99505 ( 4359) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8170.58 seconds wall clock time: 140 minutes 19.96 seconds (8419.96 seconds total)