Starting phenix.real_space_refine on Wed May 14 10:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.map" model { file = "/net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy5_36720/05_2025/8jy5_36720.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.044 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 58 5.16 5 C 7448 2.51 5 N 1908 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11511 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1457, 11511 Classifications: {'peptide': 1457} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1412} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.51, per 1000 atoms: 0.57 Number of scatterers: 11511 At special positions: 0 Unit cell: (94.16, 123.05, 160.5, 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 58 16.00 O 2097 8.00 N 1908 7.00 C 7448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 69.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.567A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.617A pdb=" N GLU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 33 through 54 removed outlier: 3.584A pdb=" N LEU A 43 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.700A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 removed outlier: 3.653A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.976A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.901A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 removed outlier: 4.087A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.535A pdb=" N ILE A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.891A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.538A pdb=" N ILE A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.981A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 352 removed outlier: 6.932A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 4.023A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 405 removed outlier: 4.220A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.672A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.768A pdb=" N MET A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 removed outlier: 4.291A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 4.067A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.128A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.548A pdb=" N PHE A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 568 removed outlier: 3.597A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Proline residue: A 554 - end of helix removed outlier: 3.549A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 595 removed outlier: 4.126A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 595 through 618 removed outlier: 3.500A pdb=" N MET A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.786A pdb=" N ILE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.601A pdb=" N GLN A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 844 through 852 removed outlier: 3.567A pdb=" N LYS A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.716A pdb=" N LYS A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.643A pdb=" N ILE A 894 " --> pdb=" O VAL A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 914 removed outlier: 3.581A pdb=" N MET A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 906 " --> pdb=" O THR A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 974 removed outlier: 3.519A pdb=" N ILE A 974 " --> pdb=" O TYR A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.625A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1005 " --> pdb=" O SER A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 Processing helix chain 'A' and resid 1022 through 1065 removed outlier: 3.591A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A1047 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.522A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1092 removed outlier: 4.086A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A1087 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1120 removed outlier: 4.150A pdb=" N GLN A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1100 " --> pdb=" O PRO A1096 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1168 removed outlier: 3.818A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.527A pdb=" N ARG A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.573A pdb=" N SER A1168 " --> pdb=" O SER A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 3.602A pdb=" N ALA A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.541A pdb=" N ASP A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A1197 " --> pdb=" O ASN A1193 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A1213 " --> pdb=" O ILE A1209 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1217 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1224 " --> pdb=" O PHE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1244 removed outlier: 4.016A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.738A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.581A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1424 through 1427 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 Processing helix chain 'A' and resid 1468 through 1483 removed outlier: 3.570A pdb=" N ILE A1479 " --> pdb=" O ILE A1475 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1480 " --> pdb=" O GLN A1476 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A1481 " --> pdb=" O THR A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1535 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.784A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 693 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 641 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 695 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 639 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 697 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 637 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.784A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 693 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 641 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 695 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 639 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 697 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 637 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.755A pdb=" N ASP A 785 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 782 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL A 818 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 784 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 667 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 833 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 714 removed outlier: 4.063A pdb=" N GLY A 713 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1315 through 1320 removed outlier: 5.781A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1315 through 1320 removed outlier: 5.781A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 4.151A pdb=" N ASP A1461 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1389 through 1390 669 hydrogen bonds defined for protein. 1941 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: 4.59 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3650 1.34 - 1.46: 2731 1.46 - 1.58: 5275 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11752 Sorted by residual: bond pdb=" C SER A 339 " pdb=" N PRO A 340 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.45e+00 bond pdb=" C ASN A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.35e+00 bond pdb=" N ASP A 656 " pdb=" CA ASP A 656 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" CA THR A 873 " pdb=" CB THR A 873 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.49e-02 4.50e+03 1.50e+00 bond pdb=" CA PRO A1384 " pdb=" C PRO A1384 " ideal model delta sigma weight residual 1.527 1.514 0.013 1.07e-02 8.73e+03 1.47e+00 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15544 1.80 - 3.59: 316 3.59 - 5.39: 62 5.39 - 7.19: 15 7.19 - 8.99: 3 Bond angle restraints: 15940 Sorted by residual: angle pdb=" C ASP A 22 " pdb=" N LEU A 23 " pdb=" CA LEU A 23 " ideal model delta sigma weight residual 120.65 125.99 -5.34 1.36e+00 5.41e-01 1.54e+01 angle pdb=" C VAL A 229 " pdb=" N ASP A 230 " pdb=" CA ASP A 230 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N SER A 462 " pdb=" CA SER A 462 " pdb=" C SER A 462 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.25e+01 angle pdb=" CA MET A 988 " pdb=" CB MET A 988 " pdb=" CG MET A 988 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C SER A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta sigma weight residual 122.26 116.35 5.91 1.73e+00 3.34e-01 1.17e+01 ... (remaining 15935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6349 17.82 - 35.64: 542 35.64 - 53.46: 91 53.46 - 71.28: 17 71.28 - 89.10: 8 Dihedral angle restraints: 7007 sinusoidal: 2760 harmonic: 4247 Sorted by residual: dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N MET A 438 " pdb=" CA MET A 438 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 26 " pdb=" CB CYS A 26 " ideal model delta sinusoidal sigma weight residual 93.00 63.78 29.22 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CA ARG A1349 " pdb=" C ARG A1349 " pdb=" N ILE A1350 " pdb=" CA ILE A1350 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 7004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1596 0.056 - 0.112: 241 0.112 - 0.168: 26 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CB ILE A 894 " pdb=" CA ILE A 894 " pdb=" CG1 ILE A 894 " pdb=" CG2 ILE A 894 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA THR A 553 " pdb=" N THR A 553 " pdb=" C THR A 553 " pdb=" CB THR A 553 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU A1170 " pdb=" CB LEU A1170 " pdb=" CD1 LEU A1170 " pdb=" CD2 LEU A1170 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 1863 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1383 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO A1384 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1384 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1384 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 442 " -0.007 2.00e-02 2.50e+03 1.26e-02 3.97e+00 pdb=" CG TRP A 442 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 442 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 442 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 442 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 442 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 442 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 442 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 474 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 475 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.022 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 189 2.68 - 3.23: 12561 3.23 - 3.79: 18320 3.79 - 4.34: 24736 4.34 - 4.90: 37678 Nonbonded interactions: 93484 Sorted by model distance: nonbonded pdb=" NE2 GLN A 767 " pdb=" O ASP A 786 " model vdw 2.119 3.120 nonbonded pdb=" OG SER A1234 " pdb=" OD1 ASP A1236 " model vdw 2.194 3.040 nonbonded pdb=" OD2 ASP A 786 " pdb=" OG SER A 789 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" O SER A1199 " model vdw 2.228 3.040 nonbonded pdb=" ND2 ASN A 409 " pdb=" O GLU A 687 " model vdw 2.235 3.120 ... (remaining 93479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 28.600 Find NCS groups from input model: 0.270 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11753 Z= 0.136 Angle : 0.656 8.987 15942 Z= 0.361 Chirality : 0.041 0.280 1866 Planarity : 0.004 0.073 1988 Dihedral : 13.663 89.097 4250 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1451 helix: 0.20 (0.17), residues: 874 sheet: 0.74 (0.53), residues: 86 loop : -0.22 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 442 HIS 0.004 0.001 HIS A1496 PHE 0.014 0.001 PHE A 981 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG A1257 Details of bonding type rmsd hydrogen bonds : bond 0.27538 ( 664) hydrogen bonds : angle 8.06349 ( 1941) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.63809 ( 2) covalent geometry : bond 0.00270 (11752) covalent geometry : angle 0.65610 (15940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9437 (tt) cc_final: 0.9093 (tp) REVERT: A 140 ILE cc_start: 0.9445 (mt) cc_final: 0.9159 (tp) REVERT: A 363 CYS cc_start: 0.8757 (m) cc_final: 0.7965 (t) REVERT: A 446 LEU cc_start: 0.9388 (tp) cc_final: 0.9078 (tp) REVERT: A 450 LEU cc_start: 0.9403 (tt) cc_final: 0.8876 (tp) REVERT: A 559 VAL cc_start: 0.9589 (t) cc_final: 0.9122 (t) REVERT: A 583 ILE cc_start: 0.9379 (pt) cc_final: 0.9174 (pt) REVERT: A 603 MET cc_start: 0.8042 (tmm) cc_final: 0.7820 (tmm) REVERT: A 685 LEU cc_start: 0.9159 (mt) cc_final: 0.8815 (tp) REVERT: A 688 MET cc_start: 0.5618 (tpt) cc_final: 0.5384 (tpp) REVERT: A 887 LEU cc_start: 0.6924 (mt) cc_final: 0.6140 (mt) REVERT: A 905 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8483 (tpt-90) REVERT: A 906 GLU cc_start: 0.9136 (tp30) cc_final: 0.8768 (tm-30) REVERT: A 1116 ILE cc_start: 0.9644 (mt) cc_final: 0.9435 (mt) REVERT: A 1141 TYR cc_start: 0.8218 (t80) cc_final: 0.7968 (t80) REVERT: A 1255 LEU cc_start: 0.9360 (tp) cc_final: 0.9109 (tp) REVERT: A 1273 THR cc_start: 0.9549 (p) cc_final: 0.9124 (p) REVERT: A 1314 ASP cc_start: 0.8851 (m-30) cc_final: 0.8572 (p0) REVERT: A 1327 MET cc_start: 0.6781 (mmp) cc_final: 0.6469 (mmp) REVERT: A 1351 LEU cc_start: 0.9217 (mt) cc_final: 0.8557 (tp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2201 time to fit residues: 86.2931 Evaluate side-chains 189 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 128 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** A1247 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 = 0.3056 r_free = 0.3056 target = 0.045120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033440 restraints weight = 96851.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.034425 restraints weight = 67187.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035156 restraints weight = 51760.086| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11753 Z= 0.209 Angle : 0.676 10.311 15942 Z= 0.362 Chirality : 0.044 0.205 1866 Planarity : 0.005 0.081 1988 Dihedral : 4.327 19.048 1553 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.31 % Allowed : 5.02 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1451 helix: 0.74 (0.17), residues: 903 sheet: 0.38 (0.53), residues: 86 loop : -0.35 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 136 HIS 0.006 0.001 HIS A1496 PHE 0.018 0.002 PHE A 135 TYR 0.013 0.002 TYR A 616 ARG 0.006 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.06116 ( 664) hydrogen bonds : angle 5.28447 ( 1941) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.53081 ( 2) covalent geometry : bond 0.00421 (11752) covalent geometry : angle 0.67636 (15940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 1.389 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 43 LEU cc_start: 0.9337 (mm) cc_final: 0.9090 (mm) REVERT: A 74 PHE cc_start: 0.9338 (m-10) cc_final: 0.9108 (m-80) REVERT: A 145 PHE cc_start: 0.9248 (m-80) cc_final: 0.8987 (m-80) REVERT: A 234 LYS cc_start: 0.9837 (tppp) cc_final: 0.9341 (mmmm) REVERT: A 470 MET cc_start: 0.9584 (mmp) cc_final: 0.9197 (mmm) REVERT: A 477 ASN cc_start: 0.9746 (m-40) cc_final: 0.9507 (m-40) REVERT: A 583 ILE cc_start: 0.9834 (pt) cc_final: 0.9502 (pt) REVERT: A 595 MET cc_start: 0.9614 (mmp) cc_final: 0.9345 (mmm) REVERT: A 598 MET cc_start: 0.9255 (tmm) cc_final: 0.8911 (tmm) REVERT: A 599 MET cc_start: 0.9516 (pmm) cc_final: 0.9252 (pmm) REVERT: A 616 TYR cc_start: 0.9412 (t80) cc_final: 0.8886 (t80) REVERT: A 617 LEU cc_start: 0.9802 (mt) cc_final: 0.9345 (tp) REVERT: A 688 MET cc_start: 0.6579 (tpt) cc_final: 0.5698 (tpp) REVERT: A 817 LEU cc_start: 0.9814 (tp) cc_final: 0.9457 (pp) REVERT: A 905 ARG cc_start: 0.9245 (tpt170) cc_final: 0.8996 (tpt-90) REVERT: A 906 GLU cc_start: 0.9542 (tp30) cc_final: 0.9160 (tm-30) REVERT: A 1123 PHE cc_start: 0.9698 (t80) cc_final: 0.9252 (t80) REVERT: A 1141 TYR cc_start: 0.9531 (t80) cc_final: 0.9145 (t80) REVERT: A 1225 MET cc_start: 0.9664 (mpp) cc_final: 0.8968 (mtt) REVERT: A 1246 LEU cc_start: 0.9760 (mm) cc_final: 0.9545 (mm) REVERT: A 1249 THR cc_start: 0.9619 (p) cc_final: 0.9416 (p) REVERT: A 1314 ASP cc_start: 0.9729 (m-30) cc_final: 0.9435 (t70) REVERT: A 1351 LEU cc_start: 0.9436 (mt) cc_final: 0.8797 (tp) outliers start: 4 outliers final: 0 residues processed: 211 average time/residue: 0.1990 time to fit residues: 64.1966 Evaluate side-chains 174 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 82 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033960 restraints weight = 95142.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035008 restraints weight = 65804.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035798 restraints weight = 50383.206| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11753 Z= 0.141 Angle : 0.640 10.852 15942 Z= 0.329 Chirality : 0.044 0.354 1866 Planarity : 0.004 0.036 1988 Dihedral : 4.232 19.024 1553 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1451 helix: 0.80 (0.17), residues: 894 sheet: 0.31 (0.53), residues: 86 loop : -0.31 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1206 HIS 0.005 0.001 HIS A1496 PHE 0.027 0.001 PHE A 981 TYR 0.028 0.001 TYR A1275 ARG 0.006 0.001 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 664) hydrogen bonds : angle 4.89685 ( 1941) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.63670 ( 2) covalent geometry : bond 0.00290 (11752) covalent geometry : angle 0.64031 (15940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.416 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 43 LEU cc_start: 0.9302 (mm) cc_final: 0.9036 (mm) REVERT: A 74 PHE cc_start: 0.9266 (m-10) cc_final: 0.9008 (m-80) REVERT: A 145 PHE cc_start: 0.9178 (m-80) cc_final: 0.8737 (m-80) REVERT: A 393 ARG cc_start: 0.9553 (ptt90) cc_final: 0.9305 (ttp80) REVERT: A 397 MET cc_start: 0.9511 (mtm) cc_final: 0.9013 (mtm) REVERT: A 440 MET cc_start: 0.9194 (mmp) cc_final: 0.8988 (mmm) REVERT: A 450 LEU cc_start: 0.9873 (tt) cc_final: 0.9482 (tt) REVERT: A 454 PHE cc_start: 0.9173 (m-80) cc_final: 0.8539 (m-80) REVERT: A 470 MET cc_start: 0.9530 (mmp) cc_final: 0.9251 (mmm) REVERT: A 477 ASN cc_start: 0.9752 (m-40) cc_final: 0.9513 (m-40) REVERT: A 583 ILE cc_start: 0.9811 (pt) cc_final: 0.9465 (pt) REVERT: A 598 MET cc_start: 0.9270 (tmm) cc_final: 0.8911 (tmm) REVERT: A 616 TYR cc_start: 0.9377 (t80) cc_final: 0.8870 (t80) REVERT: A 617 LEU cc_start: 0.9778 (mt) cc_final: 0.9387 (tp) REVERT: A 688 MET cc_start: 0.6837 (tpt) cc_final: 0.6050 (tpp) REVERT: A 817 LEU cc_start: 0.9804 (tp) cc_final: 0.9437 (pp) REVERT: A 822 MET cc_start: 0.8638 (mtt) cc_final: 0.8020 (mtp) REVERT: A 905 ARG cc_start: 0.9237 (tpt170) cc_final: 0.8945 (tpt-90) REVERT: A 906 GLU cc_start: 0.9554 (tp30) cc_final: 0.9151 (tm-30) REVERT: A 1060 LEU cc_start: 0.9639 (mp) cc_final: 0.9391 (mp) REVERT: A 1123 PHE cc_start: 0.9719 (t80) cc_final: 0.9270 (t80) REVERT: A 1141 TYR cc_start: 0.9576 (t80) cc_final: 0.9268 (t80) REVERT: A 1193 ASN cc_start: 0.9611 (t0) cc_final: 0.9168 (t0) REVERT: A 1225 MET cc_start: 0.9654 (mpp) cc_final: 0.8903 (mtp) REVERT: A 1246 LEU cc_start: 0.9730 (mm) cc_final: 0.9530 (mm) REVERT: A 1314 ASP cc_start: 0.9728 (m-30) cc_final: 0.9437 (t70) REVERT: A 1351 LEU cc_start: 0.9364 (mt) cc_final: 0.8713 (tp) outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.1940 time to fit residues: 62.8866 Evaluate side-chains 181 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 142 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 127 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.033590 restraints weight = 96051.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.034633 restraints weight = 66215.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.035414 restraints weight = 50782.907| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11753 Z= 0.136 Angle : 0.617 6.946 15942 Z= 0.319 Chirality : 0.043 0.216 1866 Planarity : 0.004 0.048 1988 Dihedral : 4.167 18.756 1553 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1451 helix: 0.79 (0.17), residues: 912 sheet: 0.41 (0.52), residues: 91 loop : -0.40 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.018 0.001 PHE A 437 TYR 0.019 0.001 TYR A1275 ARG 0.009 0.001 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 664) hydrogen bonds : angle 4.59300 ( 1941) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.59455 ( 2) covalent geometry : bond 0.00285 (11752) covalent geometry : angle 0.61664 (15940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.371 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 70 VAL cc_start: 0.9370 (p) cc_final: 0.8962 (m) REVERT: A 74 PHE cc_start: 0.9291 (m-10) cc_final: 0.8992 (m-80) REVERT: A 145 PHE cc_start: 0.9096 (m-80) cc_final: 0.8789 (m-80) REVERT: A 181 PHE cc_start: 0.9236 (m-10) cc_final: 0.8982 (m-80) REVERT: A 393 ARG cc_start: 0.9592 (ptt90) cc_final: 0.9338 (ttp80) REVERT: A 397 MET cc_start: 0.9502 (mtm) cc_final: 0.9027 (mtm) REVERT: A 440 MET cc_start: 0.9306 (mmp) cc_final: 0.9098 (mmm) REVERT: A 470 MET cc_start: 0.9548 (mmp) cc_final: 0.9255 (mmm) REVERT: A 598 MET cc_start: 0.9259 (tmm) cc_final: 0.8782 (tmm) REVERT: A 616 TYR cc_start: 0.9398 (t80) cc_final: 0.8908 (t80) REVERT: A 617 LEU cc_start: 0.9769 (mt) cc_final: 0.9381 (tp) REVERT: A 688 MET cc_start: 0.6994 (tpt) cc_final: 0.6129 (tpp) REVERT: A 817 LEU cc_start: 0.9788 (tp) cc_final: 0.9413 (pp) REVERT: A 822 MET cc_start: 0.8855 (mtt) cc_final: 0.8244 (mtp) REVERT: A 905 ARG cc_start: 0.9248 (tpt170) cc_final: 0.8923 (tpt-90) REVERT: A 906 GLU cc_start: 0.9569 (tp30) cc_final: 0.9209 (tm-30) REVERT: A 1060 LEU cc_start: 0.9684 (mp) cc_final: 0.9462 (mp) REVERT: A 1141 TYR cc_start: 0.9586 (t80) cc_final: 0.9342 (t80) REVERT: A 1193 ASN cc_start: 0.9603 (t0) cc_final: 0.9184 (t0) REVERT: A 1277 LYS cc_start: 0.9483 (ptpp) cc_final: 0.9249 (pttm) REVERT: A 1314 ASP cc_start: 0.9705 (m-30) cc_final: 0.9403 (t70) REVERT: A 1351 LEU cc_start: 0.9306 (mt) cc_final: 0.8621 (tp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2016 time to fit residues: 64.0317 Evaluate side-chains 169 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 117 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 143 optimal weight: 40.0000 chunk 83 optimal weight: 8.9990 chunk 121 optimal weight: 0.0020 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.046239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.034090 restraints weight = 93104.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035140 restraints weight = 64568.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.035937 restraints weight = 49669.027| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11753 Z= 0.120 Angle : 0.622 9.414 15942 Z= 0.311 Chirality : 0.042 0.194 1866 Planarity : 0.003 0.035 1988 Dihedral : 4.125 20.391 1553 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1451 helix: 0.86 (0.17), residues: 908 sheet: 0.45 (0.57), residues: 81 loop : -0.39 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.020 0.001 PHE A 586 TYR 0.016 0.001 TYR A1275 ARG 0.010 0.001 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 664) hydrogen bonds : angle 4.37181 ( 1941) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.52680 ( 2) covalent geometry : bond 0.00251 (11752) covalent geometry : angle 0.62167 (15940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.9325 (p) cc_final: 0.8938 (m) REVERT: A 74 PHE cc_start: 0.9251 (m-10) cc_final: 0.9036 (m-80) REVERT: A 145 PHE cc_start: 0.9106 (m-80) cc_final: 0.8775 (m-80) REVERT: A 181 PHE cc_start: 0.9227 (m-10) cc_final: 0.8951 (m-80) REVERT: A 397 MET cc_start: 0.9495 (mtm) cc_final: 0.9198 (mtt) REVERT: A 470 MET cc_start: 0.9519 (mmp) cc_final: 0.9239 (mmm) REVERT: A 583 ILE cc_start: 0.9823 (pt) cc_final: 0.9515 (pt) REVERT: A 598 MET cc_start: 0.9209 (tmm) cc_final: 0.8661 (tmm) REVERT: A 616 TYR cc_start: 0.9402 (t80) cc_final: 0.8992 (t80) REVERT: A 617 LEU cc_start: 0.9768 (mt) cc_final: 0.9544 (mt) REVERT: A 688 MET cc_start: 0.6742 (tpt) cc_final: 0.6101 (tpp) REVERT: A 817 LEU cc_start: 0.9789 (tp) cc_final: 0.9415 (pp) REVERT: A 822 MET cc_start: 0.8752 (mtt) cc_final: 0.8112 (mtp) REVERT: A 905 ARG cc_start: 0.9191 (tpt170) cc_final: 0.8868 (tpt-90) REVERT: A 906 GLU cc_start: 0.9560 (tp30) cc_final: 0.9157 (tm-30) REVERT: A 1060 LEU cc_start: 0.9684 (mp) cc_final: 0.9445 (mp) REVERT: A 1193 ASN cc_start: 0.9590 (t0) cc_final: 0.9220 (t0) REVERT: A 1209 ILE cc_start: 0.9885 (tp) cc_final: 0.9610 (tp) REVERT: A 1225 MET cc_start: 0.9641 (mpp) cc_final: 0.9309 (ptp) REVERT: A 1277 LYS cc_start: 0.9468 (ptpp) cc_final: 0.9241 (pttm) REVERT: A 1314 ASP cc_start: 0.9704 (m-30) cc_final: 0.9404 (t70) REVERT: A 1351 LEU cc_start: 0.9280 (mt) cc_final: 0.8579 (tp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2086 time to fit residues: 67.3383 Evaluate side-chains 174 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 chunk 115 optimal weight: 10.0000 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033623 restraints weight = 95486.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034656 restraints weight = 66291.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035430 restraints weight = 51056.217| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11753 Z= 0.132 Angle : 0.618 11.322 15942 Z= 0.312 Chirality : 0.042 0.188 1866 Planarity : 0.003 0.034 1988 Dihedral : 4.080 17.794 1553 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1451 helix: 0.88 (0.17), residues: 918 sheet: 0.32 (0.57), residues: 81 loop : -0.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.018 0.001 PHE A 586 TYR 0.024 0.001 TYR A1275 ARG 0.005 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 664) hydrogen bonds : angle 4.35294 ( 1941) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.54390 ( 2) covalent geometry : bond 0.00277 (11752) covalent geometry : angle 0.61753 (15940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.312 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 70 VAL cc_start: 0.9328 (p) cc_final: 0.8908 (m) REVERT: A 74 PHE cc_start: 0.9252 (m-10) cc_final: 0.9049 (m-80) REVERT: A 145 PHE cc_start: 0.9157 (m-80) cc_final: 0.8783 (m-80) REVERT: A 181 PHE cc_start: 0.9244 (m-10) cc_final: 0.8949 (m-80) REVERT: A 380 CYS cc_start: 0.9593 (t) cc_final: 0.9308 (p) REVERT: A 393 ARG cc_start: 0.9652 (ptt90) cc_final: 0.9354 (ttp-110) REVERT: A 397 MET cc_start: 0.9489 (mtm) cc_final: 0.9120 (mtm) REVERT: A 432 MET cc_start: 0.9279 (mmm) cc_final: 0.8866 (mmm) REVERT: A 438 MET cc_start: 0.8942 (mmp) cc_final: 0.8615 (mmt) REVERT: A 470 MET cc_start: 0.9549 (mmp) cc_final: 0.9274 (mmm) REVERT: A 583 ILE cc_start: 0.9835 (pt) cc_final: 0.9555 (pt) REVERT: A 598 MET cc_start: 0.9206 (tmm) cc_final: 0.8675 (tmm) REVERT: A 616 TYR cc_start: 0.9398 (t80) cc_final: 0.8957 (t80) REVERT: A 617 LEU cc_start: 0.9779 (mt) cc_final: 0.9375 (tp) REVERT: A 817 LEU cc_start: 0.9792 (tp) cc_final: 0.9435 (pp) REVERT: A 822 MET cc_start: 0.8818 (mtt) cc_final: 0.8159 (mtp) REVERT: A 905 ARG cc_start: 0.9216 (tpt170) cc_final: 0.8990 (tpt-90) REVERT: A 906 GLU cc_start: 0.9565 (tp30) cc_final: 0.9169 (tm-30) REVERT: A 1060 LEU cc_start: 0.9688 (mp) cc_final: 0.9464 (mp) REVERT: A 1193 ASN cc_start: 0.9555 (t0) cc_final: 0.9097 (t0) REVERT: A 1209 ILE cc_start: 0.9832 (tp) cc_final: 0.9541 (tp) REVERT: A 1225 MET cc_start: 0.9609 (mpp) cc_final: 0.9238 (ptp) REVERT: A 1277 LYS cc_start: 0.9454 (ptpp) cc_final: 0.9216 (pttm) REVERT: A 1314 ASP cc_start: 0.9706 (m-30) cc_final: 0.9409 (t70) REVERT: A 1351 LEU cc_start: 0.9258 (mt) cc_final: 0.8569 (tp) REVERT: A 1505 MET cc_start: 0.8864 (mmp) cc_final: 0.8569 (tpp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2077 time to fit residues: 64.8004 Evaluate side-chains 169 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.033133 restraints weight = 99738.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.034118 restraints weight = 69416.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034870 restraints weight = 53427.645| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11753 Z= 0.186 Angle : 0.637 9.676 15942 Z= 0.332 Chirality : 0.042 0.183 1866 Planarity : 0.004 0.032 1988 Dihedral : 4.177 19.260 1553 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1451 helix: 0.86 (0.17), residues: 916 sheet: 0.07 (0.56), residues: 81 loop : -0.38 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.023 0.002 PHE A1221 TYR 0.021 0.001 TYR A1275 ARG 0.010 0.001 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 664) hydrogen bonds : angle 4.51164 ( 1941) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.52278 ( 2) covalent geometry : bond 0.00374 (11752) covalent geometry : angle 0.63674 (15940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.9346 (p) cc_final: 0.8910 (m) REVERT: A 74 PHE cc_start: 0.9268 (m-10) cc_final: 0.9061 (m-80) REVERT: A 136 TRP cc_start: 0.9621 (m100) cc_final: 0.9371 (m100) REVERT: A 145 PHE cc_start: 0.9173 (m-80) cc_final: 0.8788 (m-80) REVERT: A 181 PHE cc_start: 0.9285 (m-10) cc_final: 0.8994 (m-80) REVERT: A 380 CYS cc_start: 0.9570 (t) cc_final: 0.9319 (p) REVERT: A 393 ARG cc_start: 0.9668 (ptt90) cc_final: 0.9365 (ttp-110) REVERT: A 397 MET cc_start: 0.9489 (mtm) cc_final: 0.9123 (mtm) REVERT: A 432 MET cc_start: 0.9386 (mmm) cc_final: 0.8930 (mmm) REVERT: A 470 MET cc_start: 0.9576 (mmp) cc_final: 0.9358 (mmm) REVERT: A 586 PHE cc_start: 0.9764 (m-80) cc_final: 0.9536 (m-80) REVERT: A 598 MET cc_start: 0.9206 (tmm) cc_final: 0.8701 (tmm) REVERT: A 603 MET cc_start: 0.8776 (ppp) cc_final: 0.8503 (ppp) REVERT: A 688 MET cc_start: 0.7455 (tpt) cc_final: 0.6401 (tpp) REVERT: A 817 LEU cc_start: 0.9778 (tp) cc_final: 0.9432 (pp) REVERT: A 822 MET cc_start: 0.8900 (mtt) cc_final: 0.8332 (mtp) REVERT: A 905 ARG cc_start: 0.9252 (tpt170) cc_final: 0.9004 (tpt-90) REVERT: A 906 GLU cc_start: 0.9577 (tp30) cc_final: 0.9158 (tm-30) REVERT: A 1064 ILE cc_start: 0.8243 (pt) cc_final: 0.8028 (pt) REVERT: A 1193 ASN cc_start: 0.9500 (t0) cc_final: 0.8994 (t0) REVERT: A 1225 MET cc_start: 0.9601 (mpp) cc_final: 0.9219 (ptm) REVERT: A 1314 ASP cc_start: 0.9737 (m-30) cc_final: 0.9461 (t70) REVERT: A 1351 LEU cc_start: 0.9201 (mt) cc_final: 0.8536 (tp) REVERT: A 1505 MET cc_start: 0.9018 (mmp) cc_final: 0.8658 (tpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2007 time to fit residues: 59.3174 Evaluate side-chains 161 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 12 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 116 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034312 restraints weight = 95354.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035361 restraints weight = 65901.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036149 restraints weight = 50516.895| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11753 Z= 0.124 Angle : 0.645 10.144 15942 Z= 0.320 Chirality : 0.043 0.179 1866 Planarity : 0.004 0.072 1988 Dihedral : 4.140 18.836 1553 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1451 helix: 0.90 (0.17), residues: 914 sheet: 0.02 (0.55), residues: 81 loop : -0.44 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.022 0.001 PHE A 586 TYR 0.018 0.001 TYR A1275 ARG 0.008 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 664) hydrogen bonds : angle 4.31413 ( 1941) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.44111 ( 2) covalent geometry : bond 0.00268 (11752) covalent geometry : angle 0.64547 (15940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.242 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 70 VAL cc_start: 0.9329 (p) cc_final: 0.8884 (m) REVERT: A 74 PHE cc_start: 0.9243 (m-10) cc_final: 0.8978 (m-80) REVERT: A 145 PHE cc_start: 0.9176 (m-80) cc_final: 0.8787 (m-80) REVERT: A 181 PHE cc_start: 0.9198 (m-10) cc_final: 0.8894 (m-80) REVERT: A 241 LYS cc_start: 0.9500 (ptpp) cc_final: 0.9293 (pttt) REVERT: A 380 CYS cc_start: 0.9569 (t) cc_final: 0.9289 (p) REVERT: A 393 ARG cc_start: 0.9626 (ptt90) cc_final: 0.9371 (ttp-110) REVERT: A 397 MET cc_start: 0.9503 (mtm) cc_final: 0.9162 (mtm) REVERT: A 432 MET cc_start: 0.9426 (mmm) cc_final: 0.9055 (mmm) REVERT: A 583 ILE cc_start: 0.9818 (pt) cc_final: 0.9520 (pt) REVERT: A 598 MET cc_start: 0.9169 (tmm) cc_final: 0.8730 (tmm) REVERT: A 603 MET cc_start: 0.8764 (ppp) cc_final: 0.8511 (ppp) REVERT: A 616 TYR cc_start: 0.9417 (t80) cc_final: 0.9056 (t80) REVERT: A 617 LEU cc_start: 0.9780 (mt) cc_final: 0.9486 (mt) REVERT: A 662 MET cc_start: 0.9621 (mmp) cc_final: 0.9316 (mmp) REVERT: A 688 MET cc_start: 0.7412 (tpt) cc_final: 0.6363 (tpp) REVERT: A 817 LEU cc_start: 0.9778 (tp) cc_final: 0.9424 (pp) REVERT: A 822 MET cc_start: 0.8911 (mtt) cc_final: 0.8285 (mtp) REVERT: A 905 ARG cc_start: 0.9270 (tpt170) cc_final: 0.9009 (tpt-90) REVERT: A 906 GLU cc_start: 0.9570 (tp30) cc_final: 0.9138 (tm-30) REVERT: A 1193 ASN cc_start: 0.9513 (t0) cc_final: 0.9031 (t0) REVERT: A 1225 MET cc_start: 0.9621 (mpp) cc_final: 0.9266 (ptm) REVERT: A 1314 ASP cc_start: 0.9730 (m-30) cc_final: 0.9442 (t70) REVERT: A 1351 LEU cc_start: 0.9173 (mt) cc_final: 0.8529 (tp) REVERT: A 1505 MET cc_start: 0.8982 (mmp) cc_final: 0.8662 (tpp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2007 time to fit residues: 61.8336 Evaluate side-chains 167 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 120 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 chunk 7 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034316 restraints weight = 95642.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035366 restraints weight = 66197.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.036148 restraints weight = 50787.482| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11753 Z= 0.121 Angle : 0.646 9.290 15942 Z= 0.318 Chirality : 0.043 0.186 1866 Planarity : 0.004 0.037 1988 Dihedral : 4.074 18.190 1553 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1451 helix: 0.89 (0.17), residues: 916 sheet: 0.05 (0.56), residues: 81 loop : -0.44 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 136 HIS 0.005 0.001 HIS A1371 PHE 0.018 0.001 PHE A1106 TYR 0.027 0.001 TYR A1275 ARG 0.007 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 664) hydrogen bonds : angle 4.26977 ( 1941) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.46831 ( 2) covalent geometry : bond 0.00258 (11752) covalent geometry : angle 0.64650 (15940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.253 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 42 LEU cc_start: 0.9431 (tp) cc_final: 0.9230 (pp) REVERT: A 70 VAL cc_start: 0.9250 (p) cc_final: 0.8868 (m) REVERT: A 145 PHE cc_start: 0.9195 (m-80) cc_final: 0.8819 (m-80) REVERT: A 181 PHE cc_start: 0.9204 (m-10) cc_final: 0.8912 (m-80) REVERT: A 233 MET cc_start: 0.8914 (mtm) cc_final: 0.8616 (mtm) REVERT: A 380 CYS cc_start: 0.9559 (t) cc_final: 0.9291 (p) REVERT: A 393 ARG cc_start: 0.9628 (ptt90) cc_final: 0.9364 (ttp-110) REVERT: A 397 MET cc_start: 0.9546 (mtm) cc_final: 0.9222 (mtm) REVERT: A 432 MET cc_start: 0.9445 (mmm) cc_final: 0.9086 (mmm) REVERT: A 440 MET cc_start: 0.9257 (mmp) cc_final: 0.9054 (mmm) REVERT: A 470 MET cc_start: 0.9536 (mmp) cc_final: 0.9315 (mmm) REVERT: A 583 ILE cc_start: 0.9813 (pt) cc_final: 0.9479 (pt) REVERT: A 603 MET cc_start: 0.8781 (ppp) cc_final: 0.8543 (ppp) REVERT: A 616 TYR cc_start: 0.9471 (t80) cc_final: 0.9065 (t80) REVERT: A 617 LEU cc_start: 0.9780 (mt) cc_final: 0.9491 (mt) REVERT: A 662 MET cc_start: 0.9658 (mmp) cc_final: 0.9360 (mmp) REVERT: A 688 MET cc_start: 0.7500 (tpt) cc_final: 0.6410 (tpp) REVERT: A 817 LEU cc_start: 0.9789 (tp) cc_final: 0.9396 (pp) REVERT: A 822 MET cc_start: 0.8854 (mtt) cc_final: 0.8344 (mtp) REVERT: A 905 ARG cc_start: 0.9295 (tpt170) cc_final: 0.9051 (tpt-90) REVERT: A 906 GLU cc_start: 0.9566 (tp30) cc_final: 0.9147 (tm-30) REVERT: A 1193 ASN cc_start: 0.9539 (t0) cc_final: 0.9061 (t0) REVERT: A 1225 MET cc_start: 0.9514 (mpp) cc_final: 0.9102 (mtp) REVERT: A 1226 MET cc_start: 0.9619 (mpp) cc_final: 0.9403 (mpp) REVERT: A 1258 MET cc_start: 0.9002 (mtp) cc_final: 0.8707 (mtp) REVERT: A 1277 LYS cc_start: 0.9464 (ptpp) cc_final: 0.9251 (pttm) REVERT: A 1314 ASP cc_start: 0.9751 (m-30) cc_final: 0.9484 (t70) REVERT: A 1351 LEU cc_start: 0.9110 (mt) cc_final: 0.8487 (tp) REVERT: A 1505 MET cc_start: 0.8967 (mmp) cc_final: 0.8665 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1960 time to fit residues: 60.5063 Evaluate side-chains 165 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 23 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.045285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.033729 restraints weight = 97706.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034745 restraints weight = 67991.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.035511 restraints weight = 52312.053| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11753 Z= 0.146 Angle : 0.640 7.563 15942 Z= 0.324 Chirality : 0.043 0.198 1866 Planarity : 0.004 0.035 1988 Dihedral : 4.083 17.417 1553 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1451 helix: 0.90 (0.17), residues: 917 sheet: -0.06 (0.56), residues: 81 loop : -0.44 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 136 HIS 0.004 0.001 HIS A1496 PHE 0.030 0.002 PHE A 74 TYR 0.026 0.001 TYR A1275 ARG 0.006 0.001 ARG A1289 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 664) hydrogen bonds : angle 4.33061 ( 1941) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.43353 ( 2) covalent geometry : bond 0.00307 (11752) covalent geometry : angle 0.64047 (15940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.339 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 70 VAL cc_start: 0.9330 (p) cc_final: 0.8992 (m) REVERT: A 74 PHE cc_start: 0.9260 (m-80) cc_final: 0.8832 (m-80) REVERT: A 145 PHE cc_start: 0.9217 (m-80) cc_final: 0.8834 (m-80) REVERT: A 181 PHE cc_start: 0.9246 (m-10) cc_final: 0.8944 (m-80) REVERT: A 380 CYS cc_start: 0.9562 (t) cc_final: 0.9320 (p) REVERT: A 397 MET cc_start: 0.9555 (mtm) cc_final: 0.8924 (ptm) REVERT: A 432 MET cc_start: 0.9461 (mmm) cc_final: 0.8940 (mmm) REVERT: A 440 MET cc_start: 0.9327 (mmp) cc_final: 0.9114 (mmm) REVERT: A 583 ILE cc_start: 0.9808 (pt) cc_final: 0.9504 (pt) REVERT: A 603 MET cc_start: 0.8824 (ppp) cc_final: 0.8592 (ppp) REVERT: A 616 TYR cc_start: 0.9499 (t80) cc_final: 0.9105 (t80) REVERT: A 617 LEU cc_start: 0.9790 (mt) cc_final: 0.9463 (mt) REVERT: A 662 MET cc_start: 0.9678 (mmp) cc_final: 0.9402 (mmp) REVERT: A 688 MET cc_start: 0.7498 (tpt) cc_final: 0.6416 (tpp) REVERT: A 817 LEU cc_start: 0.9791 (tp) cc_final: 0.9413 (pp) REVERT: A 822 MET cc_start: 0.8945 (mtt) cc_final: 0.8517 (mtp) REVERT: A 905 ARG cc_start: 0.9287 (tpt170) cc_final: 0.9045 (tpt-90) REVERT: A 906 GLU cc_start: 0.9602 (tp30) cc_final: 0.9176 (tm-30) REVERT: A 1037 PHE cc_start: 0.9442 (m-10) cc_final: 0.9130 (m-10) REVERT: A 1193 ASN cc_start: 0.9510 (t0) cc_final: 0.9007 (t0) REVERT: A 1225 MET cc_start: 0.9519 (mpp) cc_final: 0.9098 (mtp) REVERT: A 1226 MET cc_start: 0.9633 (mpp) cc_final: 0.9418 (mpp) REVERT: A 1258 MET cc_start: 0.9009 (mtp) cc_final: 0.8672 (mtp) REVERT: A 1314 ASP cc_start: 0.9760 (m-30) cc_final: 0.9501 (t70) REVERT: A 1351 LEU cc_start: 0.9088 (mt) cc_final: 0.8526 (tp) REVERT: A 1505 MET cc_start: 0.9001 (mmp) cc_final: 0.8657 (tpp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2024 time to fit residues: 59.7761 Evaluate side-chains 155 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.0000 chunk 15 optimal weight: 0.0570 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034544 restraints weight = 94949.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035586 restraints weight = 66216.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.036374 restraints weight = 51014.964| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11753 Z= 0.120 Angle : 0.685 13.978 15942 Z= 0.331 Chirality : 0.044 0.325 1866 Planarity : 0.004 0.040 1988 Dihedral : 4.058 17.347 1553 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1451 helix: 0.88 (0.17), residues: 917 sheet: -0.01 (0.55), residues: 81 loop : -0.38 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.025 0.001 PHE A 74 TYR 0.024 0.001 TYR A1275 ARG 0.009 0.001 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 664) hydrogen bonds : angle 4.24067 ( 1941) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.44218 ( 2) covalent geometry : bond 0.00249 (11752) covalent geometry : angle 0.68495 (15940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.66 seconds wall clock time: 67 minutes 7.31 seconds (4027.31 seconds total)