Starting phenix.real_space_refine on Wed May 14 02:53:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx7_36691/05_2025/8jx7_36691.cif" } resolution = 3.6 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= 0.006 sd= 0.053 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 7288 2.51 5 N 1858 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11237 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1416, 11237 Classifications: {'peptide': 1416} Link IDs: {'PTRANS': 44, 'TRANS': 1371} Chain breaks: 3 Time building chain proxies: 6.76, per 1000 atoms: 0.60 Number of scatterers: 11237 At special positions: 0 Unit cell: (111.28, 126.26, 148.73, 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 2033 8.00 N 1858 7.00 C 7288 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 70.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.167A pdb=" N SER A 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 54 removed outlier: 3.580A pdb=" N LEU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Proline residue: A 36 - end of helix removed outlier: 3.528A pdb=" N LEU A 43 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.562A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 4.562A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 4.086A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.708A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.883A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.842A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.540A pdb=" N ALA A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.727A pdb=" N LYS A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.572A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.604A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 407 removed outlier: 4.037A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 417 through 426 removed outlier: 4.400A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.964A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 442 through 459 Processing helix chain 'A' and resid 462 through 507 removed outlier: 3.875A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.240A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 569 removed outlier: 3.698A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 548 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Proline residue: A 554 - end of helix removed outlier: 4.302A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 596 removed outlier: 3.956A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 5.162A 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 597 through 618 removed outlier: 3.793A pdb=" N MET A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 4.299A pdb=" N ILE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.968A 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 744 removed outlier: 3.530A pdb=" N GLU A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.708A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.624A pdb=" N ASN A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 802 " --> pdb=" O HIS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.602A pdb=" N GLU A 893 " --> pdb=" O SER A 890 " (cutoff:3.500A) Proline residue: A 895 - end of helix Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.738A pdb=" N THR A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 974 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.752A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 3.687A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1067 removed outlier: 3.530A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A1047 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.616A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.774A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1094 Processing helix chain 'A' and resid 1094 through 1101 Processing helix chain 'A' and resid 1102 through 1118 removed outlier: 4.348A pdb=" N GLY A1108 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1169 removed outlier: 4.331A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.783A pdb=" N TYR A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A1155 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.616A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1243 removed outlier: 4.185A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.811A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.741A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1376 removed outlier: 4.062A pdb=" N LYS A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.576A pdb=" N SER A1427 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 3.860A pdb=" N LEU A1444 " --> pdb=" O GLY A1440 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A1445 " --> pdb=" O GLN A1441 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS A1446 " --> pdb=" O ARG A1442 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A1447 " --> pdb=" O GLN A1443 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1448 " --> pdb=" O LEU A1444 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1483 Processing helix chain 'A' and resid 1484 through 1486 No H-bonds generated for 'chain 'A' and resid 1484 through 1486' Processing helix chain 'A' and resid 1494 through 1498 removed outlier: 3.902A pdb=" N THR A1497 " --> pdb=" O ARG A1494 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A1498 " --> pdb=" O LEU A1495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1494 through 1498' Processing helix chain 'A' and resid 1517 through 1524 removed outlier: 3.504A pdb=" N GLN A1523 " --> pdb=" O GLU A1519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1524 " --> pdb=" O GLU A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1533 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 5.996A pdb=" N ARG A 628 " --> pdb=" O ILE A 697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 661 removed outlier: 6.735A pdb=" N ARG A 655 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 657 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 661 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS A 692 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.443A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASP A 785 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 704 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.995A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 1323 through 1324 Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.371A pdb=" N THR A1378 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A1330 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLY A1331 " --> pdb=" O MET A1505 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A1507 " --> pdb=" O GLY A1331 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL A1333 " --> pdb=" O LEU A1507 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1812 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: 4.53 Time building geometry restraints manager: 3.24 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: 3542 1.34 - 1.46: 2706 1.46 - 1.58: 5130 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11474 Sorted by residual: bond pdb=" C TRP A1294 " pdb=" N PRO A1295 " ideal model delta sigma weight residual 1.331 1.348 -0.016 7.90e-03 1.60e+04 4.22e+00 bond pdb=" CA LEU A1107 " pdb=" C LEU A1107 " ideal model delta sigma weight residual 1.523 1.499 0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CA ALA A 370 " pdb=" C ALA A 370 " ideal model delta sigma weight residual 1.522 1.503 0.020 1.38e-02 5.25e+03 2.01e+00 bond pdb=" C PHE A 591 " pdb=" N PRO A 592 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.36e-02 5.41e+03 1.55e+00 bond pdb=" CB GLU A 3 " pdb=" CG GLU A 3 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 11469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 15309 2.02 - 4.05: 191 4.05 - 6.07: 42 6.07 - 8.09: 17 8.09 - 10.11: 1 Bond angle restraints: 15560 Sorted by residual: angle pdb=" N ILE A 204 " pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 112.17 107.51 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 112.96 109.61 3.35 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N GLY A1031 " pdb=" CA GLY A1031 " pdb=" C GLY A1031 " ideal model delta sigma weight residual 115.32 111.10 4.22 1.31e+00 5.83e-01 1.04e+01 angle pdb=" CA LEU A 817 " pdb=" CB LEU A 817 " pdb=" CG LEU A 817 " ideal model delta sigma weight residual 116.30 126.41 -10.11 3.50e+00 8.16e-02 8.35e+00 angle pdb=" C ARG A1156 " pdb=" N SER A1157 " pdb=" CA SER A1157 " ideal model delta sigma weight residual 120.09 123.45 -3.36 1.25e+00 6.40e-01 7.22e+00 ... (remaining 15555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5844 17.66 - 35.32: 762 35.32 - 52.98: 191 52.98 - 70.64: 25 70.64 - 88.30: 20 Dihedral angle restraints: 6842 sinusoidal: 2713 harmonic: 4129 Sorted by residual: dihedral pdb=" CA PHE A 824 " pdb=" C PHE A 824 " pdb=" N LEU A 825 " pdb=" CA LEU A 825 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA MET A 438 " pdb=" C MET A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 655 " pdb=" C ARG A 655 " pdb=" N ASP A 656 " pdb=" CA ASP A 656 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1285 0.039 - 0.077: 436 0.077 - 0.116: 95 0.116 - 0.155: 6 0.155 - 0.193: 2 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ASP A1092 " pdb=" N ASP A1092 " pdb=" C ASP A1092 " pdb=" CB ASP A1092 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 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 2.37 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLU A 518 " pdb=" N GLU A 518 " pdb=" C GLU A 518 " pdb=" CB GLU A 518 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1821 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 103 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 104 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 219 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 220 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1418 " -0.011 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A1418 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A1418 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1418 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A1418 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1418 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A1418 " 0.000 2.00e-02 2.50e+03 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 125 2.63 - 3.19: 10703 3.19 - 3.76: 17761 3.76 - 4.33: 23541 4.33 - 4.90: 37743 Nonbonded interactions: 89873 Sorted by model distance: nonbonded pdb=" O LEU A 431 " pdb=" OG1 THR A 435 " model vdw 2.057 3.040 nonbonded pdb=" O VAL A 559 " pdb=" OG SER A 563 " model vdw 2.201 3.040 nonbonded pdb=" O ALA A 98 " pdb=" OG1 THR A 102 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A 22 " pdb=" NE2 GLN A 148 " model vdw 2.224 3.120 nonbonded pdb=" ND2 ASN A 409 " pdb=" O GLU A 687 " model vdw 2.230 3.120 ... (remaining 89868 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.038 11475 Z= 0.139 Angle : 0.646 10.113 15562 Z= 0.355 Chirality : 0.039 0.193 1824 Planarity : 0.004 0.064 1932 Dihedral : 17.214 88.304 4161 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 27.99 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.23), residues: 1408 helix: 0.40 (0.18), residues: 836 sheet: 0.95 (0.62), residues: 72 loop : -0.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1200 HIS 0.005 0.001 HIS A1371 PHE 0.035 0.001 PHE A1418 TYR 0.005 0.001 TYR A 206 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.26835 ( 623) hydrogen bonds : angle 8.31695 ( 1812) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.10677 ( 2) covalent geometry : bond 0.00290 (11474) covalent geometry : angle 0.64642 (15560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.8797 (tt) cc_final: 0.8456 (tt) REVERT: A 373 ILE cc_start: 0.8578 (mm) cc_final: 0.8217 (mm) REVERT: A 485 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8550 (mmmm) REVERT: A 551 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 599 MET cc_start: 0.8246 (mmm) cc_final: 0.7892 (mmm) REVERT: A 822 MET cc_start: 0.5305 (mpp) cc_final: 0.4993 (mtt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2019 time to fit residues: 83.9916 Evaluate side-chains 154 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 526 GLN A1247 ASN ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1394 ASN A1476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.054147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039880 restraints weight = 71845.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041273 restraints weight = 38235.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.042225 restraints weight = 25315.841| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11475 Z= 0.165 Angle : 0.783 12.726 15562 Z= 0.382 Chirality : 0.046 0.286 1824 Planarity : 0.005 0.051 1932 Dihedral : 4.016 20.591 1510 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.10 % Allowed : 22.73 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1408 helix: 0.26 (0.17), residues: 868 sheet: 0.58 (0.60), residues: 72 loop : -0.21 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1200 HIS 0.006 0.001 HIS A1371 PHE 0.039 0.002 PHE A 74 TYR 0.024 0.002 TYR A 616 ARG 0.010 0.001 ARG A1289 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 623) hydrogen bonds : angle 5.18507 ( 1812) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.12200 ( 2) covalent geometry : bond 0.00351 (11474) covalent geometry : angle 0.78307 (15560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 182 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9680 (tp) cc_final: 0.9449 (pp) REVERT: A 74 PHE cc_start: 0.9263 (m-80) cc_final: 0.8926 (m-80) REVERT: A 103 ASN cc_start: 0.9611 (m-40) cc_final: 0.9373 (m110) REVERT: A 138 LEU cc_start: 0.9539 (tt) cc_final: 0.9331 (tt) REVERT: A 212 ILE cc_start: 0.9746 (OUTLIER) cc_final: 0.9512 (tp) REVERT: A 230 ASP cc_start: 0.8398 (p0) cc_final: 0.7304 (p0) REVERT: A 233 MET cc_start: 0.9535 (mmm) cc_final: 0.8853 (mmm) REVERT: A 320 MET cc_start: 0.9025 (mmm) cc_final: 0.8813 (mmm) REVERT: A 397 MET cc_start: 0.9431 (mtm) cc_final: 0.9154 (mtm) REVERT: A 432 MET cc_start: 0.9507 (ttm) cc_final: 0.9125 (tpp) REVERT: A 440 MET cc_start: 0.9541 (mmm) cc_final: 0.9318 (mmm) REVERT: A 502 MET cc_start: 0.9807 (mmm) cc_final: 0.9591 (mmm) REVERT: A 593 LEU cc_start: 0.9647 (tp) cc_final: 0.9337 (tp) REVERT: A 688 MET cc_start: 0.8508 (tpp) cc_final: 0.8268 (tpp) REVERT: A 745 MET cc_start: 0.9541 (ppp) cc_final: 0.9286 (ppp) REVERT: A 892 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 903 MET cc_start: 0.9577 (mpp) cc_final: 0.9181 (mpp) REVERT: A 984 LEU cc_start: 0.9796 (tt) cc_final: 0.9447 (mm) REVERT: A 988 MET cc_start: 0.9247 (ptp) cc_final: 0.9036 (ttp) REVERT: A 1032 LEU cc_start: 0.9815 (OUTLIER) cc_final: 0.9572 (pp) REVERT: A 1139 MET cc_start: 0.8941 (tmm) cc_final: 0.8618 (ppp) REVERT: A 1225 MET cc_start: 0.9670 (mmp) cc_final: 0.9375 (mmm) REVERT: A 1226 MET cc_start: 0.9566 (mmm) cc_final: 0.9345 (mmm) REVERT: A 1258 MET cc_start: 0.9032 (mmm) cc_final: 0.8790 (mmp) REVERT: A 1349 ARG cc_start: 0.9692 (OUTLIER) cc_final: 0.9384 (mtp180) REVERT: A 1399 ASN cc_start: 0.9830 (OUTLIER) cc_final: 0.9560 (m110) REVERT: A 1505 MET cc_start: 0.9718 (mmm) cc_final: 0.9439 (mmm) outliers start: 64 outliers final: 24 residues processed: 226 average time/residue: 0.1851 time to fit residues: 64.4558 Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 5.9990 chunk 76 optimal weight: 0.0070 chunk 62 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 116 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN A1042 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.050000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036368 restraints weight = 68057.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037625 restraints weight = 37846.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038496 restraints weight = 25264.337| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11475 Z= 0.130 Angle : 0.719 11.708 15562 Z= 0.337 Chirality : 0.044 0.239 1824 Planarity : 0.004 0.048 1932 Dihedral : 3.918 20.800 1510 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.59 % Allowed : 23.44 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1408 helix: 0.43 (0.17), residues: 868 sheet: 0.70 (0.62), residues: 67 loop : -0.34 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1200 HIS 0.004 0.001 HIS A1057 PHE 0.033 0.001 PHE A1123 TYR 0.017 0.001 TYR A 885 ARG 0.009 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 623) hydrogen bonds : angle 4.75841 ( 1812) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.66397 ( 2) covalent geometry : bond 0.00269 (11474) covalent geometry : angle 0.71936 (15560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9717 (mp) cc_final: 0.9485 (pp) REVERT: A 42 LEU cc_start: 0.9662 (tp) cc_final: 0.9459 (pp) REVERT: A 74 PHE cc_start: 0.9275 (m-80) cc_final: 0.8783 (m-80) REVERT: A 107 TYR cc_start: 0.9776 (OUTLIER) cc_final: 0.9410 (m-80) REVERT: A 212 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9457 (tp) REVERT: A 320 MET cc_start: 0.8947 (mmm) cc_final: 0.8727 (mmm) REVERT: A 385 CYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9178 (p) REVERT: A 405 LEU cc_start: 0.9790 (mm) cc_final: 0.9552 (mp) REVERT: A 432 MET cc_start: 0.9505 (ttm) cc_final: 0.9193 (tpp) REVERT: A 440 MET cc_start: 0.9547 (mmm) cc_final: 0.9067 (mmm) REVERT: A 540 SER cc_start: 0.9741 (m) cc_final: 0.9471 (p) REVERT: A 542 LEU cc_start: 0.9479 (mp) cc_final: 0.9065 (tp) REVERT: A 598 MET cc_start: 0.8845 (ppp) cc_final: 0.7817 (ppp) REVERT: A 599 MET cc_start: 0.9605 (mmm) cc_final: 0.9276 (mmm) REVERT: A 603 MET cc_start: 0.9015 (tmm) cc_final: 0.8707 (ppp) REVERT: A 604 LEU cc_start: 0.9519 (pp) cc_final: 0.9208 (pp) REVERT: A 684 MET cc_start: 0.9621 (mpp) cc_final: 0.9339 (mpp) REVERT: A 688 MET cc_start: 0.8461 (tpp) cc_final: 0.8122 (tpp) REVERT: A 892 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8918 (mm-30) REVERT: A 1032 LEU cc_start: 0.9798 (OUTLIER) cc_final: 0.9587 (pp) REVERT: A 1115 MET cc_start: 0.9362 (mtp) cc_final: 0.8902 (mtt) REVERT: A 1123 PHE cc_start: 0.9719 (t80) cc_final: 0.9419 (t80) REVERT: A 1130 LEU cc_start: 0.9715 (mt) cc_final: 0.9476 (pp) REVERT: A 1184 LYS cc_start: 0.9686 (tppt) cc_final: 0.9436 (tppt) REVERT: A 1225 MET cc_start: 0.9692 (mmp) cc_final: 0.9304 (mmm) REVERT: A 1258 MET cc_start: 0.9279 (mmm) cc_final: 0.9011 (mmp) REVERT: A 1349 ARG cc_start: 0.9692 (OUTLIER) cc_final: 0.9362 (ttp-170) REVERT: A 1399 ASN cc_start: 0.9823 (OUTLIER) cc_final: 0.9584 (m-40) REVERT: A 1505 MET cc_start: 0.9692 (mmm) cc_final: 0.9370 (mmm) outliers start: 45 outliers final: 16 residues processed: 211 average time/residue: 0.1813 time to fit residues: 59.0911 Evaluate side-chains 177 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 137 optimal weight: 0.0270 chunk 114 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A1057 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** 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 = 0.3259 r_free = 0.3259 target = 0.049831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.036261 restraints weight = 67902.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037460 restraints weight = 38330.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038296 restraints weight = 26176.603| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11475 Z= 0.125 Angle : 0.716 11.046 15562 Z= 0.331 Chirality : 0.045 0.217 1824 Planarity : 0.004 0.052 1932 Dihedral : 3.830 18.222 1510 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.03 % Allowed : 25.20 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1408 helix: 0.58 (0.18), residues: 861 sheet: 0.78 (0.63), residues: 67 loop : -0.31 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1200 HIS 0.003 0.000 HIS A1057 PHE 0.018 0.001 PHE A 74 TYR 0.015 0.001 TYR A 970 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 623) hydrogen bonds : angle 4.56952 ( 1812) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.63423 ( 2) covalent geometry : bond 0.00264 (11474) covalent geometry : angle 0.71634 (15560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9643 (tp) cc_final: 0.9434 (pp) REVERT: A 74 PHE cc_start: 0.9339 (m-80) cc_final: 0.8840 (m-80) REVERT: A 107 TYR cc_start: 0.9726 (OUTLIER) cc_final: 0.9372 (m-80) REVERT: A 212 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9467 (tp) REVERT: A 222 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9331 (p) REVERT: A 230 ASP cc_start: 0.9214 (t70) cc_final: 0.8701 (p0) REVERT: A 232 GLU cc_start: 0.8636 (pp20) cc_final: 0.7730 (pp20) REVERT: A 233 MET cc_start: 0.9389 (mmm) cc_final: 0.8854 (mmm) REVERT: A 385 CYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9208 (p) REVERT: A 432 MET cc_start: 0.9484 (ttm) cc_final: 0.9159 (tpp) REVERT: A 512 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9642 (mm) REVERT: A 540 SER cc_start: 0.9739 (m) cc_final: 0.9462 (p) REVERT: A 542 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9179 (tp) REVERT: A 551 GLN cc_start: 0.9416 (tm-30) cc_final: 0.9064 (tm-30) REVERT: A 598 MET cc_start: 0.8882 (ppp) cc_final: 0.7719 (ppp) REVERT: A 599 MET cc_start: 0.9591 (mmm) cc_final: 0.9264 (mmm) REVERT: A 688 MET cc_start: 0.8427 (tpp) cc_final: 0.8099 (tpp) REVERT: A 885 TYR cc_start: 0.9116 (t80) cc_final: 0.8775 (t80) REVERT: A 892 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 988 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9255 (ttp) REVERT: A 1115 MET cc_start: 0.9357 (mtp) cc_final: 0.8900 (mtt) REVERT: A 1123 PHE cc_start: 0.9733 (t80) cc_final: 0.9531 (t80) REVERT: A 1130 LEU cc_start: 0.9711 (mt) cc_final: 0.9426 (pp) REVERT: A 1184 LYS cc_start: 0.9714 (tppt) cc_final: 0.9437 (tppt) REVERT: A 1225 MET cc_start: 0.9654 (mmp) cc_final: 0.9294 (mmm) REVERT: A 1258 MET cc_start: 0.9402 (mmm) cc_final: 0.9111 (mmp) REVERT: A 1349 ARG cc_start: 0.9686 (OUTLIER) cc_final: 0.9339 (ttp-170) REVERT: A 1399 ASN cc_start: 0.9815 (OUTLIER) cc_final: 0.9585 (m-40) REVERT: A 1505 MET cc_start: 0.9692 (mmm) cc_final: 0.9439 (mmm) outliers start: 38 outliers final: 20 residues processed: 194 average time/residue: 0.1843 time to fit residues: 55.2693 Evaluate side-chains 180 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 50.0000 chunk 100 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 997 ASN ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.048919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035662 restraints weight = 68511.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036814 restraints weight = 39122.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037637 restraints weight = 26805.333| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11475 Z= 0.133 Angle : 0.710 12.492 15562 Z= 0.331 Chirality : 0.044 0.305 1824 Planarity : 0.004 0.055 1932 Dihedral : 3.723 16.572 1510 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.99 % Allowed : 25.36 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1408 helix: 0.77 (0.18), residues: 857 sheet: 1.34 (0.71), residues: 55 loop : -0.38 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1200 HIS 0.003 0.000 HIS A1371 PHE 0.023 0.001 PHE A1037 TYR 0.014 0.001 TYR A 970 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 623) hydrogen bonds : angle 4.51591 ( 1812) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.56110 ( 2) covalent geometry : bond 0.00290 (11474) covalent geometry : angle 0.71000 (15560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9637 (tp) cc_final: 0.9422 (pp) REVERT: A 74 PHE cc_start: 0.9360 (m-80) cc_final: 0.8853 (m-80) REVERT: A 107 TYR cc_start: 0.9720 (OUTLIER) cc_final: 0.9418 (m-80) REVERT: A 118 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: A 131 PHE cc_start: 0.8703 (t80) cc_final: 0.8395 (t80) REVERT: A 169 PHE cc_start: 0.9155 (m-10) cc_final: 0.8783 (t80) REVERT: A 212 ILE cc_start: 0.9758 (OUTLIER) cc_final: 0.9554 (tp) REVERT: A 222 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9280 (p) REVERT: A 385 CYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9157 (p) REVERT: A 432 MET cc_start: 0.9479 (ttm) cc_final: 0.9184 (tpp) REVERT: A 512 LEU cc_start: 0.9854 (OUTLIER) cc_final: 0.9645 (mm) REVERT: A 540 SER cc_start: 0.9753 (m) cc_final: 0.9501 (p) REVERT: A 542 LEU cc_start: 0.9590 (mp) cc_final: 0.9182 (tp) REVERT: A 551 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9005 (tm-30) REVERT: A 595 MET cc_start: 0.9037 (ptp) cc_final: 0.8489 (tmm) REVERT: A 598 MET cc_start: 0.8890 (ppp) cc_final: 0.7135 (ppp) REVERT: A 599 MET cc_start: 0.9590 (OUTLIER) cc_final: 0.8902 (mmm) REVERT: A 688 MET cc_start: 0.8564 (tpp) cc_final: 0.8214 (tpp) REVERT: A 885 TYR cc_start: 0.9133 (t80) cc_final: 0.8669 (t80) REVERT: A 1115 MET cc_start: 0.9398 (mtp) cc_final: 0.8905 (mtt) REVERT: A 1130 LEU cc_start: 0.9711 (mt) cc_final: 0.9443 (pp) REVERT: A 1184 LYS cc_start: 0.9731 (tppt) cc_final: 0.9439 (tppt) REVERT: A 1225 MET cc_start: 0.9648 (mmp) cc_final: 0.9305 (mmm) REVERT: A 1258 MET cc_start: 0.9466 (mmm) cc_final: 0.9131 (mmp) REVERT: A 1349 ARG cc_start: 0.9691 (OUTLIER) cc_final: 0.9343 (mtp180) REVERT: A 1399 ASN cc_start: 0.9809 (OUTLIER) cc_final: 0.9578 (m-40) REVERT: A 1505 MET cc_start: 0.9665 (mmm) cc_final: 0.9451 (mmm) outliers start: 50 outliers final: 24 residues processed: 197 average time/residue: 0.1900 time to fit residues: 58.1359 Evaluate side-chains 183 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1165 GLU Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1185 HIS ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035701 restraints weight = 67805.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036858 restraints weight = 39016.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037673 restraints weight = 26919.084| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11475 Z= 0.120 Angle : 0.743 12.928 15562 Z= 0.336 Chirality : 0.044 0.351 1824 Planarity : 0.004 0.056 1932 Dihedral : 3.704 16.714 1510 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.27 % Allowed : 25.92 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1408 helix: 0.85 (0.18), residues: 857 sheet: 1.40 (0.71), residues: 55 loop : -0.44 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1200 HIS 0.002 0.000 HIS A1371 PHE 0.012 0.001 PHE A 74 TYR 0.010 0.001 TYR A1275 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 623) hydrogen bonds : angle 4.42207 ( 1812) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.52083 ( 2) covalent geometry : bond 0.00254 (11474) covalent geometry : angle 0.74287 (15560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9640 (tp) cc_final: 0.9404 (pp) REVERT: A 74 PHE cc_start: 0.9372 (m-80) cc_final: 0.8795 (m-80) REVERT: A 107 TYR cc_start: 0.9683 (OUTLIER) cc_final: 0.9376 (m-80) REVERT: A 118 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: A 131 PHE cc_start: 0.8781 (t80) cc_final: 0.8481 (t80) REVERT: A 169 PHE cc_start: 0.9144 (m-10) cc_final: 0.8779 (t80) REVERT: A 212 ILE cc_start: 0.9756 (OUTLIER) cc_final: 0.9531 (tp) REVERT: A 232 GLU cc_start: 0.8808 (pp20) cc_final: 0.8414 (pp20) REVERT: A 233 MET cc_start: 0.9432 (mmm) cc_final: 0.9139 (mmm) REVERT: A 320 MET cc_start: 0.9038 (mmm) cc_final: 0.8588 (mmm) REVERT: A 323 LEU cc_start: 0.9702 (tp) cc_final: 0.9460 (pp) REVERT: A 432 MET cc_start: 0.9469 (ttm) cc_final: 0.9242 (tpp) REVERT: A 500 LYS cc_start: 0.9330 (mtmm) cc_final: 0.9078 (ptpp) REVERT: A 512 LEU cc_start: 0.9850 (OUTLIER) cc_final: 0.9639 (mm) REVERT: A 540 SER cc_start: 0.9760 (m) cc_final: 0.9503 (p) REVERT: A 595 MET cc_start: 0.8906 (ptp) cc_final: 0.8670 (tmm) REVERT: A 598 MET cc_start: 0.8952 (ppp) cc_final: 0.7299 (ppp) REVERT: A 599 MET cc_start: 0.9573 (mmm) cc_final: 0.8931 (mmm) REVERT: A 604 LEU cc_start: 0.9520 (pp) cc_final: 0.9122 (pp) REVERT: A 605 GLN cc_start: 0.9765 (OUTLIER) cc_final: 0.9418 (mm110) REVERT: A 688 MET cc_start: 0.8588 (tpp) cc_final: 0.8250 (tpp) REVERT: A 757 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8393 (mmtm) REVERT: A 885 TYR cc_start: 0.9121 (t80) cc_final: 0.8673 (t80) REVERT: A 1115 MET cc_start: 0.9406 (mtp) cc_final: 0.8981 (mtt) REVERT: A 1130 LEU cc_start: 0.9688 (mt) cc_final: 0.9421 (pp) REVERT: A 1184 LYS cc_start: 0.9729 (tppt) cc_final: 0.9410 (tppt) REVERT: A 1200 TRP cc_start: 0.9333 (OUTLIER) cc_final: 0.9120 (p90) REVERT: A 1217 LEU cc_start: 0.9839 (OUTLIER) cc_final: 0.9596 (mm) REVERT: A 1225 MET cc_start: 0.9641 (mmp) cc_final: 0.9328 (mmm) REVERT: A 1258 MET cc_start: 0.9455 (mmm) cc_final: 0.9154 (mmp) REVERT: A 1349 ARG cc_start: 0.9668 (OUTLIER) cc_final: 0.9379 (ttp-170) REVERT: A 1399 ASN cc_start: 0.9819 (OUTLIER) cc_final: 0.9600 (m-40) REVERT: A 1505 MET cc_start: 0.9671 (mmm) cc_final: 0.9452 (mmm) outliers start: 41 outliers final: 22 residues processed: 195 average time/residue: 0.1972 time to fit residues: 58.4122 Evaluate side-chains 192 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 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 = 0.3195 r_free = 0.3195 target = 0.046979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034006 restraints weight = 72506.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035139 restraints weight = 40690.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035847 restraints weight = 27438.372| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11475 Z= 0.229 Angle : 0.761 12.028 15562 Z= 0.370 Chirality : 0.045 0.294 1824 Planarity : 0.004 0.054 1932 Dihedral : 3.727 16.931 1510 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.83 % Allowed : 26.40 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1408 helix: 0.93 (0.18), residues: 868 sheet: 1.20 (0.71), residues: 55 loop : -0.41 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1200 HIS 0.005 0.001 HIS A1371 PHE 0.016 0.001 PHE A1037 TYR 0.010 0.001 TYR A 565 ARG 0.007 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 623) hydrogen bonds : angle 4.64194 ( 1812) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.49816 ( 2) covalent geometry : bond 0.00472 (11474) covalent geometry : angle 0.76106 (15560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9395 (m-80) cc_final: 0.8830 (m-80) REVERT: A 118 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: A 362 LEU cc_start: 0.9678 (tt) cc_final: 0.9403 (tp) REVERT: A 366 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9371 (mm) REVERT: A 385 CYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9195 (p) REVERT: A 432 MET cc_start: 0.9496 (ttm) cc_final: 0.9236 (tpp) REVERT: A 440 MET cc_start: 0.9420 (mmm) cc_final: 0.9000 (mmm) REVERT: A 495 LYS cc_start: 0.9763 (tppt) cc_final: 0.9531 (tppt) REVERT: A 540 SER cc_start: 0.9796 (m) cc_final: 0.9545 (p) REVERT: A 542 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9336 (tp) REVERT: A 551 GLN cc_start: 0.9542 (tm-30) cc_final: 0.9021 (tm-30) REVERT: A 595 MET cc_start: 0.8944 (ptp) cc_final: 0.8613 (ppp) REVERT: A 598 MET cc_start: 0.9039 (ppp) cc_final: 0.7989 (ppp) REVERT: A 599 MET cc_start: 0.9631 (mmm) cc_final: 0.9073 (mmm) REVERT: A 604 LEU cc_start: 0.9541 (pp) cc_final: 0.9137 (pp) REVERT: A 605 GLN cc_start: 0.9771 (OUTLIER) cc_final: 0.9429 (mm110) REVERT: A 885 TYR cc_start: 0.9207 (t80) cc_final: 0.8717 (t80) REVERT: A 1115 MET cc_start: 0.9401 (mtp) cc_final: 0.8916 (mtp) REVERT: A 1184 LYS cc_start: 0.9762 (tppt) cc_final: 0.9445 (tppt) REVERT: A 1200 TRP cc_start: 0.9467 (OUTLIER) cc_final: 0.9213 (p90) REVERT: A 1217 LEU cc_start: 0.9852 (OUTLIER) cc_final: 0.9624 (mm) REVERT: A 1225 MET cc_start: 0.9620 (mmp) cc_final: 0.9291 (mmm) REVERT: A 1258 MET cc_start: 0.9511 (mmm) cc_final: 0.9237 (mmp) REVERT: A 1328 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (tp30) REVERT: A 1349 ARG cc_start: 0.9687 (OUTLIER) cc_final: 0.9480 (mtp180) REVERT: A 1399 ASN cc_start: 0.9798 (OUTLIER) cc_final: 0.9555 (m-40) outliers start: 48 outliers final: 31 residues processed: 179 average time/residue: 0.1886 time to fit residues: 52.8732 Evaluate side-chains 190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1328 GLU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 124 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 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 = 0.3820 r_free = 0.3820 target = 0.091949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.080076 restraints weight = 75113.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.081269 restraints weight = 26677.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.081984 restraints weight = 12837.616| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11475 Z= 0.151 Angle : 0.769 13.797 15562 Z= 0.353 Chirality : 0.046 0.307 1824 Planarity : 0.004 0.049 1932 Dihedral : 3.772 16.021 1510 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.59 % Allowed : 27.43 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1408 helix: 0.96 (0.18), residues: 869 sheet: 1.03 (0.63), residues: 70 loop : -0.45 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1200 HIS 0.004 0.000 HIS A1371 PHE 0.012 0.001 PHE A 242 TYR 0.008 0.001 TYR A 970 ARG 0.007 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 623) hydrogen bonds : angle 4.49295 ( 1812) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.54233 ( 2) covalent geometry : bond 0.00329 (11474) covalent geometry : angle 0.76885 (15560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9631 (tp) cc_final: 0.9370 (pp) REVERT: A 74 PHE cc_start: 0.9321 (m-80) cc_final: 0.8755 (m-80) REVERT: A 107 TYR cc_start: 0.9636 (OUTLIER) cc_final: 0.9334 (m-80) REVERT: A 118 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: A 169 PHE cc_start: 0.9197 (m-10) cc_final: 0.8894 (m-80) REVERT: A 232 GLU cc_start: 0.8886 (pp20) cc_final: 0.8548 (pp20) REVERT: A 233 MET cc_start: 0.9431 (mmm) cc_final: 0.9086 (mmm) REVERT: A 320 MET cc_start: 0.9082 (mmm) cc_final: 0.8624 (mmm) REVERT: A 323 LEU cc_start: 0.9736 (tp) cc_final: 0.9496 (pp) REVERT: A 362 LEU cc_start: 0.9664 (tt) cc_final: 0.9404 (tp) REVERT: A 366 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9249 (mm) REVERT: A 385 CYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9188 (p) REVERT: A 432 MET cc_start: 0.9521 (ttm) cc_final: 0.9110 (tpp) REVERT: A 440 MET cc_start: 0.9433 (mmm) cc_final: 0.9005 (mmm) REVERT: A 495 LYS cc_start: 0.9771 (tppt) cc_final: 0.9539 (tppt) REVERT: A 542 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9312 (tp) REVERT: A 595 MET cc_start: 0.8855 (ptp) cc_final: 0.8378 (ppp) REVERT: A 598 MET cc_start: 0.8984 (ppp) cc_final: 0.7839 (ppp) REVERT: A 599 MET cc_start: 0.9561 (mmm) cc_final: 0.9014 (mmm) REVERT: A 603 MET cc_start: 0.8704 (ppp) cc_final: 0.8377 (ppp) REVERT: A 604 LEU cc_start: 0.9521 (pp) cc_final: 0.9306 (pp) REVERT: A 885 TYR cc_start: 0.9004 (t80) cc_final: 0.8630 (t80) REVERT: A 1115 MET cc_start: 0.9340 (mtp) cc_final: 0.8845 (mtp) REVERT: A 1184 LYS cc_start: 0.9755 (tppt) cc_final: 0.9429 (tppt) REVERT: A 1191 ASP cc_start: 0.9620 (OUTLIER) cc_final: 0.9355 (m-30) REVERT: A 1200 TRP cc_start: 0.9514 (OUTLIER) cc_final: 0.9228 (p90) REVERT: A 1217 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9605 (mm) REVERT: A 1225 MET cc_start: 0.9594 (mmp) cc_final: 0.9258 (mmm) REVERT: A 1258 MET cc_start: 0.9475 (mmm) cc_final: 0.9176 (mmp) REVERT: A 1349 ARG cc_start: 0.9652 (OUTLIER) cc_final: 0.9217 (mtm180) REVERT: A 1399 ASN cc_start: 0.9750 (OUTLIER) cc_final: 0.9500 (m-40) outliers start: 45 outliers final: 24 residues processed: 180 average time/residue: 0.2068 time to fit residues: 57.0886 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 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 = 0.3324 r_free = 0.3324 target = 0.052338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038505 restraints weight = 74666.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039851 restraints weight = 39224.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040735 restraints weight = 25874.209| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11475 Z= 0.124 Angle : 0.781 14.172 15562 Z= 0.352 Chirality : 0.046 0.337 1824 Planarity : 0.003 0.054 1932 Dihedral : 3.786 16.194 1510 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.03 % Allowed : 27.75 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1408 helix: 0.98 (0.18), residues: 871 sheet: 1.18 (0.63), residues: 70 loop : -0.35 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1200 HIS 0.004 0.000 HIS A1371 PHE 0.013 0.001 PHE A 242 TYR 0.012 0.001 TYR A 401 ARG 0.009 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 623) hydrogen bonds : angle 4.40874 ( 1812) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.59285 ( 2) covalent geometry : bond 0.00267 (11474) covalent geometry : angle 0.78056 (15560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9657 (tp) cc_final: 0.9407 (pp) REVERT: A 74 PHE cc_start: 0.9389 (m-80) cc_final: 0.8840 (m-80) REVERT: A 107 TYR cc_start: 0.9611 (OUTLIER) cc_final: 0.9356 (m-80) REVERT: A 118 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: A 131 PHE cc_start: 0.8968 (t80) cc_final: 0.8656 (t80) REVERT: A 169 PHE cc_start: 0.9183 (m-10) cc_final: 0.8872 (m-80) REVERT: A 232 GLU cc_start: 0.8930 (pp20) cc_final: 0.8530 (pp20) REVERT: A 233 MET cc_start: 0.9449 (mmm) cc_final: 0.9090 (mmm) REVERT: A 320 MET cc_start: 0.9021 (mmm) cc_final: 0.8599 (mmm) REVERT: A 323 LEU cc_start: 0.9752 (tp) cc_final: 0.9491 (pp) REVERT: A 362 LEU cc_start: 0.9674 (tt) cc_final: 0.9393 (tp) REVERT: A 366 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9238 (mm) REVERT: A 432 MET cc_start: 0.9496 (ttm) cc_final: 0.9253 (tpp) REVERT: A 500 LYS cc_start: 0.9299 (mtmm) cc_final: 0.8956 (pttm) REVERT: A 542 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9271 (tp) REVERT: A 593 LEU cc_start: 0.9240 (pp) cc_final: 0.8982 (pt) REVERT: A 595 MET cc_start: 0.8868 (ptp) cc_final: 0.8585 (ppp) REVERT: A 598 MET cc_start: 0.9130 (ppp) cc_final: 0.8089 (ppp) REVERT: A 599 MET cc_start: 0.9609 (OUTLIER) cc_final: 0.9090 (mmm) REVERT: A 603 MET cc_start: 0.8811 (ppp) cc_final: 0.8484 (ppp) REVERT: A 604 LEU cc_start: 0.9530 (pp) cc_final: 0.9317 (pp) REVERT: A 688 MET cc_start: 0.8553 (tpt) cc_final: 0.7957 (tpp) REVERT: A 885 TYR cc_start: 0.9107 (t80) cc_final: 0.8640 (t80) REVERT: A 1061 LEU cc_start: 0.9902 (tt) cc_final: 0.9584 (pp) REVERT: A 1115 MET cc_start: 0.9376 (mtp) cc_final: 0.8950 (mtt) REVERT: A 1184 LYS cc_start: 0.9754 (tppt) cc_final: 0.9411 (tppt) REVERT: A 1191 ASP cc_start: 0.9649 (OUTLIER) cc_final: 0.9340 (m-30) REVERT: A 1200 TRP cc_start: 0.9425 (OUTLIER) cc_final: 0.9167 (p90) REVERT: A 1217 LEU cc_start: 0.9840 (OUTLIER) cc_final: 0.9616 (mm) REVERT: A 1225 MET cc_start: 0.9568 (mmp) cc_final: 0.9260 (mmm) REVERT: A 1258 MET cc_start: 0.9462 (mmm) cc_final: 0.9179 (mmp) REVERT: A 1349 ARG cc_start: 0.9679 (OUTLIER) cc_final: 0.9226 (mtm180) REVERT: A 1399 ASN cc_start: 0.9818 (OUTLIER) cc_final: 0.9572 (m-40) outliers start: 38 outliers final: 23 residues processed: 180 average time/residue: 0.1885 time to fit residues: 51.6806 Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 30 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.0470 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 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 = 0.3293 r_free = 0.3293 target = 0.050899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037231 restraints weight = 76922.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038519 restraints weight = 41039.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039392 restraints weight = 27336.269| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11475 Z= 0.196 Angle : 0.804 15.063 15562 Z= 0.373 Chirality : 0.045 0.287 1824 Planarity : 0.004 0.051 1932 Dihedral : 3.775 16.185 1510 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.87 % Allowed : 27.91 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1408 helix: 1.00 (0.18), residues: 870 sheet: 1.10 (0.62), residues: 70 loop : -0.38 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1200 HIS 0.016 0.001 HIS A1371 PHE 0.011 0.001 PHE A1182 TYR 0.020 0.001 TYR A 616 ARG 0.009 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 623) hydrogen bonds : angle 4.57929 ( 1812) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.42891 ( 2) covalent geometry : bond 0.00411 (11474) covalent geometry : angle 0.80410 (15560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9675 (tp) cc_final: 0.9438 (pp) REVERT: A 74 PHE cc_start: 0.9408 (m-80) cc_final: 0.8843 (m-80) REVERT: A 107 TYR cc_start: 0.9601 (OUTLIER) cc_final: 0.9356 (m-80) REVERT: A 118 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: A 232 GLU cc_start: 0.8947 (pp20) cc_final: 0.8695 (pp20) REVERT: A 233 MET cc_start: 0.9432 (mmm) cc_final: 0.9181 (mmm) REVERT: A 320 MET cc_start: 0.9026 (mmm) cc_final: 0.8585 (mmm) REVERT: A 322 LEU cc_start: 0.9671 (mt) cc_final: 0.9455 (tt) REVERT: A 323 LEU cc_start: 0.9750 (tp) cc_final: 0.9517 (pp) REVERT: A 362 LEU cc_start: 0.9689 (tt) cc_final: 0.9417 (tp) REVERT: A 366 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9265 (mm) REVERT: A 432 MET cc_start: 0.9519 (ttm) cc_final: 0.9190 (tpp) REVERT: A 440 MET cc_start: 0.9444 (mmm) cc_final: 0.8952 (mmm) REVERT: A 470 MET cc_start: 0.9442 (ptm) cc_final: 0.9230 (ppp) REVERT: A 492 MET cc_start: 0.9203 (mmm) cc_final: 0.8948 (mmm) REVERT: A 542 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9301 (tp) REVERT: A 595 MET cc_start: 0.8860 (ptp) cc_final: 0.8568 (ppp) REVERT: A 598 MET cc_start: 0.9171 (ppp) cc_final: 0.8164 (ppp) REVERT: A 599 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9091 (mmm) REVERT: A 603 MET cc_start: 0.8889 (ppp) cc_final: 0.8608 (ppp) REVERT: A 604 LEU cc_start: 0.9538 (pp) cc_final: 0.9315 (pp) REVERT: A 616 TYR cc_start: 0.9257 (t80) cc_final: 0.8805 (t80) REVERT: A 688 MET cc_start: 0.8547 (tpt) cc_final: 0.7999 (tpp) REVERT: A 885 TYR cc_start: 0.9168 (t80) cc_final: 0.8679 (t80) REVERT: A 1061 LEU cc_start: 0.9911 (OUTLIER) cc_final: 0.9612 (pp) REVERT: A 1184 LYS cc_start: 0.9770 (tppt) cc_final: 0.9437 (tppt) REVERT: A 1200 TRP cc_start: 0.9473 (OUTLIER) cc_final: 0.9184 (p90) REVERT: A 1217 LEU cc_start: 0.9854 (OUTLIER) cc_final: 0.9621 (mm) REVERT: A 1225 MET cc_start: 0.9558 (mmp) cc_final: 0.9258 (mmm) REVERT: A 1258 MET cc_start: 0.9504 (mmm) cc_final: 0.9253 (mmp) REVERT: A 1349 ARG cc_start: 0.9706 (OUTLIER) cc_final: 0.9299 (mtm180) REVERT: A 1399 ASN cc_start: 0.9817 (OUTLIER) cc_final: 0.9576 (m-40) outliers start: 36 outliers final: 26 residues processed: 165 average time/residue: 0.1965 time to fit residues: 50.3824 Evaluate side-chains 174 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1399 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 91 optimal weight: 0.0470 chunk 111 optimal weight: 0.0020 chunk 128 optimal weight: 5.9990 overall best weight: 0.9090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 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 = 0.3409 r_free = 0.3409 target = 0.051370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037730 restraints weight = 68360.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038953 restraints weight = 36326.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.039790 restraints weight = 24102.346| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11475 Z= 0.126 Angle : 0.817 15.846 15562 Z= 0.361 Chirality : 0.046 0.331 1824 Planarity : 0.004 0.054 1932 Dihedral : 3.784 16.395 1510 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.87 % Allowed : 28.15 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1408 helix: 0.98 (0.18), residues: 872 sheet: 1.13 (0.62), residues: 71 loop : -0.35 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1200 HIS 0.007 0.000 HIS A1371 PHE 0.012 0.001 PHE A 580 TYR 0.020 0.001 TYR A 616 ARG 0.009 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 623) hydrogen bonds : angle 4.43820 ( 1812) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.51276 ( 2) covalent geometry : bond 0.00271 (11474) covalent geometry : angle 0.81723 (15560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.09 seconds wall clock time: 65 minutes 12.71 seconds (3912.71 seconds total)