Starting phenix.real_space_refine on Sat Aug 23 09:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx7_36691/08_2025/8jx7_36691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx7_36691/08_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_36691/08_2025/8jx7_36691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx7_36691/08_2025/8jx7_36691.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx7_36691/08_2025/8jx7_36691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx7_36691/08_2025/8jx7_36691.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.39, per 1000 atoms: 0.21 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: 0.75 Conformation dependent library (CDL) restraints added in 515.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.96 Time building geometry restraints manager: 1.09 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: 0.970 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- 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 : 8.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 628 TYR 0.005 0.001 TYR A 206 PHE 0.035 0.001 PHE A1418 TRP 0.026 0.001 TRP A1200 HIS 0.005 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00290 (11474) covalent geometry : angle 0.64642 (15560) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.10677 ( 2) hydrogen bonds : bond 0.26835 ( 623) hydrogen bonds : angle 8.31695 ( 1812) *********************** 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 : 0.463 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: 0.8549 (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: 0.7890 (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: 0.0857 time to fit residues: 35.8314 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 HIS 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 = 0.3336 r_free = 0.3336 target = 0.053612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.039427 restraints weight = 72649.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.040807 restraints weight = 38405.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041726 restraints weight = 25300.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042357 restraints weight = 19009.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042803 restraints weight = 15545.844| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11475 Z= 0.191 Angle : 0.785 12.456 15562 Z= 0.386 Chirality : 0.046 0.267 1824 Planarity : 0.005 0.049 1932 Dihedral : 4.004 21.045 1510 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.26 % Allowed : 22.89 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.22), residues: 1408 helix: 0.30 (0.17), residues: 869 sheet: 0.62 (0.60), residues: 72 loop : -0.17 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1289 TYR 0.024 0.001 TYR A 616 PHE 0.036 0.002 PHE A 74 TRP 0.024 0.001 TRP A1200 HIS 0.006 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00393 (11474) covalent geometry : angle 0.78458 (15560) SS BOND : bond 0.00260 ( 1) SS BOND : angle 1.13482 ( 2) hydrogen bonds : bond 0.05845 ( 623) hydrogen bonds : angle 5.22307 ( 1812) *********************** 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 245 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9674 (tp) cc_final: 0.9424 (pp) REVERT: A 74 PHE cc_start: 0.9240 (m-80) cc_final: 0.8834 (m-80) REVERT: A 103 ASN cc_start: 0.9603 (m-40) cc_final: 0.9369 (m110) REVERT: A 138 LEU cc_start: 0.9537 (tt) cc_final: 0.9312 (tt) REVERT: A 212 ILE cc_start: 0.9748 (OUTLIER) cc_final: 0.9524 (tp) REVERT: A 230 ASP cc_start: 0.8349 (p0) cc_final: 0.7264 (p0) REVERT: A 233 MET cc_start: 0.9565 (mmm) cc_final: 0.8827 (mmm) REVERT: A 320 MET cc_start: 0.9007 (mmm) cc_final: 0.8802 (mmm) REVERT: A 397 MET cc_start: 0.9485 (mtm) cc_final: 0.9190 (mtm) REVERT: A 432 MET cc_start: 0.9497 (ttm) cc_final: 0.9121 (tpp) REVERT: A 437 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8608 (p90) REVERT: A 440 MET cc_start: 0.9527 (mmm) cc_final: 0.9231 (mmm) REVERT: A 593 LEU cc_start: 0.9655 (tp) cc_final: 0.9355 (tp) REVERT: A 598 MET cc_start: 0.8497 (ppp) cc_final: 0.8109 (ppp) REVERT: A 599 MET cc_start: 0.9457 (mmm) cc_final: 0.8903 (mmm) REVERT: A 603 MET cc_start: 0.9003 (tmm) cc_final: 0.8788 (ppp) REVERT: A 684 MET cc_start: 0.9622 (mpp) cc_final: 0.9417 (mpp) REVERT: A 688 MET cc_start: 0.8573 (tpp) cc_final: 0.8354 (tpp) REVERT: A 745 MET cc_start: 0.9536 (ppp) cc_final: 0.9278 (ppp) REVERT: A 892 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8679 (mm-30) REVERT: A 903 MET cc_start: 0.9549 (mpp) cc_final: 0.9199 (mpp) REVERT: A 984 LEU cc_start: 0.9802 (tt) cc_final: 0.9485 (mm) REVERT: A 988 MET cc_start: 0.9257 (ptp) cc_final: 0.9037 (ttp) REVERT: A 1032 LEU cc_start: 0.9814 (OUTLIER) cc_final: 0.9573 (pp) REVERT: A 1139 MET cc_start: 0.8975 (tmm) cc_final: 0.8691 (ppp) REVERT: A 1225 MET cc_start: 0.9663 (mmm) cc_final: 0.9404 (mmm) REVERT: A 1226 MET cc_start: 0.9541 (mmm) cc_final: 0.9301 (mmm) REVERT: A 1258 MET cc_start: 0.9042 (mmm) cc_final: 0.8789 (mmp) REVERT: A 1349 ARG cc_start: 0.9709 (OUTLIER) cc_final: 0.9398 (mtp180) REVERT: A 1399 ASN cc_start: 0.9825 (OUTLIER) cc_final: 0.9547 (m110) REVERT: A 1505 MET cc_start: 0.9717 (mmm) cc_final: 0.9424 (mmm) outliers start: 66 outliers final: 27 residues processed: 225 average time/residue: 0.0740 time to fit residues: 25.5832 Evaluate side-chains 190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 182 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 434 VAL Chi-restraints excluded: chain A residue 437 PHE 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 1211 LEU 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 138 optimal weight: 40.0000 chunk 11 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.034656 restraints weight = 71042.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035839 restraints weight = 38916.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036654 restraints weight = 26110.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037227 restraints weight = 19782.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037603 restraints weight = 16189.623| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3186 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= 0.202 Angle : 0.723 10.359 15562 Z= 0.355 Chirality : 0.044 0.236 1824 Planarity : 0.004 0.046 1932 Dihedral : 3.919 21.585 1510 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.10 % Allowed : 23.92 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1408 helix: 0.49 (0.17), residues: 881 sheet: 0.62 (0.62), residues: 67 loop : -0.25 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1335 TYR 0.012 0.001 TYR A 970 PHE 0.031 0.002 PHE A1123 TRP 0.018 0.001 TRP A1200 HIS 0.006 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00417 (11474) covalent geometry : angle 0.72276 (15560) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.74729 ( 2) hydrogen bonds : bond 0.05130 ( 623) hydrogen bonds : angle 4.97393 ( 1812) *********************** 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 226 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9744 (mp) cc_final: 0.9531 (pp) REVERT: A 42 LEU cc_start: 0.9648 (tp) cc_final: 0.9421 (pp) REVERT: A 74 PHE cc_start: 0.9315 (m-80) cc_final: 0.8804 (m-80) REVERT: A 107 TYR cc_start: 0.9765 (OUTLIER) cc_final: 0.9312 (m-80) REVERT: A 212 ILE cc_start: 0.9750 (OUTLIER) cc_final: 0.9530 (tp) REVERT: A 320 MET cc_start: 0.8945 (mmm) cc_final: 0.8710 (mmm) REVERT: A 385 CYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9176 (p) REVERT: A 432 MET cc_start: 0.9507 (ttm) cc_final: 0.9192 (tpp) REVERT: A 540 SER cc_start: 0.9782 (m) cc_final: 0.9538 (p) REVERT: A 595 MET cc_start: 0.8965 (ptp) cc_final: 0.8303 (ppp) REVERT: A 598 MET cc_start: 0.8571 (ppp) cc_final: 0.8185 (ppp) REVERT: A 599 MET cc_start: 0.9468 (mmm) cc_final: 0.8738 (mmm) REVERT: A 684 MET cc_start: 0.9603 (mpp) cc_final: 0.9313 (mpp) REVERT: A 688 MET cc_start: 0.8713 (tpp) cc_final: 0.8478 (tpp) REVERT: A 885 TYR cc_start: 0.9074 (t80) cc_final: 0.8770 (t80) REVERT: A 984 LEU cc_start: 0.9806 (tt) cc_final: 0.9478 (mm) REVERT: A 1032 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9586 (pp) REVERT: A 1123 PHE cc_start: 0.9672 (t80) cc_final: 0.9308 (t80) REVERT: A 1130 LEU cc_start: 0.9758 (mt) cc_final: 0.9470 (pp) REVERT: A 1185 HIS cc_start: 0.9681 (OUTLIER) cc_final: 0.9406 (t-90) REVERT: A 1225 MET cc_start: 0.9615 (mmm) cc_final: 0.9229 (mmm) REVERT: A 1258 MET cc_start: 0.9312 (mmm) cc_final: 0.9059 (mmp) REVERT: A 1349 ARG cc_start: 0.9708 (OUTLIER) cc_final: 0.9432 (mtp180) REVERT: A 1399 ASN cc_start: 0.9796 (OUTLIER) cc_final: 0.9499 (m110) REVERT: A 1505 MET cc_start: 0.9683 (mmm) cc_final: 0.9403 (mmm) outliers start: 64 outliers final: 34 residues processed: 207 average time/residue: 0.0764 time to fit residues: 24.3637 Evaluate side-chains 184 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 VAL 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 116 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER 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 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU 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 714 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1185 HIS Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1211 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.050623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036934 restraints weight = 76348.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038222 restraints weight = 39364.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039069 restraints weight = 25822.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039622 restraints weight = 19418.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.040039 restraints weight = 16026.547| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11475 Z= 0.211 Angle : 0.723 10.953 15562 Z= 0.353 Chirality : 0.045 0.230 1824 Planarity : 0.004 0.050 1932 Dihedral : 3.894 20.971 1510 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.18 % Allowed : 24.72 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.22), residues: 1408 helix: 0.73 (0.17), residues: 869 sheet: 0.70 (0.64), residues: 67 loop : -0.28 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.015 0.001 TYR A 970 PHE 0.019 0.001 PHE A 437 TRP 0.019 0.001 TRP A1200 HIS 0.005 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00434 (11474) covalent geometry : angle 0.72268 (15560) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.75250 ( 2) hydrogen bonds : bond 0.04653 ( 623) hydrogen bonds : angle 4.89189 ( 1812) *********************** 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 217 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9750 (mp) cc_final: 0.9527 (pp) REVERT: A 74 PHE cc_start: 0.9354 (m-80) cc_final: 0.8824 (m-80) REVERT: A 107 TYR cc_start: 0.9729 (OUTLIER) cc_final: 0.9281 (m-80) REVERT: A 118 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 212 ILE cc_start: 0.9755 (OUTLIER) cc_final: 0.9546 (tp) REVERT: A 320 MET cc_start: 0.8935 (mmm) cc_final: 0.8731 (pmm) REVERT: A 323 LEU cc_start: 0.9732 (tp) cc_final: 0.9511 (pp) REVERT: A 432 MET cc_start: 0.9506 (ttm) cc_final: 0.9028 (tpp) REVERT: A 440 MET cc_start: 0.9471 (mmm) cc_final: 0.9122 (mmm) REVERT: A 492 MET cc_start: 0.9206 (mmm) cc_final: 0.8840 (mmm) REVERT: A 540 SER cc_start: 0.9777 (m) cc_final: 0.9536 (p) REVERT: A 542 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9326 (tp) REVERT: A 598 MET cc_start: 0.8648 (ppp) cc_final: 0.8100 (ppp) REVERT: A 599 MET cc_start: 0.9410 (mmm) cc_final: 0.8900 (mmm) REVERT: A 603 MET cc_start: 0.9021 (tmm) cc_final: 0.8667 (ppp) REVERT: A 684 MET cc_start: 0.9519 (mpp) cc_final: 0.9266 (mpp) REVERT: A 885 TYR cc_start: 0.9111 (t80) cc_final: 0.8760 (t80) REVERT: A 988 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9182 (ttp) REVERT: A 1184 LYS cc_start: 0.9732 (tppt) cc_final: 0.9444 (tppt) REVERT: A 1185 HIS cc_start: 0.9690 (OUTLIER) cc_final: 0.9418 (t-90) REVERT: A 1200 TRP cc_start: 0.9440 (OUTLIER) cc_final: 0.9233 (p90) REVERT: A 1225 MET cc_start: 0.9585 (mmm) cc_final: 0.9336 (mmm) REVERT: A 1258 MET cc_start: 0.9396 (mmm) cc_final: 0.9116 (mmp) REVERT: A 1328 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8606 (tp30) REVERT: A 1349 ARG cc_start: 0.9709 (OUTLIER) cc_final: 0.9427 (mtp180) REVERT: A 1399 ASN cc_start: 0.9801 (OUTLIER) cc_final: 0.9576 (m-40) REVERT: A 1505 MET cc_start: 0.9728 (mmm) cc_final: 0.9473 (mmm) outliers start: 65 outliers final: 33 residues processed: 199 average time/residue: 0.0825 time to fit residues: 25.7274 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 GLN 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 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 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 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 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 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1185 HIS Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1328 GLU 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 1391 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 0 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.092840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.080927 restraints weight = 74055.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.082096 restraints weight = 25729.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.082651 restraints weight = 12394.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.083121 restraints weight = 8175.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.083388 restraints weight = 5903.376| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11475 Z= 0.137 Angle : 0.726 12.306 15562 Z= 0.339 Chirality : 0.045 0.357 1824 Planarity : 0.004 0.055 1932 Dihedral : 3.850 19.960 1510 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.99 % Allowed : 25.92 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.23), residues: 1408 helix: 0.87 (0.18), residues: 869 sheet: 0.91 (0.63), residues: 70 loop : -0.30 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.013 0.001 TYR A 970 PHE 0.030 0.001 PHE A1037 TRP 0.020 0.001 TRP A1200 HIS 0.004 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00294 (11474) covalent geometry : angle 0.72555 (15560) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.64539 ( 2) hydrogen bonds : bond 0.04454 ( 623) hydrogen bonds : angle 4.66916 ( 1812) *********************** 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 203 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9749 (mp) cc_final: 0.9522 (pp) REVERT: A 42 LEU cc_start: 0.9711 (tt) cc_final: 0.9498 (pp) REVERT: A 74 PHE cc_start: 0.9330 (m-80) cc_final: 0.8759 (m-80) REVERT: A 107 TYR cc_start: 0.9718 (OUTLIER) cc_final: 0.9408 (m-80) REVERT: A 118 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: A 169 PHE cc_start: 0.9234 (m-10) cc_final: 0.8996 (m-80) REVERT: A 212 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9496 (tp) REVERT: A 320 MET cc_start: 0.8960 (mmm) cc_final: 0.8721 (pmm) REVERT: A 336 THR cc_start: 0.9733 (OUTLIER) cc_final: 0.9395 (p) REVERT: A 385 CYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9140 (p) REVERT: A 397 MET cc_start: 0.9498 (mtm) cc_final: 0.9143 (mtm) REVERT: A 432 MET cc_start: 0.9565 (ttm) cc_final: 0.9061 (tpp) REVERT: A 440 MET cc_start: 0.9592 (mmm) cc_final: 0.9191 (mmm) REVERT: A 540 SER cc_start: 0.9766 (m) cc_final: 0.9516 (p) REVERT: A 542 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9287 (tp) REVERT: A 681 ILE cc_start: 0.9752 (OUTLIER) cc_final: 0.9383 (tt) REVERT: A 684 MET cc_start: 0.9478 (mpp) cc_final: 0.9257 (mpp) REVERT: A 688 MET cc_start: 0.8645 (tpt) cc_final: 0.8189 (tpp) REVERT: A 885 TYR cc_start: 0.9116 (t80) cc_final: 0.8265 (t80) REVERT: A 905 ARG cc_start: 0.9475 (ttp80) cc_final: 0.8646 (ttp80) REVERT: A 1061 LEU cc_start: 0.9881 (OUTLIER) cc_final: 0.9575 (pp) REVERT: A 1123 PHE cc_start: 0.9606 (t80) cc_final: 0.9162 (t80) REVERT: A 1184 LYS cc_start: 0.9738 (tppt) cc_final: 0.9454 (tppt) REVERT: A 1185 HIS cc_start: 0.9796 (OUTLIER) cc_final: 0.9535 (t-90) REVERT: A 1225 MET cc_start: 0.9668 (mmm) cc_final: 0.9246 (mmm) REVERT: A 1258 MET cc_start: 0.9426 (mmm) cc_final: 0.9091 (mmp) REVERT: A 1275 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.9298 (m-10) REVERT: A 1349 ARG cc_start: 0.9686 (OUTLIER) cc_final: 0.9314 (mtp180) REVERT: A 1399 ASN cc_start: 0.9763 (OUTLIER) cc_final: 0.9479 (m-40) REVERT: A 1505 MET cc_start: 0.9656 (mmm) cc_final: 0.9454 (mmm) outliers start: 50 outliers final: 27 residues processed: 192 average time/residue: 0.0769 time to fit residues: 23.1634 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 336 THR 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 446 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 681 ILE 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 822 MET 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 1061 LEU 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 1185 HIS Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1275 TYR 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 1386 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 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.0010 chunk 11 optimal weight: 2.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** 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 = 0.3311 r_free = 0.3311 target = 0.051876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038128 restraints weight = 74834.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.039443 restraints weight = 38809.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040338 restraints weight = 25486.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040979 restraints weight = 19024.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041364 restraints weight = 15425.378| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11475 Z= 0.124 Angle : 0.722 12.627 15562 Z= 0.334 Chirality : 0.045 0.352 1824 Planarity : 0.004 0.056 1932 Dihedral : 3.813 19.543 1510 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.83 % Allowed : 26.79 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1408 helix: 0.90 (0.18), residues: 867 sheet: 1.01 (0.63), residues: 70 loop : -0.35 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.010 0.001 TYR A 970 PHE 0.014 0.001 PHE A 74 TRP 0.020 0.001 TRP A1200 HIS 0.003 0.000 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00263 (11474) covalent geometry : angle 0.72222 (15560) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.57116 ( 2) hydrogen bonds : bond 0.04241 ( 623) hydrogen bonds : angle 4.53442 ( 1812) *********************** 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 210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9733 (mp) cc_final: 0.9482 (pp) REVERT: A 74 PHE cc_start: 0.9342 (m-80) cc_final: 0.8764 (m-80) REVERT: A 107 TYR cc_start: 0.9638 (OUTLIER) cc_final: 0.9292 (m-80) REVERT: A 118 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: A 131 PHE cc_start: 0.8892 (t80) cc_final: 0.8595 (t80) REVERT: A 169 PHE cc_start: 0.9230 (m-10) cc_final: 0.8928 (m-80) REVERT: A 212 ILE cc_start: 0.9727 (OUTLIER) cc_final: 0.9506 (tp) REVERT: A 385 CYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 432 MET cc_start: 0.9513 (ttm) cc_final: 0.9089 (tpp) REVERT: A 438 MET cc_start: 0.8822 (ppp) cc_final: 0.8585 (ppp) REVERT: A 440 MET cc_start: 0.9465 (mmm) cc_final: 0.9012 (mmm) REVERT: A 500 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9111 (pttm) REVERT: A 512 LEU cc_start: 0.9839 (OUTLIER) cc_final: 0.9634 (mm) REVERT: A 542 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9276 (tp) REVERT: A 551 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8986 (tm-30) REVERT: A 595 MET cc_start: 0.8901 (ptp) cc_final: 0.8502 (ppp) REVERT: A 598 MET cc_start: 0.8632 (ppp) cc_final: 0.7407 (ppp) REVERT: A 599 MET cc_start: 0.9149 (tpt) cc_final: 0.8390 (mmm) REVERT: A 681 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9366 (tt) REVERT: A 684 MET cc_start: 0.9431 (mpp) cc_final: 0.9229 (mpp) REVERT: A 885 TYR cc_start: 0.9019 (t80) cc_final: 0.8526 (t80) REVERT: A 1044 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.8315 (m100) REVERT: A 1061 LEU cc_start: 0.9875 (OUTLIER) cc_final: 0.9594 (pp) REVERT: A 1123 PHE cc_start: 0.9556 (t80) cc_final: 0.9258 (t80) REVERT: A 1130 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9443 (pp) REVERT: A 1184 LYS cc_start: 0.9748 (tppt) cc_final: 0.9399 (tppt) REVERT: A 1185 HIS cc_start: 0.9599 (OUTLIER) cc_final: 0.9335 (t-90) REVERT: A 1217 LEU cc_start: 0.9880 (OUTLIER) cc_final: 0.9630 (mm) REVERT: A 1225 MET cc_start: 0.9499 (mmm) cc_final: 0.9152 (mmm) REVERT: A 1258 MET cc_start: 0.9393 (mmm) cc_final: 0.9112 (mmp) REVERT: A 1275 TYR cc_start: 0.9511 (OUTLIER) cc_final: 0.9277 (m-10) REVERT: A 1328 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: A 1349 ARG cc_start: 0.9674 (OUTLIER) cc_final: 0.9296 (mtp180) REVERT: A 1399 ASN cc_start: 0.9792 (OUTLIER) cc_final: 0.9535 (m-40) outliers start: 48 outliers final: 22 residues processed: 199 average time/residue: 0.0753 time to fit residues: 23.6281 Evaluate side-chains 184 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 ILE Chi-restraints excluded: chain A residue 223 LEU 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 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 681 ILE 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 990 SER Chi-restraints excluded: chain A residue 1044 TRP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1185 HIS Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1275 TYR 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 1386 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 3 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038370 restraints weight = 74692.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039710 restraints weight = 39820.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.040603 restraints weight = 26409.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.041175 restraints weight = 19936.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041603 restraints weight = 16490.550| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4041 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= 0.127 Angle : 0.746 12.666 15562 Z= 0.340 Chirality : 0.045 0.361 1824 Planarity : 0.004 0.055 1932 Dihedral : 3.778 19.114 1510 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.27 % Allowed : 28.23 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1408 helix: 0.92 (0.18), residues: 867 sheet: 1.06 (0.63), residues: 70 loop : -0.42 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 905 TYR 0.022 0.001 TYR A 616 PHE 0.013 0.001 PHE A1240 TRP 0.020 0.001 TRP A1200 HIS 0.003 0.000 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00272 (11474) covalent geometry : angle 0.74592 (15560) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.51130 ( 2) hydrogen bonds : bond 0.04142 ( 623) hydrogen bonds : angle 4.50643 ( 1812) *********************** 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 199 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.9604 (OUTLIER) cc_final: 0.9286 (mm-40) REVERT: A 37 LEU cc_start: 0.9740 (mp) cc_final: 0.9522 (pp) REVERT: A 74 PHE cc_start: 0.9376 (m-80) cc_final: 0.8794 (m-80) REVERT: A 107 TYR cc_start: 0.9622 (OUTLIER) cc_final: 0.9318 (m-80) REVERT: A 118 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: A 131 PHE cc_start: 0.8945 (t80) cc_final: 0.8672 (t80) REVERT: A 169 PHE cc_start: 0.9157 (m-10) cc_final: 0.8849 (m-80) REVERT: A 212 ILE cc_start: 0.9738 (OUTLIER) cc_final: 0.9524 (tp) REVERT: A 232 GLU cc_start: 0.8283 (pp20) cc_final: 0.8050 (pp20) REVERT: A 233 MET cc_start: 0.9050 (mmm) cc_final: 0.8801 (mmm) REVERT: A 336 THR cc_start: 0.9772 (OUTLIER) cc_final: 0.9459 (p) REVERT: A 385 CYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9173 (p) REVERT: A 432 MET cc_start: 0.9550 (ttm) cc_final: 0.9134 (tpp) REVERT: A 438 MET cc_start: 0.8841 (ppp) cc_final: 0.8634 (ppp) REVERT: A 464 LEU cc_start: 0.9655 (mm) cc_final: 0.9395 (pp) REVERT: A 542 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9261 (tp) REVERT: A 598 MET cc_start: 0.8653 (ppp) cc_final: 0.7550 (ppp) REVERT: A 599 MET cc_start: 0.9221 (tpt) cc_final: 0.8647 (mmm) REVERT: A 603 MET cc_start: 0.9003 (tmm) cc_final: 0.8773 (ppp) REVERT: A 684 MET cc_start: 0.9441 (mpp) cc_final: 0.9214 (mpp) REVERT: A 885 TYR cc_start: 0.9133 (t80) cc_final: 0.8501 (t80) REVERT: A 1044 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.8334 (m100) REVERT: A 1061 LEU cc_start: 0.9883 (OUTLIER) cc_final: 0.9587 (pp) REVERT: A 1123 PHE cc_start: 0.9589 (t80) cc_final: 0.9384 (t80) REVERT: A 1130 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9432 (pp) REVERT: A 1184 LYS cc_start: 0.9755 (tppt) cc_final: 0.9366 (tppt) REVERT: A 1185 HIS cc_start: 0.9674 (OUTLIER) cc_final: 0.9381 (t-90) REVERT: A 1200 TRP cc_start: 0.9434 (OUTLIER) cc_final: 0.9167 (p90) REVERT: A 1217 LEU cc_start: 0.9866 (OUTLIER) cc_final: 0.9620 (mm) REVERT: A 1225 MET cc_start: 0.9560 (mmm) cc_final: 0.9242 (mmm) REVERT: A 1258 MET cc_start: 0.9475 (mmm) cc_final: 0.9185 (mmp) REVERT: A 1275 TYR cc_start: 0.9492 (OUTLIER) cc_final: 0.9276 (m-10) REVERT: A 1349 ARG cc_start: 0.9668 (OUTLIER) cc_final: 0.9458 (mtp180) REVERT: A 1399 ASN cc_start: 0.9815 (OUTLIER) cc_final: 0.9575 (m-40) outliers start: 41 outliers final: 20 residues processed: 191 average time/residue: 0.0803 time to fit residues: 24.1055 Evaluate side-chains 189 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN 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 212 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 385 CYS 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 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 990 SER Chi-restraints excluded: chain A residue 1044 TRP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1185 HIS Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1200 TRP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1275 TYR 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 1386 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 39 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 0.0770 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.092475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.080643 restraints weight = 74132.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.081839 restraints weight = 26533.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.082539 restraints weight = 12598.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.082901 restraints weight = 7653.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.083189 restraints weight = 5735.114| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4152 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= 0.135 Angle : 0.773 17.065 15562 Z= 0.351 Chirality : 0.045 0.360 1824 Planarity : 0.004 0.054 1932 Dihedral : 3.772 18.992 1510 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.19 % Allowed : 28.79 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.23), residues: 1408 helix: 0.99 (0.18), residues: 867 sheet: 1.04 (0.63), residues: 71 loop : -0.42 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 905 TYR 0.008 0.001 TYR A 401 PHE 0.012 0.001 PHE A 437 TRP 0.020 0.001 TRP A1200 HIS 0.015 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00296 (11474) covalent geometry : angle 0.77298 (15560) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.76767 ( 2) hydrogen bonds : bond 0.04100 ( 623) hydrogen bonds : angle 4.51628 ( 1812) *********************** 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 195 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9740 (mp) cc_final: 0.9536 (pp) REVERT: A 74 PHE cc_start: 0.9355 (m-80) cc_final: 0.8784 (m-80) REVERT: A 107 TYR cc_start: 0.9623 (OUTLIER) cc_final: 0.9376 (m-80) REVERT: A 118 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: A 169 PHE cc_start: 0.9113 (m-10) cc_final: 0.8824 (m-80) REVERT: A 336 THR cc_start: 0.9738 (OUTLIER) cc_final: 0.9398 (p) REVERT: A 385 CYS cc_start: 0.9594 (OUTLIER) cc_final: 0.9146 (p) REVERT: A 432 MET cc_start: 0.9573 (ttm) cc_final: 0.9371 (ttm) REVERT: A 542 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9224 (tp) REVERT: A 598 MET cc_start: 0.8621 (ppp) cc_final: 0.7667 (ppp) REVERT: A 599 MET cc_start: 0.9195 (tpt) cc_final: 0.8802 (mmm) REVERT: A 603 MET cc_start: 0.9004 (tmm) cc_final: 0.8772 (ppp) REVERT: A 604 LEU cc_start: 0.9586 (pp) cc_final: 0.9356 (pp) REVERT: A 684 MET cc_start: 0.9428 (mpp) cc_final: 0.9212 (mpp) REVERT: A 885 TYR cc_start: 0.9136 (t80) cc_final: 0.8540 (t80) REVERT: A 1044 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.8280 (m100) REVERT: A 1061 LEU cc_start: 0.9882 (OUTLIER) cc_final: 0.9550 (pp) REVERT: A 1123 PHE cc_start: 0.9595 (t80) cc_final: 0.9353 (t80) REVERT: A 1130 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9401 (pp) REVERT: A 1184 LYS cc_start: 0.9752 (tppt) cc_final: 0.9426 (tppt) REVERT: A 1185 HIS cc_start: 0.9782 (OUTLIER) cc_final: 0.9496 (t-90) REVERT: A 1200 TRP cc_start: 0.9502 (OUTLIER) cc_final: 0.9216 (p90) REVERT: A 1217 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9575 (mm) REVERT: A 1225 MET cc_start: 0.9656 (mmm) cc_final: 0.9314 (mmm) REVERT: A 1258 MET cc_start: 0.9503 (mmm) cc_final: 0.9205 (mmp) REVERT: A 1349 ARG cc_start: 0.9666 (OUTLIER) cc_final: 0.9448 (mtp180) REVERT: A 1399 ASN cc_start: 0.9779 (OUTLIER) cc_final: 0.9541 (m-40) outliers start: 40 outliers final: 23 residues processed: 184 average time/residue: 0.0726 time to fit residues: 21.0642 Evaluate side-chains 186 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 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 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 990 SER Chi-restraints excluded: chain A residue 1044 TRP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1185 HIS 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 1386 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 84 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 68 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** 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 = 0.3359 r_free = 0.3359 target = 0.050047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037023 restraints weight = 69278.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038191 restraints weight = 37527.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039011 restraints weight = 24874.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039575 restraints weight = 18626.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039971 restraints weight = 15093.814| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4288 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= 0.139 Angle : 0.792 16.017 15562 Z= 0.362 Chirality : 0.046 0.362 1824 Planarity : 0.004 0.054 1932 Dihedral : 3.816 18.576 1510 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.35 % Allowed : 29.03 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.23), residues: 1408 helix: 0.89 (0.18), residues: 871 sheet: 1.08 (0.62), residues: 71 loop : -0.54 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 905 TYR 0.016 0.001 TYR A1275 PHE 0.011 0.001 PHE A 242 TRP 0.020 0.001 TRP A1200 HIS 0.012 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00301 (11474) covalent geometry : angle 0.79228 (15560) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.57808 ( 2) hydrogen bonds : bond 0.04124 ( 623) hydrogen bonds : angle 4.54826 ( 1812) *********************** 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 190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9730 (mp) cc_final: 0.9517 (pp) REVERT: A 74 PHE cc_start: 0.9382 (m-80) cc_final: 0.8816 (m-80) REVERT: A 118 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: A 169 PHE cc_start: 0.9177 (m-10) cc_final: 0.8862 (m-80) REVERT: A 336 THR cc_start: 0.9758 (OUTLIER) cc_final: 0.9443 (p) REVERT: A 385 CYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9190 (p) REVERT: A 542 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9262 (tp) REVERT: A 598 MET cc_start: 0.8730 (ppp) cc_final: 0.7901 (ppp) REVERT: A 599 MET cc_start: 0.9154 (tpt) cc_final: 0.8849 (mmm) REVERT: A 603 MET cc_start: 0.9006 (tmm) cc_final: 0.8780 (ppp) REVERT: A 885 TYR cc_start: 0.9148 (t80) cc_final: 0.8578 (t80) REVERT: A 1044 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8248 (m100) REVERT: A 1061 LEU cc_start: 0.9888 (OUTLIER) cc_final: 0.9574 (pp) REVERT: A 1115 MET cc_start: 0.9335 (mtt) cc_final: 0.8725 (mtp) REVERT: A 1130 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9417 (pp) REVERT: A 1184 LYS cc_start: 0.9758 (tppt) cc_final: 0.9353 (tppt) REVERT: A 1185 HIS cc_start: 0.9655 (OUTLIER) cc_final: 0.9346 (t-90) REVERT: A 1200 TRP cc_start: 0.9487 (OUTLIER) cc_final: 0.9187 (p90) REVERT: A 1217 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9576 (mm) REVERT: A 1225 MET cc_start: 0.9578 (mmm) cc_final: 0.9290 (mmm) REVERT: A 1258 MET cc_start: 0.9482 (mmm) cc_final: 0.9209 (mmp) REVERT: A 1349 ARG cc_start: 0.9681 (OUTLIER) cc_final: 0.9458 (mtp180) REVERT: A 1399 ASN cc_start: 0.9794 (OUTLIER) cc_final: 0.9557 (m-40) outliers start: 42 outliers final: 24 residues processed: 179 average time/residue: 0.0717 time to fit residues: 20.0904 Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 446 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 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 990 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 TRP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1185 HIS 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 1386 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 137 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.049858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.036944 restraints weight = 68228.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038133 restraints weight = 36881.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038946 restraints weight = 24420.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039538 restraints weight = 18268.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039944 restraints weight = 14754.714| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4368 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= 0.128 Angle : 0.813 15.987 15562 Z= 0.363 Chirality : 0.045 0.367 1824 Planarity : 0.003 0.054 1932 Dihedral : 3.831 18.006 1510 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.71 % Allowed : 29.35 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.23), residues: 1408 helix: 0.88 (0.18), residues: 874 sheet: 1.19 (0.63), residues: 71 loop : -0.45 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 905 TYR 0.014 0.001 TYR A1275 PHE 0.012 0.001 PHE A 242 TRP 0.020 0.001 TRP A1200 HIS 0.009 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00278 (11474) covalent geometry : angle 0.81281 (15560) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.53588 ( 2) hydrogen bonds : bond 0.04056 ( 623) hydrogen bonds : angle 4.46486 ( 1812) ********************** 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 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9718 (mp) cc_final: 0.9503 (pp) REVERT: A 74 PHE cc_start: 0.9377 (m-80) cc_final: 0.8809 (m-80) REVERT: A 118 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: A 169 PHE cc_start: 0.9150 (m-10) cc_final: 0.8827 (m-80) REVERT: A 336 THR cc_start: 0.9756 (OUTLIER) cc_final: 0.9435 (p) REVERT: A 385 CYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9190 (p) REVERT: A 432 MET cc_start: 0.9446 (ttm) cc_final: 0.8956 (tpp) REVERT: A 441 LEU cc_start: 0.9459 (mm) cc_final: 0.9255 (mm) REVERT: A 493 LYS cc_start: 0.9647 (ptpp) cc_final: 0.9408 (ptpp) REVERT: A 542 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9231 (tp) REVERT: A 595 MET cc_start: 0.8477 (ppp) cc_final: 0.6636 (ppp) REVERT: A 598 MET cc_start: 0.8746 (ppp) cc_final: 0.7561 (ppp) REVERT: A 599 MET cc_start: 0.9168 (tpt) cc_final: 0.8717 (mmm) REVERT: A 603 MET cc_start: 0.9006 (tmm) cc_final: 0.8788 (ppp) REVERT: A 604 LEU cc_start: 0.9593 (pp) cc_final: 0.9356 (pp) REVERT: A 616 TYR cc_start: 0.9225 (t80) cc_final: 0.8498 (t80) REVERT: A 885 TYR cc_start: 0.9137 (t80) cc_final: 0.8558 (t80) REVERT: A 1044 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.8249 (m100) REVERT: A 1061 LEU cc_start: 0.9887 (OUTLIER) cc_final: 0.9568 (pp) REVERT: A 1130 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9396 (pp) REVERT: A 1184 LYS cc_start: 0.9758 (tppt) cc_final: 0.9345 (tppt) REVERT: A 1185 HIS cc_start: 0.9653 (OUTLIER) cc_final: 0.9342 (t-90) REVERT: A 1191 ASP cc_start: 0.9644 (OUTLIER) cc_final: 0.9359 (m-30) REVERT: A 1200 TRP cc_start: 0.9469 (OUTLIER) cc_final: 0.9170 (p90) REVERT: A 1217 LEU cc_start: 0.9823 (OUTLIER) cc_final: 0.9567 (mm) REVERT: A 1225 MET cc_start: 0.9590 (mmm) cc_final: 0.9242 (mmm) REVERT: A 1258 MET cc_start: 0.9470 (mmm) cc_final: 0.9188 (mmp) REVERT: A 1349 ARG cc_start: 0.9676 (OUTLIER) cc_final: 0.9258 (mtm180) REVERT: A 1399 ASN cc_start: 0.9792 (OUTLIER) cc_final: 0.9552 (m-40) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.0733 time to fit residues: 20.1114 Evaluate side-chains 182 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 385 CYS 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 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 990 SER Chi-restraints excluded: chain A residue 1044 TRP Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1185 HIS 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 67 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN ** 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 = 0.3315 r_free = 0.3315 target = 0.051473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037795 restraints weight = 75879.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039092 restraints weight = 39896.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.039973 restraints weight = 26309.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040540 restraints weight = 19746.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040978 restraints weight = 16245.244| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11475 Z= 0.142 Angle : 0.829 18.070 15562 Z= 0.374 Chirality : 0.046 0.364 1824 Planarity : 0.003 0.054 1932 Dihedral : 3.823 17.936 1510 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.79 % Allowed : 29.74 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1408 helix: 0.90 (0.18), residues: 873 sheet: 1.18 (0.62), residues: 71 loop : -0.42 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 905 TYR 0.013 0.001 TYR A1275 PHE 0.011 0.001 PHE A1182 TRP 0.020 0.001 TRP A1200 HIS 0.009 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00310 (11474) covalent geometry : angle 0.82929 (15560) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.48959 ( 2) hydrogen bonds : bond 0.04010 ( 623) hydrogen bonds : angle 4.51517 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.29 seconds wall clock time: 33 minutes 44.52 seconds (2024.52 seconds total)