Starting phenix.real_space_refine on Tue Nov 18 12:43:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l53_0836/11_2025/6l53_0836.map" } resolution = 3.63 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= 0.000 sd= 1.000 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 72 5.16 5 C 8824 2.51 5 N 2394 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13991 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1935, 13991 Classifications: {'peptide': 1935} Incomplete info: {'truncation_to_alanine': 304} Link IDs: {'CIS': 63, 'PCIS': 4, 'PTRANS': 63, 'TRANS': 1804} Chain breaks: 27 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1471 Unresolved non-hydrogen angles: 1868 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ARG:plan': 48, 'TYR:plan': 20, 'GLN:plan1': 25, 'PHE:plan': 15, 'ASN:plan1': 11, 'HIS:plan': 12, 'TRP:plan': 19, 'GLU:plan': 28, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 975 Time building chain proxies: 3.41, per 1000 atoms: 0.24 Number of scatterers: 13991 At special positions: 0 Unit cell: (130, 180.96, 132.08, 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 72 16.00 O 2701 8.00 N 2394 7.00 C 8824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 676.6 milliseconds 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 2 sheets defined 58.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.737A pdb=" N ASP A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.031A pdb=" N GLU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.759A pdb=" N ALA A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.512A pdb=" N THR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.574A pdb=" N ASN A 181 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.103A pdb=" N SER A 204 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.885A pdb=" N GLU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.695A pdb=" N PHE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.987A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 293 removed outlier: 4.217A pdb=" N SER A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.829A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.560A pdb=" N CYS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.864A pdb=" N ILE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 342 through 356 Proline residue: A 348 - end of helix removed outlier: 3.592A pdb=" N ALA A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.658A pdb=" N GLU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.668A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 removed outlier: 3.560A pdb=" N LEU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 444 through 457 removed outlier: 4.177A pdb=" N PHE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.630A pdb=" N VAL A 462 " --> pdb=" O CYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.731A pdb=" N MET A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 removed outlier: 4.400A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 5.433A pdb=" N GLN A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 582 removed outlier: 4.380A pdb=" N LYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.650A pdb=" N ASP A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.511A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.835A pdb=" N SER A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.628A pdb=" N TYR A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 removed outlier: 3.862A pdb=" N LEU A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.721A pdb=" N LYS A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 4.018A pdb=" N VAL A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.615A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.964A pdb=" N GLN A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 937 through 948 removed outlier: 3.843A pdb=" N ILE A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 985 removed outlier: 3.702A pdb=" N ASN A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 981 " --> pdb=" O GLN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.649A pdb=" N TYR A 995 " --> pdb=" O LYS A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1016 removed outlier: 3.708A pdb=" N THR A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1073 through 1078 removed outlier: 3.614A pdb=" N VAL A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1085 removed outlier: 3.766A pdb=" N LEU A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1091 through 1106 removed outlier: 3.697A pdb=" N TRP A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1105 " --> pdb=" O GLY A1101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A1106 " --> pdb=" O LYS A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1120 removed outlier: 3.873A pdb=" N LYS A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1133 removed outlier: 4.057A pdb=" N LEU A1129 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1215 removed outlier: 3.561A pdb=" N ASP A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1297 removed outlier: 3.811A pdb=" N LYS A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER A1288 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1295 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1316 through 1331 removed outlier: 3.538A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 removed outlier: 3.739A pdb=" N LEU A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.609A pdb=" N VAL A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1368 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.705A pdb=" N ASN A1404 " --> pdb=" O THR A1400 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1406 " --> pdb=" O TYR A1402 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1420 Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 3.705A pdb=" N ALA A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 4.107A pdb=" N THR A1456 " --> pdb=" O GLN A1452 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A1459 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1460 " --> pdb=" O THR A1456 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 4.134A pdb=" N THR A1471 " --> pdb=" O LYS A1467 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A1472 " --> pdb=" O LYS A1468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1484 removed outlier: 3.876A pdb=" N LEU A1483 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A1484 " --> pdb=" O PRO A1481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1480 through 1484' Processing helix chain 'A' and resid 1488 through 1497 removed outlier: 4.148A pdb=" N THR A1493 " --> pdb=" O LYS A1489 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 3.578A pdb=" N THR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1533 " --> pdb=" O ALA A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1538 removed outlier: 4.117A pdb=" N LYS A1537 " --> pdb=" O ALA A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.704A pdb=" N GLN A1603 " --> pdb=" O PHE A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1632 removed outlier: 4.163A pdb=" N ALA A1621 " --> pdb=" O LYS A1617 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1628 " --> pdb=" O SER A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'A' and resid 1644 through 1655 removed outlier: 3.799A pdb=" N LYS A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A1651 " --> pdb=" O PRO A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1675 removed outlier: 3.860A pdb=" N GLU A1665 " --> pdb=" O ILE A1661 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1668 " --> pdb=" O GLU A1664 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1708 removed outlier: 3.548A pdb=" N ILE A1707 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1708 " --> pdb=" O VAL A1704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1703 through 1708' Processing helix chain 'A' and resid 1708 through 1713 removed outlier: 4.239A pdb=" N ILE A1712 " --> pdb=" O TRP A1708 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A1713 " --> pdb=" O ARG A1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1708 through 1713' Processing helix chain 'A' and resid 1729 through 1738 removed outlier: 3.842A pdb=" N LYS A1735 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A1736 " --> pdb=" O VAL A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1759 removed outlier: 3.575A pdb=" N SER A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1797 removed outlier: 3.594A pdb=" N VAL A1797 " --> pdb=" O LEU A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1812 removed outlier: 4.197A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A1812 " --> pdb=" O GLU A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1830 Processing helix chain 'A' and resid 1837 through 1851 removed outlier: 3.985A pdb=" N ILE A1841 " --> pdb=" O VAL A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1866 Processing helix chain 'A' and resid 1927 through 1940 removed outlier: 4.042A pdb=" N SER A1931 " --> pdb=" O GLN A1927 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A1936 " --> pdb=" O LYS A1932 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 removed outlier: 3.526A pdb=" N VAL A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1948 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1971 removed outlier: 3.715A pdb=" N VAL A1969 " --> pdb=" O LEU A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.801A pdb=" N ARG A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A1980 " --> pdb=" O TYR A1976 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1981 " --> pdb=" O VAL A1977 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A1986 " --> pdb=" O GLN A1982 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A1989 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1991 " --> pdb=" O GLU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2027 removed outlier: 3.542A pdb=" N PHE A2019 " --> pdb=" O LYS A2015 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A2020 " --> pdb=" O PRO A2016 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A2025 " --> pdb=" O LEU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2072 through 2080 removed outlier: 3.653A pdb=" N LEU A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A2079 " --> pdb=" O MET A2075 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A2080 " --> pdb=" O LEU A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2101 removed outlier: 3.935A pdb=" N LEU A2099 " --> pdb=" O SER A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 removed outlier: 3.559A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2180 removed outlier: 3.941A pdb=" N THR A2179 " --> pdb=" O MET A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2231 Processing helix chain 'A' and resid 2252 through 2258 removed outlier: 3.842A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A2258 " --> pdb=" O TYR A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2289 removed outlier: 3.991A pdb=" N GLU A2285 " --> pdb=" O LYS A2281 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2286 " --> pdb=" O ALA A2282 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2287 " --> pdb=" O VAL A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2301 Processing helix chain 'A' and resid 2308 through 2331 removed outlier: 3.541A pdb=" N ARG A2319 " --> pdb=" O GLN A2315 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A2330 " --> pdb=" O MET A2326 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A2331 " --> pdb=" O VAL A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2360 through 2364 removed outlier: 3.744A pdb=" N LYS A2363 " --> pdb=" O GLU A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.955A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2396 removed outlier: 3.537A pdb=" N SER A2395 " --> pdb=" O VAL A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2396 through 2406 removed outlier: 3.892A pdb=" N LEU A2400 " --> pdb=" O CYS A2396 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A2401 " --> pdb=" O GLU A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2419 removed outlier: 3.780A pdb=" N LEU A2411 " --> pdb=" O ARG A2407 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A2417 " --> pdb=" O LEU A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 removed outlier: 3.554A pdb=" N VAL A3612 " --> pdb=" O TYR A3608 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A3613 " --> pdb=" O ALA A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3645 Processing helix chain 'A' and resid 3654 through 3658 removed outlier: 3.734A pdb=" N THR A3658 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2138 through 2140 removed outlier: 3.786A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A2154 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2212 through 2213 505 hydrogen bonds defined for protein. 1449 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: 2.21 Time building geometry restraints manager: 1.69 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: 4661 1.34 - 1.46: 2767 1.46 - 1.58: 6647 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14180 Sorted by residual: bond pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C CYS A 489 " pdb=" N GLN A 490 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.41e+00 bond pdb=" C HIS A 675 " pdb=" N ASP A 676 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" N ARG A2366 " pdb=" CA ARG A2366 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.07e+00 bond pdb=" N HIS A2278 " pdb=" CA HIS A2278 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.00e+00 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 19133 2.89 - 5.77: 160 5.77 - 8.66: 26 8.66 - 11.54: 4 11.54 - 14.43: 3 Bond angle restraints: 19326 Sorted by residual: angle pdb=" C CYS A 489 " pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 121.70 136.13 -14.43 1.80e+00 3.09e-01 6.43e+01 angle pdb=" C LEU A2277 " pdb=" N HIS A2278 " pdb=" CA HIS A2278 " ideal model delta sigma weight residual 121.70 133.67 -11.97 1.80e+00 3.09e-01 4.42e+01 angle pdb=" C HIS A 675 " pdb=" N ASP A 676 " pdb=" CA ASP A 676 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" N PRO A3627 " pdb=" CA PRO A3627 " pdb=" CB PRO A3627 " ideal model delta sigma weight residual 102.60 110.03 -7.43 1.17e+00 7.31e-01 4.03e+01 angle pdb=" C ASN A1019 " pdb=" N ARG A1020 " pdb=" CA ARG A1020 " ideal model delta sigma weight residual 121.70 132.28 -10.58 1.80e+00 3.09e-01 3.45e+01 ... (remaining 19321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8194 17.07 - 34.15: 310 34.15 - 51.22: 50 51.22 - 68.30: 12 68.30 - 85.37: 5 Dihedral angle restraints: 8571 sinusoidal: 2929 harmonic: 5642 Sorted by residual: dihedral pdb=" CA ILE A 901 " pdb=" C ILE A 901 " pdb=" N PRO A 902 " pdb=" CA PRO A 902 " ideal model delta harmonic sigma weight residual 180.00 128.38 51.62 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA LEU A1657 " pdb=" C LEU A1657 " pdb=" N PRO A1658 " pdb=" CA PRO A1658 " ideal model delta harmonic sigma weight residual -180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA ILE A1089 " pdb=" C ILE A1089 " pdb=" N GLN A1090 " pdb=" CA GLN A1090 " ideal model delta harmonic sigma weight residual -180.00 -147.02 -32.98 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2023 0.051 - 0.103: 351 0.103 - 0.154: 35 0.154 - 0.205: 7 0.205 - 0.257: 1 Chirality restraints: 2417 Sorted by residual: chirality pdb=" CA PRO A3627 " pdb=" N PRO A3627 " pdb=" C PRO A3627 " pdb=" CB PRO A3627 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLN A 490 " pdb=" N GLN A 490 " pdb=" C GLN A 490 " pdb=" CB GLN A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PRO A2276 " pdb=" N PRO A2276 " pdb=" C PRO A2276 " pdb=" CB PRO A2276 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 2414 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 901 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 902 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A2275 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A2276 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2276 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2276 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1346 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A1347 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1347 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1347 " 0.024 5.00e-02 4.00e+02 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 801 2.73 - 3.28: 14768 3.28 - 3.82: 20909 3.82 - 4.36: 25364 4.36 - 4.90: 41180 Nonbonded interactions: 103022 Sorted by model distance: nonbonded pdb=" O VAL A1094 " pdb=" OG SER A1097 " model vdw 2.193 3.040 nonbonded pdb=" O CYS A 492 " pdb=" OH TYR A 565 " model vdw 2.199 3.040 nonbonded pdb=" O ALA A 259 " pdb=" OG1 THR A 262 " model vdw 2.200 3.040 nonbonded pdb=" O SER A1608 " pdb=" OG SER A1618 " model vdw 2.233 3.040 nonbonded pdb=" O ASN A 111 " pdb=" OG SER A 115 " model vdw 2.250 3.040 ... (remaining 103017 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: 2.410 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.002 0.047 14180 Z= 0.129 Angle : 0.688 14.431 19326 Z= 0.387 Chirality : 0.040 0.257 2417 Planarity : 0.004 0.078 2459 Dihedral : 9.711 85.375 4875 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.85 % Favored : 89.89 % Rotamer: Outliers : 3.49 % Allowed : 7.48 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.16), residues: 1879 helix: -2.77 (0.13), residues: 917 sheet: -3.39 (0.85), residues: 29 loop : -3.83 (0.17), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.005 0.001 TYR A 998 PHE 0.006 0.001 PHE A2188 TRP 0.008 0.001 TRP A1819 HIS 0.001 0.000 HIS A2023 Details of bonding type rmsd covalent geometry : bond 0.00233 (14180) covalent geometry : angle 0.68757 (19326) hydrogen bonds : bond 0.22786 ( 505) hydrogen bonds : angle 7.62689 ( 1449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4702 (pp) REVERT: A 820 LEU cc_start: 0.7194 (mt) cc_final: 0.6473 (mt) REVERT: A 1205 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6433 (mt-10) REVERT: A 1525 ILE cc_start: 0.7044 (mt) cc_final: 0.6158 (mt) REVERT: A 1526 LEU cc_start: 0.8323 (mm) cc_final: 0.7961 (pp) outliers start: 49 outliers final: 16 residues processed: 444 average time/residue: 0.1221 time to fit residues: 78.1960 Evaluate side-chains 279 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 123 HIS A 171 GLN A 178 GLN A 309 HIS A 326 HIS A 490 GLN A 671 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 GLN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 ASN A1825 GLN A1832 HIS ** A2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2229 GLN A2337 HIS A2352 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.144110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.122991 restraints weight = 42550.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124796 restraints weight = 24541.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.126001 restraints weight = 16815.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.126816 restraints weight = 12987.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.127369 restraints weight = 10869.571| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14180 Z= 0.162 Angle : 0.815 14.620 19326 Z= 0.414 Chirality : 0.044 0.283 2417 Planarity : 0.005 0.076 2459 Dihedral : 6.066 56.859 2024 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.55 % Favored : 88.34 % Rotamer: Outliers : 4.70 % Allowed : 14.90 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.17), residues: 1879 helix: -1.81 (0.15), residues: 960 sheet: -2.84 (0.94), residues: 29 loop : -3.59 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1433 TYR 0.023 0.001 TYR A1194 PHE 0.026 0.002 PHE A 237 TRP 0.035 0.002 TRP A 235 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00349 (14180) covalent geometry : angle 0.81460 (19326) hydrogen bonds : bond 0.03862 ( 505) hydrogen bonds : angle 4.94258 ( 1449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8601 (m-80) cc_final: 0.8230 (m-10) REVERT: A 267 LYS cc_start: 0.8442 (pttp) cc_final: 0.7886 (tptt) REVERT: A 506 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8256 (mm) REVERT: A 561 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.4946 (pp) REVERT: A 577 ASN cc_start: 0.8357 (p0) cc_final: 0.7853 (p0) REVERT: A 720 LYS cc_start: 0.8267 (mmtm) cc_final: 0.8031 (mmtp) REVERT: A 906 LEU cc_start: 0.4023 (OUTLIER) cc_final: 0.3547 (mp) REVERT: A 1186 LEU cc_start: 0.2588 (OUTLIER) cc_final: 0.1793 (tt) REVERT: A 1474 GLN cc_start: 0.8632 (tp40) cc_final: 0.8431 (tp40) REVERT: A 1526 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7405 (pp) REVERT: A 2193 TYR cc_start: 0.6684 (t80) cc_final: 0.6170 (t80) REVERT: A 2345 MET cc_start: 0.7466 (mmm) cc_final: 0.7155 (mmp) outliers start: 66 outliers final: 31 residues processed: 312 average time/residue: 0.1161 time to fit residues: 53.7067 Evaluate side-chains 274 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1118 PHE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2217 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 93 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 557 ASN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.119481 restraints weight = 42414.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.121353 restraints weight = 24555.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.122538 restraints weight = 16774.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123424 restraints weight = 12935.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.123843 restraints weight = 10831.995| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14180 Z= 0.158 Angle : 0.800 14.602 19326 Z= 0.406 Chirality : 0.044 0.224 2417 Planarity : 0.005 0.075 2459 Dihedral : 6.138 57.929 2020 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.44 % Favored : 88.45 % Rotamer: Outliers : 5.06 % Allowed : 17.32 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.18), residues: 1879 helix: -1.38 (0.16), residues: 980 sheet: -2.48 (1.00), residues: 29 loop : -3.52 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1433 TYR 0.025 0.001 TYR A 434 PHE 0.032 0.001 PHE A 349 TRP 0.054 0.002 TRP A 235 HIS 0.003 0.001 HIS A2189 Details of bonding type rmsd covalent geometry : bond 0.00347 (14180) covalent geometry : angle 0.80016 (19326) hydrogen bonds : bond 0.03318 ( 505) hydrogen bonds : angle 4.56199 ( 1449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8354 (pttp) cc_final: 0.8007 (tptt) REVERT: A 349 PHE cc_start: 0.8010 (m-80) cc_final: 0.7761 (m-80) REVERT: A 561 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5029 (pp) REVERT: A 577 ASN cc_start: 0.8409 (p0) cc_final: 0.7908 (p0) REVERT: A 1526 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7422 (pp) REVERT: A 1790 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8885 (mm) outliers start: 71 outliers final: 39 residues processed: 303 average time/residue: 0.1126 time to fit residues: 51.6433 Evaluate side-chains 276 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1118 PHE Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 166 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 550 GLN A 557 ASN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1362 ASN A2192 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.141385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120443 restraints weight = 42441.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121378 restraints weight = 25887.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.122238 restraints weight = 21079.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122855 restraints weight = 16094.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122866 restraints weight = 13264.362| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14180 Z= 0.147 Angle : 0.796 14.593 19326 Z= 0.403 Chirality : 0.044 0.224 2417 Planarity : 0.005 0.074 2459 Dihedral : 6.181 58.942 2019 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.55 % Favored : 88.34 % Rotamer: Outliers : 5.13 % Allowed : 18.10 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.19), residues: 1879 helix: -1.15 (0.16), residues: 987 sheet: -2.21 (1.05), residues: 29 loop : -3.44 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1433 TYR 0.017 0.001 TYR A 434 PHE 0.020 0.002 PHE A 349 TRP 0.060 0.002 TRP A 235 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00321 (14180) covalent geometry : angle 0.79623 (19326) hydrogen bonds : bond 0.02868 ( 505) hydrogen bonds : angle 4.43721 ( 1449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8334 (pttp) cc_final: 0.7930 (tppt) REVERT: A 277 MET cc_start: 0.5941 (pmm) cc_final: 0.5717 (pmm) REVERT: A 368 MET cc_start: 0.5889 (mmt) cc_final: 0.5492 (ptp) REVERT: A 561 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5475 (pp) REVERT: A 1046 VAL cc_start: 0.5671 (OUTLIER) cc_final: 0.5379 (t) REVERT: A 1113 GLN cc_start: 0.6930 (pm20) cc_final: 0.6656 (pm20) REVERT: A 1526 LEU cc_start: 0.8310 (mm) cc_final: 0.7398 (pp) REVERT: A 2102 MET cc_start: 0.6496 (ptm) cc_final: 0.6111 (ptp) outliers start: 72 outliers final: 39 residues processed: 295 average time/residue: 0.1137 time to fit residues: 50.6217 Evaluate side-chains 267 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2214 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2351 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2403 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 140 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 0.0070 chunk 160 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 309 HIS A 550 GLN A 671 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1021 GLN A1326 GLN A1413 GLN A2356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.133918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111878 restraints weight = 41652.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.112043 restraints weight = 28337.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112731 restraints weight = 21215.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113283 restraints weight = 17920.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113267 restraints weight = 16080.684| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14180 Z= 0.253 Angle : 0.931 14.935 19326 Z= 0.475 Chirality : 0.049 0.221 2417 Planarity : 0.006 0.075 2459 Dihedral : 6.817 55.107 2018 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.77 % Favored : 86.96 % Rotamer: Outliers : 5.20 % Allowed : 18.89 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.19), residues: 1879 helix: -1.31 (0.16), residues: 1010 sheet: -2.51 (1.01), residues: 29 loop : -3.49 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2404 TYR 0.023 0.002 TYR A2193 PHE 0.032 0.002 PHE A1741 TRP 0.065 0.003 TRP A 235 HIS 0.007 0.002 HIS A2189 Details of bonding type rmsd covalent geometry : bond 0.00568 (14180) covalent geometry : angle 0.93083 (19326) hydrogen bonds : bond 0.03972 ( 505) hydrogen bonds : angle 4.84063 ( 1449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 247 time to evaluate : 0.547 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 96 GLU cc_start: 0.6328 (tt0) cc_final: 0.6102 (tt0) REVERT: A 267 LYS cc_start: 0.8317 (pttp) cc_final: 0.8000 (tppt) REVERT: A 277 MET cc_start: 0.6150 (pmm) cc_final: 0.5804 (pmm) REVERT: A 295 LYS cc_start: 0.5565 (tttt) cc_final: 0.5237 (tptt) REVERT: A 350 TRP cc_start: 0.7332 (t-100) cc_final: 0.7033 (t-100) REVERT: A 368 MET cc_start: 0.5912 (mmt) cc_final: 0.5380 (ptp) REVERT: A 561 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5756 (pp) REVERT: A 577 ASN cc_start: 0.8493 (p0) cc_final: 0.8022 (p0) REVERT: A 1046 VAL cc_start: 0.5729 (OUTLIER) cc_final: 0.5470 (t) REVERT: A 1132 MET cc_start: 0.7382 (tpp) cc_final: 0.7088 (tpp) REVERT: A 1184 ASN cc_start: 0.5132 (m-40) cc_final: 0.4163 (p0) REVERT: A 1185 TYR cc_start: 0.2874 (OUTLIER) cc_final: 0.2640 (t80) REVERT: A 1347 PRO cc_start: 0.6188 (Cg_endo) cc_final: 0.5975 (Cg_endo) REVERT: A 1422 MET cc_start: 0.7598 (mtt) cc_final: 0.7270 (mtp) REVERT: A 1526 LEU cc_start: 0.8481 (mm) cc_final: 0.7650 (pp) REVERT: A 2419 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.4506 (t80) outliers start: 73 outliers final: 42 residues processed: 299 average time/residue: 0.1091 time to fit residues: 48.6182 Evaluate side-chains 277 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1465 HIS Chi-restraints excluded: chain A residue 1596 GLU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1837 VAL Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2355 TYR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 166 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 133 optimal weight: 0.0670 chunk 47 optimal weight: 0.0040 chunk 114 optimal weight: 0.2980 chunk 154 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN A1326 GLN A1825 GLN A2168 GLN A2356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.116463 restraints weight = 41556.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116930 restraints weight = 28137.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117331 restraints weight = 19719.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117816 restraints weight = 18870.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.117885 restraints weight = 16250.297| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14180 Z= 0.149 Angle : 0.841 14.684 19326 Z= 0.425 Chirality : 0.045 0.233 2417 Planarity : 0.006 0.084 2459 Dihedral : 6.428 57.091 2017 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.55 % Favored : 88.34 % Rotamer: Outliers : 4.28 % Allowed : 20.46 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.19), residues: 1879 helix: -1.02 (0.16), residues: 999 sheet: -2.41 (0.99), residues: 29 loop : -3.38 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1990 TYR 0.024 0.001 TYR A 434 PHE 0.018 0.002 PHE A 349 TRP 0.065 0.002 TRP A 235 HIS 0.016 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00325 (14180) covalent geometry : angle 0.84093 (19326) hydrogen bonds : bond 0.02884 ( 505) hydrogen bonds : angle 4.54651 ( 1449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8268 (pttp) cc_final: 0.7889 (tppt) REVERT: A 277 MET cc_start: 0.6023 (pmm) cc_final: 0.5797 (pmm) REVERT: A 302 LEU cc_start: 0.8285 (tt) cc_final: 0.7966 (mt) REVERT: A 349 PHE cc_start: 0.8257 (m-80) cc_final: 0.7825 (m-80) REVERT: A 368 MET cc_start: 0.5944 (mmt) cc_final: 0.5467 (ptp) REVERT: A 437 MET cc_start: 0.6537 (mmm) cc_final: 0.5879 (ppp) REVERT: A 561 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5549 (pp) REVERT: A 577 ASN cc_start: 0.8399 (p0) cc_final: 0.7978 (p0) REVERT: A 1046 VAL cc_start: 0.5585 (OUTLIER) cc_final: 0.5327 (t) REVERT: A 1308 GLU cc_start: 0.6507 (mp0) cc_final: 0.5868 (tp30) REVERT: A 1526 LEU cc_start: 0.8390 (mm) cc_final: 0.7712 (pp) REVERT: A 2419 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.4359 (t80) outliers start: 60 outliers final: 34 residues processed: 294 average time/residue: 0.1103 time to fit residues: 48.0724 Evaluate side-chains 259 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 190 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1413 GLN A1472 GLN A2356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.116065 restraints weight = 41768.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.115818 restraints weight = 30164.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.116417 restraints weight = 21456.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.116730 restraints weight = 19872.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116985 restraints weight = 17922.607| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14180 Z= 0.157 Angle : 0.854 14.674 19326 Z= 0.430 Chirality : 0.045 0.224 2417 Planarity : 0.006 0.083 2459 Dihedral : 6.389 56.176 2017 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.35 % Favored : 87.55 % Rotamer: Outliers : 4.56 % Allowed : 20.10 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.19), residues: 1879 helix: -0.92 (0.17), residues: 1000 sheet: -2.18 (1.04), residues: 29 loop : -3.35 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2182 TYR 0.015 0.001 TYR A 434 PHE 0.015 0.001 PHE A 923 TRP 0.068 0.002 TRP A 235 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00347 (14180) covalent geometry : angle 0.85366 (19326) hydrogen bonds : bond 0.02879 ( 505) hydrogen bonds : angle 4.50527 ( 1449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 234 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8290 (pttp) cc_final: 0.8036 (tppt) REVERT: A 302 LEU cc_start: 0.8166 (tt) cc_final: 0.7880 (mt) REVERT: A 350 TRP cc_start: 0.7343 (t-100) cc_final: 0.6970 (t-100) REVERT: A 368 MET cc_start: 0.5942 (mmt) cc_final: 0.5475 (ptp) REVERT: A 561 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5698 (pp) REVERT: A 577 ASN cc_start: 0.8426 (p0) cc_final: 0.7984 (p0) REVERT: A 1184 ASN cc_start: 0.4767 (m-40) cc_final: 0.4070 (p0) REVERT: A 1308 GLU cc_start: 0.6463 (mp0) cc_final: 0.5780 (tm-30) REVERT: A 1526 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7586 (pp) REVERT: A 2419 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.4387 (t80) outliers start: 64 outliers final: 41 residues processed: 281 average time/residue: 0.1060 time to fit residues: 44.9136 Evaluate side-chains 271 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2305 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 13 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 78 optimal weight: 0.0070 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 485 GLN A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1472 GLN A2356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.116023 restraints weight = 41660.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.117814 restraints weight = 24590.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.118953 restraints weight = 17034.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.119695 restraints weight = 13322.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120016 restraints weight = 11277.874| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14180 Z= 0.147 Angle : 0.849 14.650 19326 Z= 0.426 Chirality : 0.045 0.223 2417 Planarity : 0.006 0.089 2459 Dihedral : 6.323 58.577 2017 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.55 % Favored : 88.34 % Rotamer: Outliers : 3.99 % Allowed : 21.03 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1879 helix: -0.81 (0.17), residues: 999 sheet: -2.01 (1.08), residues: 29 loop : -3.26 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2182 TYR 0.016 0.001 TYR A 434 PHE 0.014 0.001 PHE A 240 TRP 0.070 0.002 TRP A 235 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00319 (14180) covalent geometry : angle 0.84935 (19326) hydrogen bonds : bond 0.02683 ( 505) hydrogen bonds : angle 4.43639 ( 1449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8326 (pttp) cc_final: 0.7985 (tppt) REVERT: A 349 PHE cc_start: 0.7928 (m-80) cc_final: 0.7694 (m-80) REVERT: A 350 TRP cc_start: 0.7016 (t-100) cc_final: 0.6658 (t-100) REVERT: A 368 MET cc_start: 0.5833 (mmt) cc_final: 0.5491 (ptp) REVERT: A 561 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5584 (pp) REVERT: A 577 ASN cc_start: 0.8340 (p0) cc_final: 0.7936 (p0) REVERT: A 1184 ASN cc_start: 0.4345 (m-40) cc_final: 0.3870 (p0) REVERT: A 1526 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7171 (pp) REVERT: A 2375 MET cc_start: 0.8248 (tpp) cc_final: 0.7505 (tpt) REVERT: A 2419 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.4171 (t80) outliers start: 56 outliers final: 38 residues processed: 274 average time/residue: 0.1109 time to fit residues: 45.8772 Evaluate side-chains 260 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1472 GLN Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.135818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112985 restraints weight = 41968.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.114649 restraints weight = 25105.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115831 restraints weight = 17403.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116611 restraints weight = 13585.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.117138 restraints weight = 11498.570| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14180 Z= 0.181 Angle : 0.883 14.791 19326 Z= 0.444 Chirality : 0.047 0.311 2417 Planarity : 0.006 0.096 2459 Dihedral : 6.402 57.760 2015 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.61 % Favored : 87.33 % Rotamer: Outliers : 3.64 % Allowed : 21.95 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1879 helix: -0.77 (0.17), residues: 996 sheet: -1.97 (1.11), residues: 29 loop : -3.32 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1433 TYR 0.015 0.001 TYR A 434 PHE 0.016 0.001 PHE A1741 TRP 0.063 0.003 TRP A 235 HIS 0.004 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00406 (14180) covalent geometry : angle 0.88326 (19326) hydrogen bonds : bond 0.03046 ( 505) hydrogen bonds : angle 4.52260 ( 1449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 PHE cc_start: 0.8044 (m-80) cc_final: 0.7772 (m-80) REVERT: A 350 TRP cc_start: 0.7139 (t-100) cc_final: 0.6758 (t-100) REVERT: A 368 MET cc_start: 0.5833 (mmt) cc_final: 0.5493 (ptp) REVERT: A 437 MET cc_start: 0.6485 (mmm) cc_final: 0.5979 (ppp) REVERT: A 561 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5873 (pp) REVERT: A 577 ASN cc_start: 0.8404 (p0) cc_final: 0.7981 (p0) REVERT: A 674 ARG cc_start: 0.6666 (mmp80) cc_final: 0.6405 (mmp-170) REVERT: A 1184 ASN cc_start: 0.4816 (m-40) cc_final: 0.4274 (p0) REVERT: A 1185 TYR cc_start: 0.2766 (OUTLIER) cc_final: 0.2437 (t80) REVERT: A 1526 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7327 (pp) REVERT: A 2375 MET cc_start: 0.8239 (tpp) cc_final: 0.7998 (tpt) REVERT: A 2419 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.4309 (t80) outliers start: 51 outliers final: 42 residues processed: 259 average time/residue: 0.1110 time to fit residues: 43.3080 Evaluate side-chains 267 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1465 HIS Chi-restraints excluded: chain A residue 1472 GLN Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2305 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2386 THR Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 68 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 165 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A2356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.137383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116829 restraints weight = 41690.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116790 restraints weight = 26176.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117319 restraints weight = 21695.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117672 restraints weight = 18108.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.117732 restraints weight = 17034.947| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14180 Z= 0.151 Angle : 0.873 14.701 19326 Z= 0.437 Chirality : 0.046 0.241 2417 Planarity : 0.006 0.098 2459 Dihedral : 6.339 59.396 2015 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.60 % Favored : 88.29 % Rotamer: Outliers : 3.28 % Allowed : 22.74 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.20), residues: 1879 helix: -0.72 (0.17), residues: 999 sheet: -1.91 (1.12), residues: 29 loop : -3.26 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2182 TYR 0.013 0.001 TYR A 434 PHE 0.021 0.001 PHE A 356 TRP 0.075 0.002 TRP A 235 HIS 0.007 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00329 (14180) covalent geometry : angle 0.87316 (19326) hydrogen bonds : bond 0.02763 ( 505) hydrogen bonds : angle 4.50692 ( 1449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 PHE cc_start: 0.8181 (m-80) cc_final: 0.7879 (m-80) REVERT: A 350 TRP cc_start: 0.7330 (t-100) cc_final: 0.7000 (t-100) REVERT: A 368 MET cc_start: 0.5745 (mmt) cc_final: 0.5464 (ptp) REVERT: A 437 MET cc_start: 0.6485 (mmm) cc_final: 0.6026 (ppp) REVERT: A 506 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 561 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5754 (pp) REVERT: A 577 ASN cc_start: 0.8348 (p0) cc_final: 0.7959 (p0) REVERT: A 674 ARG cc_start: 0.6498 (mmp80) cc_final: 0.6210 (mmp-170) REVERT: A 1075 MET cc_start: 0.7256 (mmm) cc_final: 0.6957 (mmm) REVERT: A 1184 ASN cc_start: 0.4843 (m-40) cc_final: 0.4199 (p0) REVERT: A 1185 TYR cc_start: 0.2512 (OUTLIER) cc_final: 0.2205 (t80) REVERT: A 1526 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7319 (pp) REVERT: A 2370 LYS cc_start: 0.2458 (tttt) cc_final: 0.2177 (tttt) REVERT: A 2375 MET cc_start: 0.8178 (tpp) cc_final: 0.7420 (tpt) REVERT: A 2419 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.4293 (t80) outliers start: 46 outliers final: 39 residues processed: 260 average time/residue: 0.1106 time to fit residues: 43.4762 Evaluate side-chains 262 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1211 HIS Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1636 ASN Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2383 LEU Chi-restraints excluded: chain A residue 2386 THR Chi-restraints excluded: chain A residue 2419 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 182 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.135285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112527 restraints weight = 41297.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.114212 restraints weight = 24677.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.115365 restraints weight = 17184.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116114 restraints weight = 13398.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.116554 restraints weight = 11398.998| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14180 Z= 0.178 Angle : 0.895 14.804 19326 Z= 0.448 Chirality : 0.047 0.223 2417 Planarity : 0.006 0.099 2459 Dihedral : 6.497 59.226 2015 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.04 % Favored : 86.91 % Rotamer: Outliers : 3.71 % Allowed : 22.45 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.19), residues: 1879 helix: -0.70 (0.17), residues: 1000 sheet: -2.01 (1.12), residues: 29 loop : -3.33 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1433 TYR 0.012 0.001 TYR A 434 PHE 0.015 0.001 PHE A1741 TRP 0.075 0.003 TRP A 235 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00398 (14180) covalent geometry : angle 0.89532 (19326) hydrogen bonds : bond 0.03040 ( 505) hydrogen bonds : angle 4.59848 ( 1449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.96 seconds wall clock time: 49 minutes 36.40 seconds (2976.40 seconds total)