Starting phenix.real_space_refine on Tue Jun 17 15:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.map" model { file = "/net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dut_47177/06_2025/9dut_47177.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 111 5.16 5 C 12763 2.51 5 N 3407 2.21 5 O 3631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19912 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1946, 15582 Classifications: {'peptide': 1946} Link IDs: {'PTRANS': 82, 'TRANS': 1863} Chain breaks: 15 Chain: "B" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 575 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 74, 575 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 bond proxies already assigned to first conformer: 572 Chain: "C" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Chain: "D" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "E" Number of atoms: 576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} bond proxies already assigned to first conformer: 571 Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 891 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Time building chain proxies: 12.18, per 1000 atoms: 0.61 Number of scatterers: 19912 At special positions: 0 Unit cell: (115.093, 154.048, 146.08, 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 111 16.00 O 3631 8.00 N 3407 7.00 C 12763 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: 4.57 Conformation dependent library (CDL) restraints added in 2.8 seconds 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4734 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 12 sheets defined 62.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.854A pdb=" N ILE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS A 50 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 103 through 136 removed outlier: 3.548A pdb=" N ARG A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.908A pdb=" N GLU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 161 through 182 removed outlier: 3.655A pdb=" N PHE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Processing helix chain 'A' and resid 251 through 273 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.997A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.288A pdb=" N LEU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.619A pdb=" N ARG A 301 " --> pdb=" O VAL A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 302 through 319 removed outlier: 3.835A pdb=" N ASN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.669A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.792A pdb=" N ILE A 349 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 353 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.918A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.805A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 465' Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.766A pdb=" N TRP A 476 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP A 477 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 removed outlier: 3.699A pdb=" N VAL A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.672A pdb=" N VAL A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.642A pdb=" N GLY A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.552A pdb=" N PHE A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.581A pdb=" N ASN A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.760A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.660A pdb=" N LYS A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 743 through 763 Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 788 through 815 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.593A pdb=" N ALA A 867 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 923 through 933 removed outlier: 3.586A pdb=" N LEU A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 970 Processing helix chain 'A' and resid 975 through 983 removed outlier: 3.864A pdb=" N HIS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.562A pdb=" N LEU A1012 " --> pdb=" O SER A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 3.577A pdb=" N GLU A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1066 removed outlier: 4.110A pdb=" N ALA A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1079 removed outlier: 3.916A pdb=" N LEU A1079 " --> pdb=" O ILE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.632A pdb=" N ILE A1086 " --> pdb=" O THR A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1104 Processing helix chain 'A' and resid 1105 through 1120 Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1161 through 1165 removed outlier: 3.599A pdb=" N SER A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1161 through 1165' Processing helix chain 'A' and resid 1176 through 1182 Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1252 through 1265 removed outlier: 3.596A pdb=" N ASN A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A1258 " --> pdb=" O SER A1254 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A1265 " --> pdb=" O LEU A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1303 through 1307 removed outlier: 3.974A pdb=" N ARG A1306 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1348 removed outlier: 3.546A pdb=" N PHE A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1451 Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1503 removed outlier: 3.546A pdb=" N PHE A1483 " --> pdb=" O GLU A1479 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE A1497 " --> pdb=" O ILE A1493 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP A1498 " --> pdb=" O ASN A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1521 removed outlier: 4.244A pdb=" N GLN A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.819A pdb=" N HIS A1535 " --> pdb=" O ASN A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1542 Processing helix chain 'A' and resid 1561 through 1582 removed outlier: 3.757A pdb=" N ASN A1582 " --> pdb=" O ASP A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1620 Processing helix chain 'A' and resid 1632 through 1651 Processing helix chain 'A' and resid 1670 through 1685 Processing helix chain 'A' and resid 1725 through 1735 Processing helix chain 'A' and resid 1750 through 1755 removed outlier: 4.080A pdb=" N PHE A1754 " --> pdb=" O GLU A1750 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A1755 " --> pdb=" O ILE A1751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1750 through 1755' Processing helix chain 'A' and resid 1763 through 1772 Processing helix chain 'A' and resid 1792 through 1803 Processing helix chain 'A' and resid 1828 through 1839 Processing helix chain 'A' and resid 1859 through 1870 Processing helix chain 'A' and resid 1889 through 1907 Processing helix chain 'A' and resid 1925 through 1934 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.574A pdb=" N ILE A1973 " --> pdb=" O ASN A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1999 removed outlier: 3.614A pdb=" N ILE A1989 " --> pdb=" O SER A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2006 removed outlier: 3.513A pdb=" N VAL A2005 " --> pdb=" O ILE A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2019 Processing helix chain 'A' and resid 2022 through 2030 removed outlier: 3.595A pdb=" N ASN A2030 " --> pdb=" O GLN A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2039 through 2045 Processing helix chain 'A' and resid 2057 through 2070 Processing helix chain 'A' and resid 2083 through 2110 removed outlier: 3.522A pdb=" N LEU A2087 " --> pdb=" O ALA A2083 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A2088 " --> pdb=" O TYR A2084 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A2089 " --> pdb=" O PRO A2085 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A2094 " --> pdb=" O SER A2090 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A2110 " --> pdb=" O HIS A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2127 Processing helix chain 'A' and resid 2143 through 2153 removed outlier: 3.816A pdb=" N GLY A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2164 through 2182 removed outlier: 3.894A pdb=" N LEU A2180 " --> pdb=" O GLY A2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.630A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 371 removed outlier: 3.665A pdb=" N SER B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.978A pdb=" N ALA B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 372 removed outlier: 3.882A pdb=" N GLU C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.688A pdb=" N ARG C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 488 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'D' and resid 325 through 369 removed outlier: 4.157A pdb=" N GLY D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 340 Processing helix chain 'E' and resid 342 through 374 Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.763A pdb=" N ASP E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 85 Processing helix chain 'F' and resid 101 through 115 removed outlier: 3.812A pdb=" N MET F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR F 108 " --> pdb=" O MET F 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 109 " --> pdb=" O PHE F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 156 through 161 Processing helix chain 'F' and resid 162 through 170 removed outlier: 3.637A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY F 169 " --> pdb=" O PRO F 165 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 85 removed outlier: 3.519A pdb=" N ALA G 72 " --> pdb=" O HIS G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 115 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'G' and resid 134 through 152 removed outlier: 3.816A pdb=" N ILE G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 162 through 170 removed outlier: 4.116A pdb=" N SER G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 6.589A pdb=" N ILE A 20 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.363A pdb=" N SER A 83 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR A 222 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS A 219 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 378 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.680A pdb=" N LYS A 447 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.857A pdb=" N TYR A 706 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 771 removed outlier: 3.573A pdb=" N ASN A 774 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AA8, first strand: chain 'A' and resid 1166 through 1171 Processing sheet with id=AA9, first strand: chain 'A' and resid 1196 through 1197 removed outlier: 3.830A pdb=" N CYS A1196 " --> pdb=" O THR A1354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1592 through 1593 removed outlier: 6.227A pdb=" N LEU A1592 " --> pdb=" O TYR A1667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1722 through 1724 removed outlier: 6.916A pdb=" N TYR A1937 " --> pdb=" O LEU A1962 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A1962 " --> pdb=" O TYR A1937 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1961 " --> pdb=" O SER A1912 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A1912 " --> pdb=" O ASP A1961 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A1876 " --> pdb=" O GLY A1911 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2128 through 2131 1126 hydrogen bonds defined for protein. 3295 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: 8.87 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4412 1.33 - 1.45: 4120 1.45 - 1.57: 11585 1.57 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 20302 Sorted by residual: bond pdb=" CA HIS A1174 " pdb=" C HIS A1174 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.21e-02 6.83e+03 2.98e+01 bond pdb=" CA THR A1176 " pdb=" C THR A1176 " ideal model delta sigma weight residual 1.524 1.460 0.063 1.30e-02 5.92e+03 2.37e+01 bond pdb=" N ARG A1173 " pdb=" CA ARG A1173 " ideal model delta sigma weight residual 1.459 1.499 -0.039 9.10e-03 1.21e+04 1.88e+01 bond pdb=" N HIS A1174 " pdb=" CA HIS A1174 " ideal model delta sigma weight residual 1.454 1.415 0.039 1.23e-02 6.61e+03 9.90e+00 bond pdb=" C ASP A1687 " pdb=" N PRO A1688 " ideal model delta sigma weight residual 1.336 1.365 -0.030 9.80e-03 1.04e+04 9.08e+00 ... (remaining 20297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 27212 3.72 - 7.43: 202 7.43 - 11.15: 21 11.15 - 14.86: 5 14.86 - 18.58: 1 Bond angle restraints: 27441 Sorted by residual: angle pdb=" N THR A1176 " pdb=" CA THR A1176 " pdb=" C THR A1176 " ideal model delta sigma weight residual 110.28 101.02 9.26 1.48e+00 4.57e-01 3.91e+01 angle pdb=" C PRO A2038 " pdb=" N LYS A2039 " pdb=" CA LYS A2039 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 angle pdb=" N ARG A1173 " pdb=" CA ARG A1173 " pdb=" C ARG A1173 " ideal model delta sigma weight residual 112.99 104.23 8.76 1.61e+00 3.86e-01 2.96e+01 angle pdb=" CA LEU A1739 " pdb=" CB LEU A1739 " pdb=" CG LEU A1739 " ideal model delta sigma weight residual 116.30 134.88 -18.58 3.50e+00 8.16e-02 2.82e+01 angle pdb=" C LEU E 394 " pdb=" N LYS E 395 " pdb=" CA LYS E 395 " ideal model delta sigma weight residual 124.21 130.24 -6.03 1.21e+00 6.83e-01 2.48e+01 ... (remaining 27436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 11212 14.53 - 29.07: 915 29.07 - 43.60: 179 43.60 - 58.13: 32 58.13 - 72.67: 7 Dihedral angle restraints: 12345 sinusoidal: 5046 harmonic: 7299 Sorted by residual: dihedral pdb=" CA GLN A2135 " pdb=" C GLN A2135 " pdb=" N ASN A2136 " pdb=" CA ASN A2136 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN A 64 " pdb=" C ASN A 64 " pdb=" N ASN A 65 " pdb=" CA ASN A 65 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C THR A1176 " pdb=" N THR A1176 " pdb=" CA THR A1176 " pdb=" CB THR A1176 " ideal model delta harmonic sigma weight residual -122.00 -109.67 -12.33 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 12342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2959 0.099 - 0.198: 184 0.198 - 0.297: 11 0.297 - 0.396: 4 0.396 - 0.495: 1 Chirality restraints: 3159 Sorted by residual: chirality pdb=" CB ILE C 442 " pdb=" CA ILE C 442 " pdb=" CG1 ILE C 442 " pdb=" CG2 ILE C 442 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CA HIS A1174 " pdb=" N HIS A1174 " pdb=" C HIS A1174 " pdb=" CB HIS A1174 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB VAL A 298 " pdb=" CA VAL A 298 " pdb=" CG1 VAL A 298 " pdb=" CG2 VAL A 298 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 3156 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 408 " 0.015 2.00e-02 2.50e+03 2.47e-02 1.53e+01 pdb=" CG TRP A 408 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 408 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP A 408 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 408 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 408 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 408 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 408 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 408 " 0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 408 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1687 " 0.060 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO A1688 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1688 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1688 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 284 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 285 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.049 5.00e-02 4.00e+02 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3950 2.78 - 3.31: 18570 3.31 - 3.84: 31960 3.84 - 4.37: 38079 4.37 - 4.90: 64814 Nonbonded interactions: 157373 Sorted by model distance: nonbonded pdb=" O GLN A2148 " pdb=" OG1 THR A2152 " model vdw 2.255 3.040 nonbonded pdb=" O TRP A 747 " pdb=" OG1 THR A 751 " model vdw 2.269 3.040 nonbonded pdb=" O TYR A 117 " pdb=" OG SER A 121 " model vdw 2.269 3.040 nonbonded pdb=" O GLN G 135 " pdb=" OG1 THR G 138 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OD1 ASP A 335 " model vdw 2.302 3.040 ... (remaining 157368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 65 through 86 or resid 99 through 175)) selection = (chain 'G' and (resid 65 through 86 or resid 99 through 175)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 49.840 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.004 0.067 20302 Z= 0.229 Angle : 0.869 18.578 27441 Z= 0.468 Chirality : 0.054 0.495 3159 Planarity : 0.009 0.099 3436 Dihedral : 11.127 72.667 7611 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2449 helix: -0.50 (0.12), residues: 1417 sheet: 1.21 (0.42), residues: 150 loop : -1.77 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 408 HIS 0.018 0.001 HIS A 157 PHE 0.025 0.002 PHE A 546 TYR 0.026 0.002 TYR A 742 ARG 0.009 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.17163 ( 1126) hydrogen bonds : angle 6.22824 ( 3295) covalent geometry : bond 0.00429 (20302) covalent geometry : angle 0.86911 (27441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7859 (mt) cc_final: 0.7521 (mp) REVERT: A 240 MET cc_start: 0.8366 (mmm) cc_final: 0.8067 (mmm) REVERT: A 243 THR cc_start: 0.7609 (m) cc_final: 0.6759 (p) REVERT: A 265 ILE cc_start: 0.7664 (mm) cc_final: 0.7458 (mm) REVERT: A 328 HIS cc_start: 0.7576 (m-70) cc_final: 0.7348 (m170) REVERT: A 422 ARG cc_start: 0.6511 (tpp80) cc_final: 0.6294 (mtt90) REVERT: A 461 THR cc_start: 0.8575 (p) cc_final: 0.8252 (t) REVERT: A 516 TYR cc_start: 0.8151 (t80) cc_final: 0.7625 (t80) REVERT: A 650 MET cc_start: 0.6193 (tpt) cc_final: 0.5796 (tpt) REVERT: A 803 TYR cc_start: 0.7986 (t80) cc_final: 0.7622 (t80) REVERT: A 852 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6957 (mtt180) REVERT: A 869 SER cc_start: 0.7578 (t) cc_final: 0.7327 (p) REVERT: A 925 ASP cc_start: 0.7707 (m-30) cc_final: 0.7500 (m-30) REVERT: A 1014 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7381 (mmtp) REVERT: A 1023 ILE cc_start: 0.8432 (tp) cc_final: 0.8128 (tt) REVERT: A 1058 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7737 (mtm-85) REVERT: A 1078 MET cc_start: 0.7446 (ptp) cc_final: 0.7141 (ptp) REVERT: A 1126 LEU cc_start: 0.8168 (mt) cc_final: 0.7871 (mt) REVERT: A 1275 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6756 (ttt-90) REVERT: A 1359 THR cc_start: 0.8206 (m) cc_final: 0.7929 (m) REVERT: A 1444 MET cc_start: 0.8015 (tpp) cc_final: 0.7641 (tpp) REVERT: A 1574 MET cc_start: 0.6589 (mmp) cc_final: 0.6356 (mmp) REVERT: A 1590 PHE cc_start: 0.7472 (t80) cc_final: 0.7208 (t80) REVERT: A 1713 MET cc_start: 0.4355 (mtp) cc_final: 0.4038 (mtp) REVERT: A 1730 LYS cc_start: 0.7464 (mttt) cc_final: 0.7186 (mttp) REVERT: A 1892 GLU cc_start: 0.7420 (tt0) cc_final: 0.7103 (tt0) REVERT: A 1906 LEU cc_start: 0.8033 (tp) cc_final: 0.7733 (tt) REVERT: A 1924 ASP cc_start: 0.7220 (m-30) cc_final: 0.6868 (m-30) REVERT: A 1959 MET cc_start: 0.7685 (mtm) cc_final: 0.7243 (mtm) REVERT: A 2017 THR cc_start: 0.6949 (p) cc_final: 0.6681 (m) REVERT: A 2125 LYS cc_start: 0.8307 (mttt) cc_final: 0.7815 (mtpp) REVERT: A 2128 TYR cc_start: 0.6513 (m-80) cc_final: 0.6228 (m-10) REVERT: C 447 SER cc_start: 0.7646 (t) cc_final: 0.7352 (p) REVERT: C 500 MET cc_start: 0.8023 (ttp) cc_final: 0.7798 (ttm) REVERT: E 371 MET cc_start: 0.6942 (ptm) cc_final: 0.6638 (ttt) REVERT: F 104 MET cc_start: 0.6809 (mpp) cc_final: 0.6470 (mpp) REVERT: F 106 MET cc_start: 0.7424 (tpp) cc_final: 0.6779 (tpp) REVERT: F 118 MET cc_start: 0.6783 (mmm) cc_final: 0.6549 (mmm) REVERT: G 77 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6679 (tm-30) REVERT: G 118 MET cc_start: 0.5564 (tpt) cc_final: 0.5079 (tpt) REVERT: G 128 LEU cc_start: 0.8330 (mt) cc_final: 0.8031 (mt) REVERT: G 129 MET cc_start: 0.7341 (mmt) cc_final: 0.6972 (mmt) REVERT: G 163 LEU cc_start: 0.8068 (mt) cc_final: 0.7844 (mt) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.3397 time to fit residues: 225.4276 Evaluate side-chains 368 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.0010 chunk 187 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 144 optimal weight: 0.0370 chunk 224 optimal weight: 0.9990 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 423 ASN A 435 GLN A 681 GLN A 812 HIS A1124 ASN A1317 ASN A2030 ASN A2106 HIS G 150 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137828 restraints weight = 51268.402| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.99 r_work: 0.3517 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20302 Z= 0.148 Angle : 0.599 12.495 27441 Z= 0.309 Chirality : 0.041 0.183 3159 Planarity : 0.006 0.055 3436 Dihedral : 4.620 23.849 2696 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.94 % Allowed : 5.24 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 2449 helix: 1.31 (0.13), residues: 1450 sheet: 0.94 (0.42), residues: 138 loop : -1.48 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 86 HIS 0.010 0.001 HIS A2134 PHE 0.020 0.002 PHE A 546 TYR 0.020 0.001 TYR A 400 ARG 0.013 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 1126) hydrogen bonds : angle 4.36772 ( 3295) covalent geometry : bond 0.00320 (20302) covalent geometry : angle 0.59856 (27441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 385 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 TYR cc_start: 0.8439 (m-10) cc_final: 0.8235 (m-10) REVERT: A 29 LEU cc_start: 0.7842 (mt) cc_final: 0.7560 (mp) REVERT: A 38 TYR cc_start: 0.7931 (m-80) cc_final: 0.7730 (m-80) REVERT: A 196 PHE cc_start: 0.8307 (t80) cc_final: 0.8049 (t80) REVERT: A 263 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7911 (mtpp) REVERT: A 422 ARG cc_start: 0.6541 (tpp80) cc_final: 0.6304 (mtt90) REVERT: A 467 LYS cc_start: 0.7206 (mtmm) cc_final: 0.6800 (mtmm) REVERT: A 516 TYR cc_start: 0.8136 (t80) cc_final: 0.7865 (t80) REVERT: A 650 MET cc_start: 0.6079 (tpt) cc_final: 0.5721 (tpt) REVERT: A 750 SER cc_start: 0.8480 (t) cc_final: 0.8020 (m) REVERT: A 765 ARG cc_start: 0.6804 (mmm-85) cc_final: 0.6566 (mmm-85) REVERT: A 848 LYS cc_start: 0.7466 (ttmt) cc_final: 0.7212 (ttmt) REVERT: A 852 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6864 (mtt180) REVERT: A 877 LYS cc_start: 0.8283 (tptt) cc_final: 0.7984 (tptt) REVERT: A 925 ASP cc_start: 0.7692 (m-30) cc_final: 0.7489 (m-30) REVERT: A 1014 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7483 (mmtp) REVERT: A 1023 ILE cc_start: 0.8420 (tp) cc_final: 0.8152 (tt) REVERT: A 1069 THR cc_start: 0.8042 (m) cc_final: 0.7799 (m) REVERT: A 1078 MET cc_start: 0.7274 (ptp) cc_final: 0.7061 (ptp) REVERT: A 1145 TRP cc_start: 0.8528 (m100) cc_final: 0.8317 (m100) REVERT: A 1275 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6706 (ttm-80) REVERT: A 1359 THR cc_start: 0.8191 (m) cc_final: 0.7916 (m) REVERT: A 1424 PHE cc_start: 0.7884 (m-80) cc_final: 0.6860 (m-80) REVERT: A 1444 MET cc_start: 0.8148 (tpp) cc_final: 0.7852 (tpp) REVERT: A 1590 PHE cc_start: 0.7582 (t80) cc_final: 0.7310 (t80) REVERT: A 1713 MET cc_start: 0.4201 (mtp) cc_final: 0.3923 (mtp) REVERT: A 1906 LEU cc_start: 0.8097 (tp) cc_final: 0.7809 (tt) REVERT: A 1924 ASP cc_start: 0.7190 (m-30) cc_final: 0.6808 (m-30) REVERT: A 1959 MET cc_start: 0.7896 (mtm) cc_final: 0.7438 (mtm) REVERT: A 2017 THR cc_start: 0.7230 (p) cc_final: 0.6945 (m) REVERT: A 2106 HIS cc_start: 0.8248 (t-170) cc_final: 0.7901 (t70) REVERT: A 2125 LYS cc_start: 0.8302 (mttt) cc_final: 0.7869 (mtpp) REVERT: C 447 SER cc_start: 0.7645 (t) cc_final: 0.7356 (p) REVERT: F 106 MET cc_start: 0.7252 (tpp) cc_final: 0.6596 (tpp) REVERT: F 159 LEU cc_start: 0.7801 (mt) cc_final: 0.7057 (mp) REVERT: F 174 MET cc_start: 0.4039 (tpp) cc_final: 0.3718 (mpp) REVERT: G 77 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6704 (tm-30) REVERT: G 118 MET cc_start: 0.5549 (tpt) cc_final: 0.5123 (tpt) REVERT: G 128 LEU cc_start: 0.8418 (mt) cc_final: 0.8099 (mt) REVERT: G 129 MET cc_start: 0.7427 (mmt) cc_final: 0.7048 (mmt) outliers start: 21 outliers final: 12 residues processed: 390 average time/residue: 0.3603 time to fit residues: 214.4488 Evaluate side-chains 372 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 360 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1837 ARG Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2130 ILE Chi-restraints excluded: chain E residue 367 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 27 optimal weight: 0.0970 chunk 144 optimal weight: 0.0370 chunk 212 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 439 ASN A1169 HIS ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 GLN A2002 GLN A2134 HIS B 366 HIS E 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136855 restraints weight = 62422.647| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.61 r_work: 0.3512 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20302 Z= 0.132 Angle : 0.558 15.321 27441 Z= 0.285 Chirality : 0.041 0.195 3159 Planarity : 0.005 0.053 3436 Dihedral : 4.405 25.637 2696 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.30 % Allowed : 7.22 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2449 helix: 1.96 (0.13), residues: 1444 sheet: 0.80 (0.42), residues: 139 loop : -1.29 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1856 HIS 0.009 0.001 HIS A2134 PHE 0.021 0.001 PHE A1604 TYR 0.017 0.001 TYR A 400 ARG 0.010 0.000 ARG A1172 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 1126) hydrogen bonds : angle 4.11434 ( 3295) covalent geometry : bond 0.00287 (20302) covalent geometry : angle 0.55817 (27441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7856 (mt) cc_final: 0.7581 (mp) REVERT: A 263 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7941 (mtpp) REVERT: A 282 MET cc_start: 0.7647 (mmm) cc_final: 0.7397 (mmt) REVERT: A 351 SER cc_start: 0.7774 (t) cc_final: 0.7264 (m) REVERT: A 467 LYS cc_start: 0.7235 (mtmm) cc_final: 0.6817 (mtmm) REVERT: A 515 MET cc_start: 0.8127 (tpp) cc_final: 0.7656 (mpp) REVERT: A 545 LEU cc_start: 0.6980 (mt) cc_final: 0.6773 (mp) REVERT: A 650 MET cc_start: 0.6021 (tpt) cc_final: 0.5641 (tpt) REVERT: A 765 ARG cc_start: 0.6909 (mmm-85) cc_final: 0.6609 (mmm-85) REVERT: A 848 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7048 (ttmt) REVERT: A 852 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6920 (mtt180) REVERT: A 877 LYS cc_start: 0.8319 (tptt) cc_final: 0.7982 (tptt) REVERT: A 880 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: A 1014 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7538 (mmtp) REVERT: A 1023 ILE cc_start: 0.8421 (tp) cc_final: 0.8140 (tt) REVERT: A 1126 LEU cc_start: 0.8224 (mt) cc_final: 0.7970 (mt) REVERT: A 1275 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6707 (ttm-80) REVERT: A 1424 PHE cc_start: 0.7893 (m-80) cc_final: 0.6741 (m-80) REVERT: A 1444 MET cc_start: 0.8178 (tpp) cc_final: 0.7869 (tpp) REVERT: A 1590 PHE cc_start: 0.7660 (t80) cc_final: 0.7363 (t80) REVERT: A 1604 PHE cc_start: 0.7346 (t80) cc_final: 0.7111 (t80) REVERT: A 1608 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 1673 TYR cc_start: 0.7758 (t80) cc_final: 0.7415 (t80) REVERT: A 1713 MET cc_start: 0.4170 (mtp) cc_final: 0.3940 (mtp) REVERT: A 1729 LEU cc_start: 0.6805 (mm) cc_final: 0.6533 (mt) REVERT: A 1730 LYS cc_start: 0.7395 (mttm) cc_final: 0.7195 (mttp) REVERT: A 1890 THR cc_start: 0.7657 (p) cc_final: 0.7448 (m) REVERT: A 1906 LEU cc_start: 0.8096 (tp) cc_final: 0.7845 (tt) REVERT: A 1924 ASP cc_start: 0.7230 (m-30) cc_final: 0.6831 (m-30) REVERT: A 1959 MET cc_start: 0.7901 (mtm) cc_final: 0.7516 (mtm) REVERT: A 2017 THR cc_start: 0.7169 (p) cc_final: 0.6904 (m) REVERT: A 2125 LYS cc_start: 0.8322 (mttt) cc_final: 0.7891 (mtpp) REVERT: C 447 SER cc_start: 0.7662 (t) cc_final: 0.7380 (p) REVERT: E 372 ILE cc_start: 0.6392 (mt) cc_final: 0.6028 (mt) REVERT: F 106 MET cc_start: 0.7256 (tpp) cc_final: 0.6775 (tpp) REVERT: F 118 MET cc_start: 0.7438 (mmt) cc_final: 0.6951 (mmt) REVERT: F 159 LEU cc_start: 0.7729 (mt) cc_final: 0.7227 (mt) REVERT: F 174 MET cc_start: 0.4071 (tpp) cc_final: 0.3781 (mpp) REVERT: G 77 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6706 (tm-30) REVERT: G 80 MET cc_start: 0.7013 (mmt) cc_final: 0.6755 (mmt) REVERT: G 118 MET cc_start: 0.5581 (tpt) cc_final: 0.5164 (tpt) REVERT: G 128 LEU cc_start: 0.8449 (mt) cc_final: 0.8126 (mt) REVERT: G 129 MET cc_start: 0.7432 (mmt) cc_final: 0.7077 (mmt) outliers start: 29 outliers final: 22 residues processed: 377 average time/residue: 0.3397 time to fit residues: 193.7952 Evaluate side-chains 381 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 358 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1772 THR Chi-restraints excluded: chain A residue 1837 ARG Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2134 HIS Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 234 optimal weight: 0.6980 chunk 232 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 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 157 HIS A 562 ASN A 566 ASN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN C 438 GLN G 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134752 restraints weight = 56856.194| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.48 r_work: 0.3449 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20302 Z= 0.180 Angle : 0.595 18.476 27441 Z= 0.303 Chirality : 0.043 0.211 3159 Planarity : 0.005 0.053 3436 Dihedral : 4.499 24.843 2696 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 2.29 % Allowed : 8.20 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.17), residues: 2449 helix: 2.02 (0.13), residues: 1449 sheet: 0.67 (0.40), residues: 138 loop : -1.29 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 408 HIS 0.038 0.001 HIS A2134 PHE 0.022 0.002 PHE A 546 TYR 0.025 0.002 TYR A 400 ARG 0.006 0.001 ARG A1172 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 1126) hydrogen bonds : angle 4.16500 ( 3295) covalent geometry : bond 0.00414 (20302) covalent geometry : angle 0.59460 (27441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 371 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7856 (mt) cc_final: 0.7585 (mp) REVERT: A 240 MET cc_start: 0.8293 (mmm) cc_final: 0.7985 (mmp) REVERT: A 263 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7903 (mtpp) REVERT: A 351 SER cc_start: 0.7743 (t) cc_final: 0.7210 (m) REVERT: A 352 PHE cc_start: 0.8161 (m-80) cc_final: 0.7731 (m-80) REVERT: A 650 MET cc_start: 0.6048 (tpt) cc_final: 0.5674 (tpt) REVERT: A 750 SER cc_start: 0.8560 (t) cc_final: 0.8098 (m) REVERT: A 765 ARG cc_start: 0.6927 (mmm-85) cc_final: 0.6576 (mmm-85) REVERT: A 848 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7155 (ttmt) REVERT: A 852 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6998 (mtt180) REVERT: A 877 LYS cc_start: 0.8301 (tptt) cc_final: 0.8034 (tptt) REVERT: A 880 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 1023 ILE cc_start: 0.8408 (tp) cc_final: 0.8147 (tt) REVERT: A 1126 LEU cc_start: 0.8296 (mt) cc_final: 0.8078 (mt) REVERT: A 1127 ILE cc_start: 0.8180 (mt) cc_final: 0.7801 (tt) REVERT: A 1275 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6648 (ttm-80) REVERT: A 1424 PHE cc_start: 0.7980 (m-80) cc_final: 0.6802 (m-80) REVERT: A 1432 LEU cc_start: 0.8240 (mt) cc_final: 0.7997 (mm) REVERT: A 1444 MET cc_start: 0.8183 (tpp) cc_final: 0.7896 (tpp) REVERT: A 1590 PHE cc_start: 0.7803 (t80) cc_final: 0.7431 (t80) REVERT: A 1729 LEU cc_start: 0.6787 (mm) cc_final: 0.6515 (mt) REVERT: A 1730 LYS cc_start: 0.7367 (mttm) cc_final: 0.7161 (mttp) REVERT: A 1906 LEU cc_start: 0.8082 (tp) cc_final: 0.7852 (tt) REVERT: A 1924 ASP cc_start: 0.7188 (m-30) cc_final: 0.6778 (m-30) REVERT: A 1959 MET cc_start: 0.7969 (mtm) cc_final: 0.7573 (mtm) REVERT: A 2001 ILE cc_start: 0.7721 (tp) cc_final: 0.7472 (tp) REVERT: A 2017 THR cc_start: 0.7317 (p) cc_final: 0.7093 (m) REVERT: A 2125 LYS cc_start: 0.8319 (mttt) cc_final: 0.7864 (mtpp) REVERT: A 2129 LEU cc_start: 0.7878 (mt) cc_final: 0.7578 (mt) REVERT: C 447 SER cc_start: 0.7695 (t) cc_final: 0.7456 (p) REVERT: F 106 MET cc_start: 0.7266 (tpp) cc_final: 0.6899 (tpp) REVERT: F 118 MET cc_start: 0.7521 (mmt) cc_final: 0.6992 (mmt) REVERT: F 159 LEU cc_start: 0.7752 (mt) cc_final: 0.7262 (mp) REVERT: F 174 MET cc_start: 0.4141 (tpp) cc_final: 0.3850 (mpp) REVERT: G 77 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6707 (tm-30) REVERT: G 80 MET cc_start: 0.7026 (mmt) cc_final: 0.6792 (mmt) REVERT: G 118 MET cc_start: 0.5553 (tpt) cc_final: 0.5162 (tpt) REVERT: G 128 LEU cc_start: 0.8484 (mt) cc_final: 0.8213 (mt) REVERT: G 129 MET cc_start: 0.7541 (mmt) cc_final: 0.7164 (mmt) outliers start: 51 outliers final: 35 residues processed: 395 average time/residue: 0.4238 time to fit residues: 263.2976 Evaluate side-chains 396 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 360 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1359 THR Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1772 THR Chi-restraints excluded: chain A residue 1837 ARG Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 27 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 209 optimal weight: 0.9980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 423 ASN A 473 GLN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131789 restraints weight = 57456.705| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.48 r_work: 0.3409 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20302 Z= 0.226 Angle : 0.647 20.461 27441 Z= 0.329 Chirality : 0.045 0.213 3159 Planarity : 0.005 0.072 3436 Dihedral : 4.685 25.798 2696 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.73 % Allowed : 9.32 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2449 helix: 1.85 (0.13), residues: 1454 sheet: 0.41 (0.39), residues: 144 loop : -1.36 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 408 HIS 0.008 0.001 HIS A1174 PHE 0.022 0.002 PHE A 546 TYR 0.028 0.002 TYR A 400 ARG 0.009 0.001 ARG A2101 Details of bonding type rmsd hydrogen bonds : bond 0.05760 ( 1126) hydrogen bonds : angle 4.28392 ( 3295) covalent geometry : bond 0.00527 (20302) covalent geometry : angle 0.64674 (27441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 381 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7841 (mt) cc_final: 0.7588 (mp) REVERT: A 263 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7892 (mtpp) REVERT: A 352 PHE cc_start: 0.8124 (m-80) cc_final: 0.7755 (m-80) REVERT: A 431 LEU cc_start: 0.7921 (mt) cc_final: 0.7675 (mt) REVERT: A 545 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6950 (mt) REVERT: A 553 MET cc_start: 0.7882 (tpt) cc_final: 0.7455 (mmm) REVERT: A 650 MET cc_start: 0.5994 (tpt) cc_final: 0.5637 (tpt) REVERT: A 750 SER cc_start: 0.8594 (t) cc_final: 0.8146 (m) REVERT: A 765 ARG cc_start: 0.6960 (mmm-85) cc_final: 0.6645 (mmm-85) REVERT: A 768 SER cc_start: 0.7626 (t) cc_final: 0.7266 (p) REVERT: A 848 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7413 (ttmt) REVERT: A 852 ARG cc_start: 0.7327 (mtt180) cc_final: 0.7040 (mtt180) REVERT: A 877 LYS cc_start: 0.8303 (tptt) cc_final: 0.8009 (tptt) REVERT: A 880 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: A 1023 ILE cc_start: 0.8438 (tp) cc_final: 0.8182 (tt) REVERT: A 1126 LEU cc_start: 0.8337 (mt) cc_final: 0.8106 (mt) REVERT: A 1176 THR cc_start: 0.5545 (m) cc_final: 0.4273 (p) REVERT: A 1275 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6707 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7280 (mmmm) REVERT: A 1424 PHE cc_start: 0.8088 (m-80) cc_final: 0.6892 (m-80) REVERT: A 1432 LEU cc_start: 0.8297 (mt) cc_final: 0.8048 (mm) REVERT: A 1444 MET cc_start: 0.8190 (tpp) cc_final: 0.7950 (tpp) REVERT: A 1590 PHE cc_start: 0.7873 (t80) cc_final: 0.7663 (t80) REVERT: A 1608 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8093 (mm-40) REVERT: A 1673 TYR cc_start: 0.7995 (t80) cc_final: 0.7725 (t80) REVERT: A 1729 LEU cc_start: 0.6762 (mm) cc_final: 0.6482 (mt) REVERT: A 1906 LEU cc_start: 0.8076 (tp) cc_final: 0.7866 (tt) REVERT: A 1924 ASP cc_start: 0.7328 (m-30) cc_final: 0.6923 (m-30) REVERT: A 1959 MET cc_start: 0.7980 (mtm) cc_final: 0.7616 (mtm) REVERT: A 2001 ILE cc_start: 0.7748 (tp) cc_final: 0.7508 (tp) REVERT: A 2125 LYS cc_start: 0.8316 (mttt) cc_final: 0.7878 (mtpp) REVERT: A 2129 LEU cc_start: 0.7991 (mt) cc_final: 0.7611 (mt) REVERT: A 2181 ILE cc_start: 0.3879 (OUTLIER) cc_final: 0.3604 (mt) REVERT: C 447 SER cc_start: 0.7713 (t) cc_final: 0.7457 (p) REVERT: F 106 MET cc_start: 0.7354 (tpp) cc_final: 0.7008 (tpp) REVERT: F 118 MET cc_start: 0.7669 (mmt) cc_final: 0.7157 (mmt) REVERT: F 129 MET cc_start: 0.7436 (mtm) cc_final: 0.7192 (mpp) REVERT: F 159 LEU cc_start: 0.7785 (mt) cc_final: 0.7397 (mp) REVERT: F 174 MET cc_start: 0.4176 (tpp) cc_final: 0.3881 (mpp) REVERT: G 77 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6679 (tm-30) REVERT: G 80 MET cc_start: 0.7083 (mmt) cc_final: 0.6839 (mmt) REVERT: G 118 MET cc_start: 0.5496 (tpt) cc_final: 0.5133 (tpt) REVERT: G 128 LEU cc_start: 0.8514 (mt) cc_final: 0.8186 (mt) REVERT: G 129 MET cc_start: 0.7596 (mmt) cc_final: 0.7256 (mmt) outliers start: 61 outliers final: 44 residues processed: 411 average time/residue: 0.4377 time to fit residues: 277.7793 Evaluate side-chains 414 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1177 CYS Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 1968 MET Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 236 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 423 ASN A 774 ASN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133416 restraints weight = 60063.156| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.90 r_work: 0.3405 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20302 Z= 0.164 Angle : 0.615 29.348 27441 Z= 0.304 Chirality : 0.042 0.183 3159 Planarity : 0.005 0.067 3436 Dihedral : 4.551 26.587 2696 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.15 % Allowed : 10.85 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2449 helix: 1.99 (0.13), residues: 1468 sheet: 0.09 (0.39), residues: 148 loop : -1.34 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.006 0.001 HIS A1174 PHE 0.022 0.002 PHE A 546 TYR 0.029 0.002 TYR A 400 ARG 0.005 0.000 ARG A2101 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 1126) hydrogen bonds : angle 4.14475 ( 3295) covalent geometry : bond 0.00376 (20302) covalent geometry : angle 0.61482 (27441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7823 (mt) cc_final: 0.7562 (mp) REVERT: A 110 LEU cc_start: 0.7488 (mt) cc_final: 0.7240 (mt) REVERT: A 240 MET cc_start: 0.8287 (mmm) cc_final: 0.8078 (mmp) REVERT: A 263 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7882 (mtpp) REVERT: A 351 SER cc_start: 0.7717 (t) cc_final: 0.7121 (m) REVERT: A 352 PHE cc_start: 0.8080 (m-80) cc_final: 0.7723 (m-80) REVERT: A 515 MET cc_start: 0.8200 (mmm) cc_final: 0.7788 (tpp) REVERT: A 545 LEU cc_start: 0.7284 (mp) cc_final: 0.6964 (mt) REVERT: A 553 MET cc_start: 0.7889 (tpt) cc_final: 0.7463 (mmm) REVERT: A 650 MET cc_start: 0.6049 (tpt) cc_final: 0.5681 (tpt) REVERT: A 750 SER cc_start: 0.8591 (t) cc_final: 0.8134 (m) REVERT: A 765 ARG cc_start: 0.6997 (mmm-85) cc_final: 0.6707 (mmm-85) REVERT: A 768 SER cc_start: 0.7565 (t) cc_final: 0.7149 (p) REVERT: A 792 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7433 (mtmt) REVERT: A 848 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7151 (ttmt) REVERT: A 852 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7052 (mtt180) REVERT: A 877 LYS cc_start: 0.8340 (tptt) cc_final: 0.8026 (tptt) REVERT: A 880 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: A 1023 ILE cc_start: 0.8451 (tp) cc_final: 0.8181 (tt) REVERT: A 1127 ILE cc_start: 0.8167 (mt) cc_final: 0.7855 (tt) REVERT: A 1176 THR cc_start: 0.5457 (m) cc_final: 0.4205 (p) REVERT: A 1275 ARG cc_start: 0.7101 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7260 (mmmm) REVERT: A 1444 MET cc_start: 0.8227 (tpp) cc_final: 0.8001 (tpp) REVERT: A 1590 PHE cc_start: 0.7941 (t80) cc_final: 0.7579 (t80) REVERT: A 1673 TYR cc_start: 0.7996 (t80) cc_final: 0.7759 (t80) REVERT: A 1729 LEU cc_start: 0.6746 (mm) cc_final: 0.6462 (mt) REVERT: A 1750 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6900 (tm-30) REVERT: A 1906 LEU cc_start: 0.8093 (tp) cc_final: 0.7866 (tt) REVERT: A 1924 ASP cc_start: 0.7371 (m-30) cc_final: 0.6952 (m-30) REVERT: A 1959 MET cc_start: 0.7969 (mtm) cc_final: 0.7578 (mtm) REVERT: A 2001 ILE cc_start: 0.7728 (tp) cc_final: 0.7477 (tp) REVERT: A 2125 LYS cc_start: 0.8320 (mttt) cc_final: 0.7976 (mmmm) REVERT: A 2181 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.3566 (mt) REVERT: C 447 SER cc_start: 0.7721 (t) cc_final: 0.7461 (p) REVERT: F 104 MET cc_start: 0.7209 (mmm) cc_final: 0.6818 (mmt) REVERT: F 106 MET cc_start: 0.7275 (tpp) cc_final: 0.6949 (tpp) REVERT: F 118 MET cc_start: 0.7696 (mmt) cc_final: 0.7229 (mmt) REVERT: F 159 LEU cc_start: 0.7760 (mt) cc_final: 0.7387 (mp) REVERT: F 174 MET cc_start: 0.4233 (tpp) cc_final: 0.3985 (mpp) REVERT: G 77 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6724 (tm-30) REVERT: G 80 MET cc_start: 0.7081 (mmt) cc_final: 0.6861 (mmt) REVERT: G 118 MET cc_start: 0.5460 (tpt) cc_final: 0.5114 (tpt) REVERT: G 128 LEU cc_start: 0.8500 (mt) cc_final: 0.8222 (mt) REVERT: G 129 MET cc_start: 0.7597 (mmt) cc_final: 0.7286 (mmt) outliers start: 48 outliers final: 36 residues processed: 404 average time/residue: 0.5590 time to fit residues: 346.8339 Evaluate side-chains 404 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 366 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 1968 MET Chi-restraints excluded: chain A residue 2024 ILE Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 176 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 423 ASN A 473 GLN A1315 ASN A1317 ASN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133793 restraints weight = 62310.316| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.01 r_work: 0.3412 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20302 Z= 0.146 Angle : 0.600 29.431 27441 Z= 0.294 Chirality : 0.041 0.186 3159 Planarity : 0.005 0.062 3436 Dihedral : 4.467 27.564 2696 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.38 % Allowed : 11.25 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2449 helix: 2.13 (0.13), residues: 1461 sheet: 0.03 (0.39), residues: 150 loop : -1.32 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1189 HIS 0.007 0.001 HIS A 404 PHE 0.020 0.001 PHE A 546 TYR 0.023 0.001 TYR A 400 ARG 0.008 0.000 ARG A2101 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 1126) hydrogen bonds : angle 4.06492 ( 3295) covalent geometry : bond 0.00331 (20302) covalent geometry : angle 0.59986 (27441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 374 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7846 (mt) cc_final: 0.7586 (mp) REVERT: A 263 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7852 (mtpp) REVERT: A 351 SER cc_start: 0.7717 (t) cc_final: 0.7169 (m) REVERT: A 352 PHE cc_start: 0.8068 (m-80) cc_final: 0.7740 (m-80) REVERT: A 467 LYS cc_start: 0.7268 (mtmm) cc_final: 0.6848 (mtmm) REVERT: A 515 MET cc_start: 0.8209 (mmm) cc_final: 0.7776 (tpp) REVERT: A 545 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7002 (mt) REVERT: A 553 MET cc_start: 0.7863 (tpt) cc_final: 0.7442 (mmm) REVERT: A 650 MET cc_start: 0.5998 (tpt) cc_final: 0.5641 (tpt) REVERT: A 750 SER cc_start: 0.8571 (t) cc_final: 0.8127 (m) REVERT: A 765 ARG cc_start: 0.6934 (mmm-85) cc_final: 0.6682 (mmm-85) REVERT: A 768 SER cc_start: 0.7476 (t) cc_final: 0.7098 (p) REVERT: A 792 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7491 (mtmt) REVERT: A 848 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7091 (ttmt) REVERT: A 852 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7036 (mtt180) REVERT: A 877 LYS cc_start: 0.8361 (tptt) cc_final: 0.8059 (tptt) REVERT: A 880 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 1023 ILE cc_start: 0.8490 (tp) cc_final: 0.8203 (tt) REVERT: A 1127 ILE cc_start: 0.8172 (mt) cc_final: 0.7861 (tt) REVERT: A 1176 THR cc_start: 0.5483 (m) cc_final: 0.4235 (p) REVERT: A 1275 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.6812 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7276 (mmmm) REVERT: A 1444 MET cc_start: 0.8209 (tpp) cc_final: 0.7988 (tpp) REVERT: A 1590 PHE cc_start: 0.7940 (t80) cc_final: 0.7515 (t80) REVERT: A 1673 TYR cc_start: 0.7998 (t80) cc_final: 0.7767 (t80) REVERT: A 1716 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7269 (ptpp) REVERT: A 1729 LEU cc_start: 0.6812 (mm) cc_final: 0.6529 (mt) REVERT: A 1750 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6917 (tm-30) REVERT: A 1906 LEU cc_start: 0.8084 (tp) cc_final: 0.7873 (tt) REVERT: A 1924 ASP cc_start: 0.7412 (m-30) cc_final: 0.6998 (m-30) REVERT: A 1959 MET cc_start: 0.7925 (mtm) cc_final: 0.7542 (mtm) REVERT: A 2001 ILE cc_start: 0.7718 (tp) cc_final: 0.7462 (tp) REVERT: A 2125 LYS cc_start: 0.8345 (mttt) cc_final: 0.8004 (mmmm) REVERT: A 2181 ILE cc_start: 0.3803 (OUTLIER) cc_final: 0.3554 (mt) REVERT: C 447 SER cc_start: 0.7697 (t) cc_final: 0.7452 (p) REVERT: F 104 MET cc_start: 0.7259 (mmm) cc_final: 0.6965 (mmt) REVERT: F 106 MET cc_start: 0.7211 (tpp) cc_final: 0.6882 (tpp) REVERT: F 118 MET cc_start: 0.7659 (mmt) cc_final: 0.7227 (mmt) REVERT: F 159 LEU cc_start: 0.7729 (mt) cc_final: 0.7350 (mp) REVERT: F 174 MET cc_start: 0.4257 (tpp) cc_final: 0.4034 (mpp) REVERT: G 77 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6687 (tm-30) REVERT: G 80 MET cc_start: 0.7064 (mmt) cc_final: 0.6859 (mmt) REVERT: G 118 MET cc_start: 0.5403 (tpt) cc_final: 0.5077 (tpt) REVERT: G 128 LEU cc_start: 0.8505 (mt) cc_final: 0.8222 (mt) REVERT: G 129 MET cc_start: 0.7460 (mmt) cc_final: 0.7173 (mmt) outliers start: 53 outliers final: 37 residues processed: 400 average time/residue: 0.5664 time to fit residues: 357.7440 Evaluate side-chains 406 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 365 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1836 HIS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 1968 MET Chi-restraints excluded: chain A residue 2024 ILE Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 473 GLN ** A1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132882 restraints weight = 57808.392| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.53 r_work: 0.3441 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20302 Z= 0.163 Angle : 0.620 29.715 27441 Z= 0.303 Chirality : 0.042 0.195 3159 Planarity : 0.005 0.069 3436 Dihedral : 4.477 29.260 2696 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.06 % Allowed : 11.70 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2449 helix: 2.12 (0.13), residues: 1460 sheet: -0.02 (0.38), residues: 155 loop : -1.35 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 747 HIS 0.006 0.001 HIS A 404 PHE 0.020 0.001 PHE A 546 TYR 0.014 0.001 TYR A 832 ARG 0.006 0.000 ARG A2101 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 1126) hydrogen bonds : angle 4.08480 ( 3295) covalent geometry : bond 0.00378 (20302) covalent geometry : angle 0.61962 (27441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7832 (mt) cc_final: 0.7585 (mp) REVERT: A 263 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7801 (mtpp) REVERT: A 467 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6859 (mtmm) REVERT: A 515 MET cc_start: 0.8166 (mmm) cc_final: 0.7704 (tpp) REVERT: A 538 GLU cc_start: 0.7158 (pm20) cc_final: 0.6895 (pm20) REVERT: A 545 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6873 (mt) REVERT: A 553 MET cc_start: 0.7828 (tpt) cc_final: 0.7402 (mmm) REVERT: A 650 MET cc_start: 0.6072 (tpt) cc_final: 0.5764 (tpt) REVERT: A 736 MET cc_start: 0.5377 (mtp) cc_final: 0.5052 (mtp) REVERT: A 765 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6629 (mmm-85) REVERT: A 768 SER cc_start: 0.7514 (t) cc_final: 0.7117 (p) REVERT: A 792 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7408 (mtmt) REVERT: A 848 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7228 (ttmt) REVERT: A 852 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6941 (mtt180) REVERT: A 877 LYS cc_start: 0.8313 (tptt) cc_final: 0.8014 (tptt) REVERT: A 880 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: A 1023 ILE cc_start: 0.8470 (tp) cc_final: 0.8181 (tt) REVERT: A 1127 ILE cc_start: 0.8138 (mt) cc_final: 0.7854 (tt) REVERT: A 1176 THR cc_start: 0.5477 (m) cc_final: 0.4374 (p) REVERT: A 1275 ARG cc_start: 0.7159 (ttm-80) cc_final: 0.6804 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7526 (mtpt) cc_final: 0.7295 (mmmm) REVERT: A 1424 PHE cc_start: 0.7886 (m-80) cc_final: 0.6590 (m-80) REVERT: A 1444 MET cc_start: 0.8185 (tpp) cc_final: 0.7947 (tpp) REVERT: A 1590 PHE cc_start: 0.7930 (t80) cc_final: 0.7475 (t80) REVERT: A 1729 LEU cc_start: 0.6810 (mm) cc_final: 0.6515 (mt) REVERT: A 1924 ASP cc_start: 0.7353 (m-30) cc_final: 0.6932 (m-30) REVERT: A 1959 MET cc_start: 0.7903 (mtm) cc_final: 0.7521 (mtm) REVERT: A 2001 ILE cc_start: 0.7714 (tp) cc_final: 0.7455 (tp) REVERT: A 2125 LYS cc_start: 0.8307 (mttt) cc_final: 0.7975 (mmmm) REVERT: A 2181 ILE cc_start: 0.3776 (OUTLIER) cc_final: 0.3523 (mt) REVERT: C 447 SER cc_start: 0.7658 (t) cc_final: 0.7416 (p) REVERT: F 104 MET cc_start: 0.7122 (mmm) cc_final: 0.6904 (mmt) REVERT: F 106 MET cc_start: 0.7174 (tpp) cc_final: 0.6835 (tpp) REVERT: F 118 MET cc_start: 0.7634 (mmt) cc_final: 0.7216 (mmt) REVERT: F 159 LEU cc_start: 0.7723 (mt) cc_final: 0.7353 (mp) REVERT: F 174 MET cc_start: 0.4261 (tpp) cc_final: 0.4039 (mpp) REVERT: G 77 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6670 (tm-30) REVERT: G 118 MET cc_start: 0.5356 (tpt) cc_final: 0.5030 (tpt) REVERT: G 128 LEU cc_start: 0.8514 (mt) cc_final: 0.8237 (mt) REVERT: G 129 MET cc_start: 0.7496 (mmt) cc_final: 0.7205 (mmt) outliers start: 46 outliers final: 37 residues processed: 382 average time/residue: 0.3561 time to fit residues: 205.8490 Evaluate side-chains 400 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 360 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1836 HIS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 1968 MET Chi-restraints excluded: chain A residue 2024 ILE Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.0000 chunk 154 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 181 optimal weight: 0.2980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 473 GLN A1315 ASN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2015 ASN B 329 ASN C 438 GLN G 150 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134769 restraints weight = 56367.248| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.73 r_work: 0.3433 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20302 Z= 0.137 Angle : 0.602 29.109 27441 Z= 0.292 Chirality : 0.041 0.199 3159 Planarity : 0.005 0.070 3436 Dihedral : 4.394 32.040 2696 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 12.01 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2449 helix: 2.22 (0.13), residues: 1465 sheet: -0.03 (0.38), residues: 155 loop : -1.34 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1189 HIS 0.006 0.001 HIS A 157 PHE 0.019 0.001 PHE A 546 TYR 0.015 0.001 TYR A 754 ARG 0.006 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1126) hydrogen bonds : angle 3.98649 ( 3295) covalent geometry : bond 0.00310 (20302) covalent geometry : angle 0.60178 (27441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7855 (mt) cc_final: 0.7588 (mp) REVERT: A 263 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7819 (mtpp) REVERT: A 294 ARG cc_start: 0.8533 (ttm170) cc_final: 0.8298 (ptp-170) REVERT: A 467 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6862 (mtmm) REVERT: A 515 MET cc_start: 0.8173 (mmm) cc_final: 0.7721 (tpp) REVERT: A 538 GLU cc_start: 0.7133 (pm20) cc_final: 0.6895 (pm20) REVERT: A 545 LEU cc_start: 0.7207 (mp) cc_final: 0.6912 (mt) REVERT: A 553 MET cc_start: 0.7844 (tpt) cc_final: 0.7432 (mmm) REVERT: A 650 MET cc_start: 0.6040 (tpt) cc_final: 0.5732 (tpt) REVERT: A 736 MET cc_start: 0.5371 (mtp) cc_final: 0.5091 (mtp) REVERT: A 765 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6702 (mmm-85) REVERT: A 768 SER cc_start: 0.7457 (t) cc_final: 0.7074 (p) REVERT: A 848 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7241 (ttmt) REVERT: A 852 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6991 (mtt180) REVERT: A 877 LYS cc_start: 0.8368 (tptt) cc_final: 0.8055 (tptt) REVERT: A 880 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: A 1023 ILE cc_start: 0.8474 (tp) cc_final: 0.8201 (tt) REVERT: A 1176 THR cc_start: 0.5484 (m) cc_final: 0.4254 (p) REVERT: A 1275 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6790 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7316 (mmmm) REVERT: A 1424 PHE cc_start: 0.7903 (m-80) cc_final: 0.6530 (m-80) REVERT: A 1444 MET cc_start: 0.8204 (tpp) cc_final: 0.7959 (tpp) REVERT: A 1590 PHE cc_start: 0.7941 (t80) cc_final: 0.7502 (t80) REVERT: A 1716 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7141 (ptpp) REVERT: A 1729 LEU cc_start: 0.6845 (mm) cc_final: 0.6553 (mt) REVERT: A 1907 LEU cc_start: 0.7613 (mt) cc_final: 0.7395 (mp) REVERT: A 1924 ASP cc_start: 0.7359 (m-30) cc_final: 0.6980 (m-30) REVERT: A 1959 MET cc_start: 0.7888 (mtm) cc_final: 0.7487 (mtm) REVERT: A 2001 ILE cc_start: 0.7706 (tp) cc_final: 0.7466 (tp) REVERT: A 2125 LYS cc_start: 0.8288 (mttt) cc_final: 0.7973 (mmmm) REVERT: A 2181 ILE cc_start: 0.3719 (OUTLIER) cc_final: 0.3460 (mt) REVERT: C 371 MET cc_start: 0.4229 (mmt) cc_final: 0.3699 (mmm) REVERT: C 447 SER cc_start: 0.7662 (t) cc_final: 0.7420 (p) REVERT: F 82 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6658 (t) REVERT: F 106 MET cc_start: 0.7173 (tpp) cc_final: 0.6835 (tpp) REVERT: F 118 MET cc_start: 0.7473 (mmt) cc_final: 0.7128 (mmt) REVERT: F 159 LEU cc_start: 0.7717 (mt) cc_final: 0.7435 (mt) REVERT: G 77 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6729 (tm-30) REVERT: G 118 MET cc_start: 0.5315 (tpt) cc_final: 0.4997 (tpt) REVERT: G 128 LEU cc_start: 0.8505 (mt) cc_final: 0.8218 (mt) REVERT: G 129 MET cc_start: 0.7491 (mmt) cc_final: 0.7216 (mmt) outliers start: 43 outliers final: 33 residues processed: 384 average time/residue: 0.3689 time to fit residues: 217.1545 Evaluate side-chains 392 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1836 HIS Chi-restraints excluded: chain A residue 1915 VAL Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2024 ILE Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 5 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 473 GLN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN G 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133940 restraints weight = 55186.260| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.39 r_work: 0.3456 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 20302 Z= 0.180 Angle : 0.879 59.200 27441 Z= 0.500 Chirality : 0.042 0.400 3159 Planarity : 0.005 0.069 3436 Dihedral : 4.439 31.925 2696 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.70 % Allowed : 12.77 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2449 helix: 2.21 (0.13), residues: 1465 sheet: -0.03 (0.38), residues: 155 loop : -1.36 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1189 HIS 0.007 0.001 HIS A 404 PHE 0.019 0.001 PHE A 546 TYR 0.015 0.001 TYR A 754 ARG 0.055 0.001 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1126) hydrogen bonds : angle 3.98999 ( 3295) covalent geometry : bond 0.00397 (20302) covalent geometry : angle 0.87877 (27441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 355 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7834 (mt) cc_final: 0.7571 (mp) REVERT: A 263 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7791 (mtpp) REVERT: A 294 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8261 (ptp-170) REVERT: A 467 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6858 (mtmm) REVERT: A 515 MET cc_start: 0.8151 (mmm) cc_final: 0.7688 (tpp) REVERT: A 538 GLU cc_start: 0.7123 (pm20) cc_final: 0.6887 (pm20) REVERT: A 545 LEU cc_start: 0.7161 (mp) cc_final: 0.6866 (mt) REVERT: A 553 MET cc_start: 0.7831 (tpt) cc_final: 0.7416 (mmm) REVERT: A 650 MET cc_start: 0.6037 (tpt) cc_final: 0.5736 (tpt) REVERT: A 736 MET cc_start: 0.5277 (mtp) cc_final: 0.5002 (mtp) REVERT: A 765 ARG cc_start: 0.6874 (mmm-85) cc_final: 0.6658 (mmm-85) REVERT: A 768 SER cc_start: 0.7434 (t) cc_final: 0.7048 (p) REVERT: A 848 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7203 (ttmt) REVERT: A 852 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6963 (mtt180) REVERT: A 877 LYS cc_start: 0.8333 (tptt) cc_final: 0.8021 (tptt) REVERT: A 880 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 1023 ILE cc_start: 0.8454 (tp) cc_final: 0.8176 (tt) REVERT: A 1176 THR cc_start: 0.5445 (m) cc_final: 0.4247 (p) REVERT: A 1275 ARG cc_start: 0.7132 (ttm-80) cc_final: 0.6773 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7286 (mmmm) REVERT: A 1424 PHE cc_start: 0.7884 (m-80) cc_final: 0.6532 (m-80) REVERT: A 1444 MET cc_start: 0.8167 (tpp) cc_final: 0.7925 (tpp) REVERT: A 1590 PHE cc_start: 0.7935 (t80) cc_final: 0.7498 (t80) REVERT: A 1716 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7143 (ptpp) REVERT: A 1729 LEU cc_start: 0.6849 (mm) cc_final: 0.6558 (mt) REVERT: A 1907 LEU cc_start: 0.7572 (mt) cc_final: 0.7349 (mp) REVERT: A 1924 ASP cc_start: 0.7324 (m-30) cc_final: 0.6937 (m-30) REVERT: A 1959 MET cc_start: 0.7853 (mtm) cc_final: 0.7445 (mtm) REVERT: A 2001 ILE cc_start: 0.7692 (tp) cc_final: 0.7456 (tp) REVERT: A 2123 ASN cc_start: 0.7569 (m-40) cc_final: 0.7362 (m-40) REVERT: A 2125 LYS cc_start: 0.8257 (mttt) cc_final: 0.7935 (mmmm) REVERT: A 2181 ILE cc_start: 0.3724 (OUTLIER) cc_final: 0.3476 (mt) REVERT: C 371 MET cc_start: 0.4193 (mmt) cc_final: 0.3674 (mmm) REVERT: C 447 SER cc_start: 0.7644 (t) cc_final: 0.7407 (p) REVERT: F 82 THR cc_start: 0.6963 (OUTLIER) cc_final: 0.6618 (t) REVERT: F 106 MET cc_start: 0.7102 (tpp) cc_final: 0.6768 (tpp) REVERT: F 118 MET cc_start: 0.7456 (mmt) cc_final: 0.7082 (mmt) REVERT: F 159 LEU cc_start: 0.7704 (mt) cc_final: 0.7410 (mt) REVERT: F 174 MET cc_start: 0.3892 (mpp) cc_final: 0.3607 (mpp) REVERT: G 77 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6709 (tm-30) REVERT: G 118 MET cc_start: 0.5287 (tpt) cc_final: 0.4981 (tpt) REVERT: G 128 LEU cc_start: 0.8489 (mt) cc_final: 0.8197 (mt) REVERT: G 129 MET cc_start: 0.7487 (mmt) cc_final: 0.7214 (mmt) outliers start: 38 outliers final: 30 residues processed: 378 average time/residue: 0.3452 time to fit residues: 196.8464 Evaluate side-chains 388 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 354 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1716 LYS Chi-restraints excluded: chain A residue 1836 HIS Chi-restraints excluded: chain A residue 1915 VAL Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 1953 THR Chi-restraints excluded: chain A residue 1954 GLU Chi-restraints excluded: chain A residue 2024 ILE Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 174 optimal weight: 0.0270 chunk 171 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 473 GLN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134939 restraints weight = 51773.091| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.29 r_work: 0.3466 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 20302 Z= 0.180 Angle : 0.879 59.200 27441 Z= 0.500 Chirality : 0.042 0.400 3159 Planarity : 0.005 0.069 3436 Dihedral : 4.439 31.925 2696 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.52 % Allowed : 12.95 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2449 helix: 2.21 (0.13), residues: 1465 sheet: -0.03 (0.38), residues: 155 loop : -1.36 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1189 HIS 0.007 0.001 HIS A 404 PHE 0.019 0.001 PHE A 546 TYR 0.015 0.001 TYR A 754 ARG 0.055 0.001 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1126) hydrogen bonds : angle 3.98999 ( 3295) covalent geometry : bond 0.00397 (20302) covalent geometry : angle 0.87877 (27441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13219.71 seconds wall clock time: 238 minutes 43.48 seconds (14323.48 seconds total)