Starting phenix.real_space_refine on Thu Sep 18 20:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dut_47177/09_2025/9dut_47177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dut_47177/09_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_47177/09_2025/9dut_47177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dut_47177/09_2025/9dut_47177.map" model { file = "/net/cci-nas-00/data/ceres_data/9dut_47177/09_2025/9dut_47177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dut_47177/09_2025/9dut_47177.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.03, per 1000 atoms: 0.25 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: 1.74 Conformation dependent library (CDL) restraints added in 934.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.96 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: 4.59 Time building geometry restraints manager: 2.33 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: 3.660 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 554 TYR 0.026 0.002 TYR A 742 PHE 0.025 0.002 PHE A 546 TRP 0.059 0.003 TRP A 408 HIS 0.018 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00429 (20302) covalent geometry : angle 0.86911 (27441) hydrogen bonds : bond 0.17163 ( 1126) hydrogen bonds : angle 6.22824 ( 3295) *********************** 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 : 0.803 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: 0.1683 time to fit residues: 111.3951 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 : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN A 423 ASN A 435 GLN A 774 ASN A 812 HIS A1124 ASN A1169 HIS A1317 ASN A2030 ASN A2106 HIS B 366 HIS C 438 GLN D 330 GLN G 150 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133980 restraints weight = 55069.320| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.33 r_work: 0.3458 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- 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: 0.7183 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20302 Z= 0.217 Angle : 0.676 13.222 27441 Z= 0.349 Chirality : 0.045 0.214 3159 Planarity : 0.006 0.061 3436 Dihedral : 4.840 25.994 2696 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.21 % Allowed : 5.15 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2449 helix: 1.09 (0.13), residues: 1442 sheet: 0.44 (0.40), residues: 153 loop : -1.41 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 951 TYR 0.019 0.002 TYR A 400 PHE 0.022 0.002 PHE A 546 TRP 0.023 0.002 TRP A 408 HIS 0.010 0.002 HIS A1991 Details of bonding type rmsd covalent geometry : bond 0.00499 (20302) covalent geometry : angle 0.67552 (27441) hydrogen bonds : bond 0.06420 ( 1126) hydrogen bonds : angle 4.49736 ( 3295) *********************** 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 428 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 401 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7838 (mt) cc_final: 0.7582 (mp) REVERT: A 240 MET cc_start: 0.8317 (mmm) cc_final: 0.8097 (mmp) REVERT: A 263 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7907 (mtpp) REVERT: A 336 TYR cc_start: 0.8482 (t80) cc_final: 0.8199 (t80) REVERT: A 467 LYS cc_start: 0.7234 (mtmm) cc_final: 0.6859 (mtmm) REVERT: A 515 MET cc_start: 0.7960 (tpp) cc_final: 0.7711 (tpp) REVERT: A 516 TYR cc_start: 0.8139 (t80) cc_final: 0.7927 (t80) REVERT: A 549 MET cc_start: 0.7854 (ptp) cc_final: 0.7634 (ptm) REVERT: A 650 MET cc_start: 0.6064 (tpt) cc_final: 0.5693 (tpt) REVERT: A 750 SER cc_start: 0.8537 (t) cc_final: 0.8132 (m) REVERT: A 765 ARG cc_start: 0.6874 (mmm-85) cc_final: 0.6585 (mmm-85) REVERT: A 852 ARG cc_start: 0.7291 (mtt180) cc_final: 0.7026 (mtt180) REVERT: A 877 LYS cc_start: 0.8282 (tptt) cc_final: 0.7948 (tptt) REVERT: A 1023 ILE cc_start: 0.8377 (tp) cc_final: 0.8125 (tt) REVERT: A 1078 MET cc_start: 0.7343 (ptp) cc_final: 0.7102 (ptp) REVERT: A 1145 TRP cc_start: 0.8535 (m100) cc_final: 0.8304 (m100) REVERT: A 1275 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6970 (ttm-80) REVERT: A 1359 THR cc_start: 0.8209 (m) cc_final: 0.7992 (m) REVERT: A 1424 PHE cc_start: 0.8031 (m-80) cc_final: 0.7131 (m-80) REVERT: A 1444 MET cc_start: 0.8189 (tpp) cc_final: 0.7919 (tpp) REVERT: A 1510 MET cc_start: 0.7177 (mtp) cc_final: 0.6966 (mtp) REVERT: A 1590 PHE cc_start: 0.7710 (t80) cc_final: 0.7341 (t80) REVERT: A 1713 MET cc_start: 0.4364 (mtp) cc_final: 0.4052 (mtp) REVERT: A 1906 LEU cc_start: 0.8086 (tp) cc_final: 0.7826 (tt) REVERT: A 1924 ASP cc_start: 0.7212 (m-30) cc_final: 0.6789 (m-30) REVERT: A 1959 MET cc_start: 0.8003 (mtm) cc_final: 0.7617 (mtm) REVERT: A 2001 ILE cc_start: 0.7735 (tp) cc_final: 0.7490 (tp) REVERT: A 2017 THR cc_start: 0.7370 (p) cc_final: 0.7130 (m) REVERT: A 2106 HIS cc_start: 0.8317 (t-170) cc_final: 0.7914 (t70) REVERT: A 2125 LYS cc_start: 0.8328 (mttt) cc_final: 0.7883 (mtpp) REVERT: C 447 SER cc_start: 0.7701 (t) cc_final: 0.7435 (p) REVERT: E 372 ILE cc_start: 0.6457 (mt) cc_final: 0.6177 (mt) REVERT: F 106 MET cc_start: 0.7230 (tpp) cc_final: 0.6660 (tpp) REVERT: F 159 LEU cc_start: 0.7804 (mt) cc_final: 0.7136 (mp) REVERT: F 174 MET cc_start: 0.4089 (tpp) cc_final: 0.3766 (mpp) REVERT: G 77 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6694 (tm-30) REVERT: G 80 MET cc_start: 0.7025 (mmt) cc_final: 0.6750 (mmt) REVERT: G 118 MET cc_start: 0.5552 (tpt) cc_final: 0.5102 (tpt) REVERT: G 128 LEU cc_start: 0.8449 (mt) cc_final: 0.8120 (mt) REVERT: G 129 MET cc_start: 0.7489 (mmt) cc_final: 0.7105 (mmt) outliers start: 27 outliers final: 16 residues processed: 409 average time/residue: 0.1648 time to fit residues: 101.6991 Evaluate side-chains 396 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 380 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 1613 CYS 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 2063 LEU Chi-restraints excluded: chain A residue 2130 ILE Chi-restraints excluded: chain C residue 438 GLN 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 144 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 244 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 439 ASN A 562 ASN A 774 ASN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 GLN A2002 GLN A2134 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 = 0.4080 r_free = 0.4080 target = 0.166766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133635 restraints weight = 61160.086| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.88 r_work: 0.3411 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 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 = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20302 Z= 0.173 Angle : 0.608 16.295 27441 Z= 0.312 Chirality : 0.042 0.174 3159 Planarity : 0.005 0.058 3436 Dihedral : 4.697 26.372 2696 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 8.11 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2449 helix: 1.66 (0.13), residues: 1442 sheet: 0.68 (0.41), residues: 143 loop : -1.34 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1172 TYR 0.025 0.002 TYR A 400 PHE 0.020 0.002 PHE A 546 TRP 0.016 0.001 TRP A 408 HIS 0.008 0.001 HIS A2134 Details of bonding type rmsd covalent geometry : bond 0.00393 (20302) covalent geometry : angle 0.60784 (27441) hydrogen bonds : bond 0.05685 ( 1126) hydrogen bonds : angle 4.34001 ( 3295) *********************** 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 415 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 374 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7874 (mt) cc_final: 0.7612 (mp) REVERT: A 240 MET cc_start: 0.8317 (mmm) cc_final: 0.7900 (mmp) REVERT: A 243 THR cc_start: 0.7663 (m) cc_final: 0.6919 (p) REVERT: A 263 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7954 (mtpp) REVERT: A 336 TYR cc_start: 0.8458 (t80) cc_final: 0.8256 (t80) REVERT: A 351 SER cc_start: 0.7790 (t) cc_final: 0.7305 (m) REVERT: A 431 LEU cc_start: 0.7907 (mt) cc_final: 0.7632 (mt) REVERT: A 467 LYS cc_start: 0.7261 (mtmm) cc_final: 0.6853 (mtmm) REVERT: A 650 MET cc_start: 0.6004 (tpt) cc_final: 0.5586 (tpt) REVERT: A 666 LYS cc_start: 0.7514 (mttt) cc_final: 0.7120 (mttt) REVERT: A 750 SER cc_start: 0.8585 (t) cc_final: 0.8154 (m) REVERT: A 765 ARG cc_start: 0.7014 (mmm-85) cc_final: 0.6703 (mmm-85) REVERT: A 803 TYR cc_start: 0.8120 (t80) cc_final: 0.7603 (t80) REVERT: A 852 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7055 (mtt180) REVERT: A 877 LYS cc_start: 0.8327 (tptt) cc_final: 0.7994 (tptt) REVERT: A 880 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 1023 ILE cc_start: 0.8416 (tp) cc_final: 0.8166 (tt) REVERT: A 1058 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: A 1121 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7522 (mtm110) REVERT: A 1275 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6772 (ttm-80) REVERT: A 1424 PHE cc_start: 0.8037 (m-80) cc_final: 0.7013 (m-80) REVERT: A 1444 MET cc_start: 0.8241 (tpp) cc_final: 0.7946 (tpp) REVERT: A 1590 PHE cc_start: 0.7792 (t80) cc_final: 0.7400 (t80) REVERT: A 1608 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8105 (mm-40) REVERT: A 1673 TYR cc_start: 0.7820 (t80) cc_final: 0.7493 (t80) REVERT: A 1713 MET cc_start: 0.4380 (mtp) cc_final: 0.4099 (mtp) REVERT: A 1729 LEU cc_start: 0.6804 (mm) cc_final: 0.6569 (mt) REVERT: A 1730 LYS cc_start: 0.7394 (mttm) cc_final: 0.7180 (mttp) REVERT: A 1906 LEU cc_start: 0.8116 (tp) cc_final: 0.7858 (tt) REVERT: A 1924 ASP cc_start: 0.7259 (m-30) cc_final: 0.6855 (m-30) REVERT: A 1959 MET cc_start: 0.8027 (mtm) cc_final: 0.7630 (mtm) REVERT: A 2001 ILE cc_start: 0.7723 (tp) cc_final: 0.7488 (tp) REVERT: A 2017 THR cc_start: 0.7309 (p) cc_final: 0.7085 (m) REVERT: A 2106 HIS cc_start: 0.8335 (t-170) cc_final: 0.8112 (t-170) REVERT: A 2125 LYS cc_start: 0.8374 (mttt) cc_final: 0.7918 (mtpp) REVERT: C 447 SER cc_start: 0.7729 (t) cc_final: 0.7464 (p) REVERT: E 372 ILE cc_start: 0.6532 (mt) cc_final: 0.6021 (mt) REVERT: F 106 MET cc_start: 0.7395 (tpp) cc_final: 0.6934 (tpp) REVERT: F 118 MET cc_start: 0.7489 (mmt) cc_final: 0.7059 (mmt) REVERT: F 159 LEU cc_start: 0.7804 (mt) cc_final: 0.7329 (mp) REVERT: F 174 MET cc_start: 0.4199 (tpp) cc_final: 0.3886 (mpp) REVERT: G 77 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6701 (tm-30) REVERT: G 118 MET cc_start: 0.5562 (tpt) cc_final: 0.5142 (tpt) REVERT: G 128 LEU cc_start: 0.8506 (mt) cc_final: 0.8176 (mt) REVERT: G 129 MET cc_start: 0.7602 (mmt) cc_final: 0.7196 (mmt) outliers start: 41 outliers final: 29 residues processed: 390 average time/residue: 0.1646 time to fit residues: 97.0099 Evaluate side-chains 393 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 363 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 774 ASN 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 1050 MET Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1311 THR 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 1968 MET 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 C residue 359 SER Chi-restraints excluded: chain F residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 184 optimal weight: 0.0570 chunk 171 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN A1531 ASN C 356 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 = 0.4082 r_free = 0.4082 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134191 restraints weight = 55372.672| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.30 r_work: 0.3449 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 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 = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20302 Z= 0.154 Angle : 0.577 17.951 27441 Z= 0.294 Chirality : 0.041 0.217 3159 Planarity : 0.005 0.068 3436 Dihedral : 4.557 24.513 2696 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.11 % Allowed : 9.32 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.17), residues: 2449 helix: 1.95 (0.13), residues: 1450 sheet: 0.58 (0.41), residues: 138 loop : -1.34 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2101 TYR 0.019 0.001 TYR A 400 PHE 0.020 0.001 PHE A 546 TRP 0.012 0.001 TRP A 408 HIS 0.022 0.001 HIS A2134 Details of bonding type rmsd covalent geometry : bond 0.00344 (20302) covalent geometry : angle 0.57729 (27441) hydrogen bonds : bond 0.05202 ( 1126) hydrogen bonds : angle 4.19343 ( 3295) *********************** 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 417 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7853 (mt) cc_final: 0.7572 (mp) REVERT: A 243 THR cc_start: 0.7628 (m) cc_final: 0.6796 (p) REVERT: A 263 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7928 (mtpp) REVERT: A 351 SER cc_start: 0.7720 (t) cc_final: 0.7197 (m) REVERT: A 352 PHE cc_start: 0.8129 (m-80) cc_final: 0.7744 (m-80) REVERT: A 354 ARG cc_start: 0.7444 (mmt90) cc_final: 0.7242 (mtt90) REVERT: A 431 LEU cc_start: 0.7916 (mt) cc_final: 0.7642 (mt) REVERT: A 515 MET cc_start: 0.8128 (tpp) cc_final: 0.7796 (mpp) REVERT: A 650 MET cc_start: 0.6003 (tpt) cc_final: 0.5644 (tpt) REVERT: A 750 SER cc_start: 0.8552 (t) cc_final: 0.8110 (m) REVERT: A 765 ARG cc_start: 0.6908 (mmm-85) cc_final: 0.6603 (mmm-85) REVERT: A 852 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6967 (mtt180) REVERT: A 877 LYS cc_start: 0.8290 (tptt) cc_final: 0.8020 (tptt) REVERT: A 880 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: A 1023 ILE cc_start: 0.8417 (tp) cc_final: 0.8150 (tt) REVERT: A 1275 ARG cc_start: 0.7159 (ttm-80) cc_final: 0.6728 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7292 (mmmm) REVERT: A 1424 PHE cc_start: 0.8040 (m-80) cc_final: 0.6953 (m-80) REVERT: A 1432 LEU cc_start: 0.8181 (mp) cc_final: 0.7973 (mm) REVERT: A 1444 MET cc_start: 0.8197 (tpp) cc_final: 0.7909 (tpp) REVERT: A 1713 MET cc_start: 0.4484 (mtp) cc_final: 0.4215 (mtp) REVERT: A 1729 LEU cc_start: 0.6723 (mm) cc_final: 0.6473 (mt) REVERT: A 1730 LYS cc_start: 0.7329 (mttm) cc_final: 0.7125 (mttp) REVERT: A 1906 LEU cc_start: 0.8068 (tp) cc_final: 0.7823 (tt) REVERT: A 1924 ASP cc_start: 0.7305 (m-30) cc_final: 0.6890 (m-30) REVERT: A 1959 MET cc_start: 0.7938 (mtm) cc_final: 0.7567 (mtm) REVERT: A 2001 ILE cc_start: 0.7685 (tp) cc_final: 0.7470 (tp) REVERT: A 2125 LYS cc_start: 0.8316 (mttt) cc_final: 0.7868 (mtpp) REVERT: C 447 SER cc_start: 0.7698 (t) cc_final: 0.7458 (p) REVERT: E 371 MET cc_start: 0.7718 (tmm) cc_final: 0.7518 (tmm) REVERT: F 106 MET cc_start: 0.7297 (tpp) cc_final: 0.6886 (tpp) REVERT: F 118 MET cc_start: 0.7439 (mmt) cc_final: 0.7048 (mmt) REVERT: F 159 LEU cc_start: 0.7795 (mt) cc_final: 0.7335 (mp) REVERT: F 174 MET cc_start: 0.4214 (tpp) cc_final: 0.3908 (mpp) REVERT: G 77 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6685 (tm-30) REVERT: G 80 MET cc_start: 0.7049 (mmt) cc_final: 0.6810 (mmt) REVERT: G 118 MET cc_start: 0.5503 (tpt) cc_final: 0.5116 (tpt) REVERT: G 128 LEU cc_start: 0.8477 (mt) cc_final: 0.8213 (mt) REVERT: G 129 MET cc_start: 0.7546 (mmt) cc_final: 0.7168 (mmt) outliers start: 47 outliers final: 36 residues processed: 392 average time/residue: 0.1604 time to fit residues: 95.2417 Evaluate side-chains 400 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ASP 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 736 MET Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1178 VAL 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 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 1968 MET 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 C residue 359 SER Chi-restraints excluded: chain C residue 470 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 134 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A 566 ASN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132440 restraints weight = 52656.669| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.15 r_work: 0.3429 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 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 = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20302 Z= 0.195 Angle : 0.623 20.004 27441 Z= 0.315 Chirality : 0.043 0.207 3159 Planarity : 0.005 0.063 3436 Dihedral : 4.643 25.048 2696 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.51 % Allowed : 10.22 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2449 helix: 1.89 (0.13), residues: 1452 sheet: 0.39 (0.39), residues: 138 loop : -1.35 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2101 TYR 0.023 0.002 TYR A 400 PHE 0.021 0.002 PHE A 546 TRP 0.022 0.002 TRP A 408 HIS 0.008 0.001 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00454 (20302) covalent geometry : angle 0.62279 (27441) hydrogen bonds : bond 0.05567 ( 1126) hydrogen bonds : angle 4.24369 ( 3295) *********************** 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 428 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7844 (mt) cc_final: 0.7596 (mp) REVERT: A 240 MET cc_start: 0.8302 (mmm) cc_final: 0.7865 (mmp) REVERT: A 243 THR cc_start: 0.7653 (m) cc_final: 0.6846 (p) REVERT: A 263 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7865 (mtpp) REVERT: A 352 PHE cc_start: 0.8127 (m-80) cc_final: 0.7774 (m-80) REVERT: A 431 LEU cc_start: 0.7966 (mt) cc_final: 0.7698 (mt) REVERT: A 545 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6868 (mt) REVERT: A 553 MET cc_start: 0.7852 (tpt) cc_final: 0.7440 (mmm) REVERT: A 650 MET cc_start: 0.5989 (tpt) cc_final: 0.5641 (tpt) REVERT: A 750 SER cc_start: 0.8574 (t) cc_final: 0.8109 (m) REVERT: A 765 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.6611 (mmm-85) REVERT: A 768 SER cc_start: 0.7590 (t) cc_final: 0.7195 (p) REVERT: A 852 ARG cc_start: 0.7303 (mtt180) cc_final: 0.7027 (mtt180) REVERT: A 877 LYS cc_start: 0.8278 (tptt) cc_final: 0.8024 (tptt) REVERT: A 880 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: A 1023 ILE cc_start: 0.8459 (tp) cc_final: 0.8188 (tt) REVERT: A 1056 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7742 (m) REVERT: A 1275 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6801 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7244 (mmmm) REVERT: A 1424 PHE cc_start: 0.8138 (m-80) cc_final: 0.7039 (m-80) REVERT: A 1432 LEU cc_start: 0.8229 (mp) cc_final: 0.8016 (mm) REVERT: A 1444 MET cc_start: 0.8155 (tpp) cc_final: 0.7911 (tpp) REVERT: A 1729 LEU cc_start: 0.6764 (mm) cc_final: 0.6487 (mt) REVERT: A 1730 LYS cc_start: 0.7406 (mttm) cc_final: 0.7189 (mttp) REVERT: A 1750 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6918 (tm-30) REVERT: A 1906 LEU cc_start: 0.8057 (tp) cc_final: 0.7824 (tt) REVERT: A 1924 ASP cc_start: 0.7310 (m-30) cc_final: 0.6921 (m-30) REVERT: A 1959 MET cc_start: 0.7942 (mtm) cc_final: 0.7589 (mtm) REVERT: A 2001 ILE cc_start: 0.7712 (tp) cc_final: 0.7485 (tp) REVERT: A 2125 LYS cc_start: 0.8267 (mttt) cc_final: 0.7810 (mtpp) REVERT: A 2181 ILE cc_start: 0.3835 (OUTLIER) cc_final: 0.3608 (mt) REVERT: C 447 SER cc_start: 0.7698 (t) cc_final: 0.7453 (p) REVERT: E 371 MET cc_start: 0.7698 (tmm) cc_final: 0.7371 (ttt) REVERT: F 106 MET cc_start: 0.7294 (tpp) cc_final: 0.6965 (tpp) REVERT: F 118 MET cc_start: 0.7568 (mmt) cc_final: 0.7154 (mmt) REVERT: F 159 LEU cc_start: 0.7813 (mt) cc_final: 0.7423 (mp) REVERT: F 174 MET cc_start: 0.4208 (tpp) cc_final: 0.3918 (mpp) REVERT: G 77 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6699 (tm-30) REVERT: G 80 MET cc_start: 0.7066 (mmt) cc_final: 0.6829 (mmt) REVERT: G 118 MET cc_start: 0.5472 (tpt) cc_final: 0.5117 (tpt) REVERT: G 128 LEU cc_start: 0.8491 (mt) cc_final: 0.8161 (mt) REVERT: G 129 MET cc_start: 0.7546 (mmt) cc_final: 0.7231 (mmt) outliers start: 56 outliers final: 41 residues processed: 405 average time/residue: 0.1658 time to fit residues: 101.0056 Evaluate side-chains 405 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 194 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 413 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 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 1056 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1178 VAL 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 1993 LEU 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 470 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 185 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 246 optimal weight: 0.5980 chunk 203 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 A1315 ASN 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 = 0.166084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133194 restraints weight = 56152.269| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.39 r_work: 0.3438 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 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 = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20302 Z= 0.170 Angle : 0.619 29.332 27441 Z= 0.306 Chirality : 0.042 0.182 3159 Planarity : 0.005 0.059 3436 Dihedral : 4.573 25.823 2696 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.33 % Allowed : 11.07 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.17), residues: 2449 helix: 2.00 (0.13), residues: 1453 sheet: 0.37 (0.38), residues: 143 loop : -1.31 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1058 TYR 0.023 0.002 TYR A 400 PHE 0.022 0.002 PHE A 546 TRP 0.010 0.001 TRP A 168 HIS 0.007 0.001 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00392 (20302) covalent geometry : angle 0.61862 (27441) hydrogen bonds : bond 0.05194 ( 1126) hydrogen bonds : angle 4.15934 ( 3295) *********************** 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 422 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7809 (mt) cc_final: 0.7557 (mp) REVERT: A 263 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7829 (mtpp) REVERT: A 294 ARG cc_start: 0.8557 (ttm170) cc_final: 0.8194 (ptp-170) REVERT: A 351 SER cc_start: 0.7733 (t) cc_final: 0.7163 (m) REVERT: A 352 PHE cc_start: 0.8070 (m-80) cc_final: 0.7743 (m-80) REVERT: A 545 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 553 MET cc_start: 0.7828 (tpt) cc_final: 0.7419 (mmm) REVERT: A 650 MET cc_start: 0.6049 (tpt) cc_final: 0.5681 (tpt) REVERT: A 750 SER cc_start: 0.8565 (t) cc_final: 0.8100 (m) REVERT: A 765 ARG cc_start: 0.6884 (mmm-85) cc_final: 0.6652 (mmm-85) REVERT: A 768 SER cc_start: 0.7533 (t) cc_final: 0.7119 (p) REVERT: A 852 ARG cc_start: 0.7321 (mtt180) cc_final: 0.7017 (mtt180) REVERT: A 877 LYS cc_start: 0.8273 (tptt) cc_final: 0.7974 (tptt) REVERT: A 880 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 1023 ILE cc_start: 0.8425 (tp) cc_final: 0.8159 (tt) REVERT: A 1056 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7756 (m) REVERT: A 1275 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7185 (mmmm) REVERT: A 1432 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 1444 MET cc_start: 0.8178 (tpp) cc_final: 0.7969 (tpp) REVERT: A 1729 LEU cc_start: 0.6762 (mm) cc_final: 0.6495 (mt) REVERT: A 1750 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6882 (tm-30) REVERT: A 1892 GLU cc_start: 0.7707 (tt0) cc_final: 0.7467 (tt0) REVERT: A 1906 LEU cc_start: 0.8052 (tp) cc_final: 0.7820 (tt) REVERT: A 1924 ASP cc_start: 0.7316 (m-30) cc_final: 0.6892 (m-30) REVERT: A 1959 MET cc_start: 0.7932 (mtm) cc_final: 0.7562 (mtm) REVERT: A 2125 LYS cc_start: 0.8290 (mttt) cc_final: 0.7943 (mmmm) REVERT: A 2181 ILE cc_start: 0.3797 (OUTLIER) cc_final: 0.3566 (mt) REVERT: C 447 SER cc_start: 0.7717 (t) cc_final: 0.7447 (p) REVERT: E 371 MET cc_start: 0.7621 (tmm) cc_final: 0.7303 (ttt) REVERT: F 104 MET cc_start: 0.7060 (mmm) cc_final: 0.6591 (mmt) REVERT: F 106 MET cc_start: 0.7245 (tpp) cc_final: 0.6892 (tpp) REVERT: F 118 MET cc_start: 0.7528 (mmt) cc_final: 0.7149 (mmt) REVERT: F 159 LEU cc_start: 0.7794 (mt) cc_final: 0.7415 (mp) REVERT: F 174 MET cc_start: 0.4277 (tpp) cc_final: 0.3965 (mpp) REVERT: G 77 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6689 (tm-30) REVERT: G 80 MET cc_start: 0.7043 (mmt) cc_final: 0.6833 (mmt) REVERT: G 118 MET cc_start: 0.5439 (tpt) cc_final: 0.5092 (tpt) REVERT: G 128 LEU cc_start: 0.8484 (mt) cc_final: 0.8205 (mt) REVERT: G 129 MET cc_start: 0.7580 (mmt) cc_final: 0.7233 (mmt) outliers start: 52 outliers final: 38 residues processed: 400 average time/residue: 0.1625 time to fit residues: 97.9706 Evaluate side-chains 411 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 368 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 268 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 413 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 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 1056 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1432 LEU 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 1993 LEU 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 470 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 108 optimal weight: 0.2980 chunk 172 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 47 optimal weight: 0.2980 chunk 242 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 358 HIS A 423 ASN A 473 GLN B 329 ASN G 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.168157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135947 restraints weight = 57846.158| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.75 r_work: 0.3445 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 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 = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20302 Z= 0.117 Angle : 0.576 28.351 27441 Z= 0.281 Chirality : 0.040 0.188 3159 Planarity : 0.004 0.065 3436 Dihedral : 4.325 26.783 2696 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.15 % Allowed : 11.74 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.17), residues: 2449 helix: 2.28 (0.14), residues: 1453 sheet: 0.45 (0.39), residues: 144 loop : -1.28 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2101 TYR 0.019 0.001 TYR A 400 PHE 0.020 0.001 PHE A 546 TRP 0.014 0.001 TRP A1189 HIS 0.010 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00251 (20302) covalent geometry : angle 0.57607 (27441) hydrogen bonds : bond 0.04317 ( 1126) hydrogen bonds : angle 3.95194 ( 3295) *********************** 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 420 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 372 time to evaluate : 0.781 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: 0.7820 (mt) cc_final: 0.7540 (mp) REVERT: A 263 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7872 (mtpp) REVERT: A 294 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8261 (ptp-170) REVERT: A 351 SER cc_start: 0.7716 (t) cc_final: 0.7103 (m) REVERT: A 352 PHE cc_start: 0.8062 (m-80) cc_final: 0.7736 (m-80) REVERT: A 467 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6805 (mtmm) REVERT: A 545 LEU cc_start: 0.7146 (mp) cc_final: 0.6752 (mt) REVERT: A 553 MET cc_start: 0.7814 (tpt) cc_final: 0.7395 (mmm) REVERT: A 650 MET cc_start: 0.6026 (tpt) cc_final: 0.5738 (tpt) REVERT: A 750 SER cc_start: 0.8540 (t) cc_final: 0.8100 (m) REVERT: A 765 ARG cc_start: 0.6924 (mmm-85) cc_final: 0.6718 (mmm-85) REVERT: A 768 SER cc_start: 0.7409 (t) cc_final: 0.6990 (p) REVERT: A 852 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7005 (mtt180) REVERT: A 877 LYS cc_start: 0.8320 (tptt) cc_final: 0.8019 (tptt) REVERT: A 880 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: A 912 MET cc_start: 0.7729 (mmm) cc_final: 0.7394 (tpp) REVERT: A 1023 ILE cc_start: 0.8438 (tp) cc_final: 0.8171 (tt) REVERT: A 1078 MET cc_start: 0.7324 (ptp) cc_final: 0.7122 (ptp) REVERT: A 1275 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6749 (ttm-80) REVERT: A 1345 GLU cc_start: 0.7102 (tt0) cc_final: 0.6785 (tt0) REVERT: A 1385 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7255 (mmmm) REVERT: A 1444 MET cc_start: 0.8197 (tpp) cc_final: 0.7949 (tpp) REVERT: A 1673 TYR cc_start: 0.7960 (t80) cc_final: 0.7691 (t80) REVERT: A 1716 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7222 (ptpp) REVERT: A 1729 LEU cc_start: 0.6777 (mm) cc_final: 0.6501 (mt) REVERT: A 1906 LEU cc_start: 0.8065 (tp) cc_final: 0.7860 (tt) REVERT: A 1924 ASP cc_start: 0.7350 (m-30) cc_final: 0.6905 (m-30) REVERT: A 1959 MET cc_start: 0.7867 (mtm) cc_final: 0.7447 (mtm) REVERT: A 2001 ILE cc_start: 0.7667 (tp) cc_final: 0.7412 (tp) REVERT: A 2017 THR cc_start: 0.7303 (p) cc_final: 0.7071 (m) REVERT: A 2125 LYS cc_start: 0.8326 (mttt) cc_final: 0.8018 (mmmm) REVERT: A 2136 ASN cc_start: 0.6488 (t0) cc_final: 0.5925 (m-40) REVERT: A 2181 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3452 (mt) REVERT: C 447 SER cc_start: 0.7673 (t) cc_final: 0.7413 (p) REVERT: E 371 MET cc_start: 0.7555 (tmm) cc_final: 0.7224 (ttt) REVERT: F 104 MET cc_start: 0.7143 (mmm) cc_final: 0.6816 (mmt) REVERT: F 106 MET cc_start: 0.7202 (tpp) cc_final: 0.6816 (tpp) REVERT: F 118 MET cc_start: 0.7468 (mmt) cc_final: 0.7122 (mmt) REVERT: F 159 LEU cc_start: 0.7744 (mt) cc_final: 0.7302 (mp) REVERT: F 174 MET cc_start: 0.4254 (tpp) cc_final: 0.4025 (mpp) REVERT: G 77 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6692 (tm-30) REVERT: G 80 MET cc_start: 0.7034 (mmt) cc_final: 0.6831 (mmt) REVERT: G 118 MET cc_start: 0.5396 (tpt) cc_final: 0.5060 (tpt) REVERT: G 128 LEU cc_start: 0.8498 (mt) cc_final: 0.8221 (mt) REVERT: G 129 MET cc_start: 0.7554 (mmt) cc_final: 0.7244 (mmt) outliers start: 48 outliers final: 32 residues processed: 400 average time/residue: 0.1624 time to fit residues: 98.2550 Evaluate side-chains 399 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 413 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 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 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 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 1993 LEU 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 470 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 130 VAL 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 55 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 A1186 ASN A1315 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132798 restraints weight = 50996.224| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.08 r_work: 0.3452 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 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 = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20302 Z= 0.185 Angle : 0.629 28.220 27441 Z= 0.310 Chirality : 0.043 0.197 3159 Planarity : 0.005 0.071 3436 Dihedral : 4.461 28.196 2696 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.97 % Allowed : 12.55 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.17), residues: 2449 helix: 2.09 (0.13), residues: 1453 sheet: 0.26 (0.38), residues: 156 loop : -1.31 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1837 TYR 0.015 0.002 TYR A 832 PHE 0.022 0.002 PHE A 546 TRP 0.012 0.002 TRP A 476 HIS 0.007 0.001 HIS A1991 Details of bonding type rmsd covalent geometry : bond 0.00433 (20302) covalent geometry : angle 0.62878 (27441) hydrogen bonds : bond 0.05121 ( 1126) hydrogen bonds : angle 4.08879 ( 3295) *********************** 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 405 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7820 (mt) cc_final: 0.7590 (mp) REVERT: A 263 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7808 (mtpp) REVERT: A 467 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6871 (mtmm) REVERT: A 515 MET cc_start: 0.8135 (tpp) cc_final: 0.7896 (tpp) REVERT: A 545 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6848 (mt) REVERT: A 553 MET cc_start: 0.7784 (tpt) cc_final: 0.7385 (mmm) REVERT: A 650 MET cc_start: 0.6049 (tpt) cc_final: 0.5752 (tpt) REVERT: A 765 ARG cc_start: 0.6790 (mmm-85) cc_final: 0.6550 (mmm-85) REVERT: A 768 SER cc_start: 0.7482 (t) cc_final: 0.7075 (p) REVERT: A 852 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6961 (mtt180) REVERT: A 877 LYS cc_start: 0.8283 (tptt) cc_final: 0.8008 (tptt) REVERT: A 880 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 912 MET cc_start: 0.7805 (mmm) cc_final: 0.7493 (tpp) REVERT: A 1023 ILE cc_start: 0.8452 (tp) cc_final: 0.8176 (tt) REVERT: A 1107 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 1176 THR cc_start: 0.5534 (m) cc_final: 0.4256 (p) REVERT: A 1275 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6768 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7253 (mmmm) REVERT: A 1444 MET cc_start: 0.8115 (tpp) cc_final: 0.7890 (tpp) REVERT: A 1716 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7192 (ptpp) REVERT: A 1729 LEU cc_start: 0.6820 (mm) cc_final: 0.6532 (mt) REVERT: A 1924 ASP cc_start: 0.7274 (m-30) cc_final: 0.6867 (m-30) REVERT: A 1959 MET cc_start: 0.7860 (mtm) cc_final: 0.7476 (mtm) REVERT: A 2001 ILE cc_start: 0.7682 (tp) cc_final: 0.7423 (tp) REVERT: A 2123 ASN cc_start: 0.7710 (m-40) cc_final: 0.7498 (m-40) REVERT: A 2125 LYS cc_start: 0.8292 (mttt) cc_final: 0.7958 (mmmm) REVERT: A 2181 ILE cc_start: 0.3710 (OUTLIER) cc_final: 0.3485 (mt) REVERT: C 447 SER cc_start: 0.7680 (t) cc_final: 0.7445 (p) REVERT: E 371 MET cc_start: 0.7573 (tmm) cc_final: 0.7298 (ttt) REVERT: F 104 MET cc_start: 0.7115 (mmm) cc_final: 0.6891 (mmt) REVERT: F 106 MET cc_start: 0.7125 (tpp) cc_final: 0.6781 (tpp) REVERT: F 118 MET cc_start: 0.7438 (mmt) cc_final: 0.7071 (mmt) REVERT: F 159 LEU cc_start: 0.7797 (mt) cc_final: 0.7397 (mp) REVERT: F 174 MET cc_start: 0.4251 (tpp) cc_final: 0.4043 (mpp) REVERT: G 77 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6692 (tm-30) REVERT: G 118 MET cc_start: 0.5365 (tpt) cc_final: 0.5047 (tpt) REVERT: G 128 LEU cc_start: 0.8482 (mt) cc_final: 0.8217 (mt) REVERT: G 129 MET cc_start: 0.7568 (mmt) cc_final: 0.7277 (mmt) outliers start: 44 outliers final: 36 residues processed: 387 average time/residue: 0.1498 time to fit residues: 86.2650 Evaluate side-chains 399 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 358 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU 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 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 413 LEU 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 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 1089 SER Chi-restraints excluded: chain A residue 1107 ASP 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 1993 LEU 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 C residue 470 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 185 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 A1174 HIS ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134105 restraints weight = 46226.803| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.74 r_work: 0.3483 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20302 Z= 0.143 Angle : 0.608 27.965 27441 Z= 0.297 Chirality : 0.041 0.186 3159 Planarity : 0.005 0.070 3436 Dihedral : 4.412 31.492 2696 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.11 % Allowed : 12.55 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.17), residues: 2449 helix: 2.20 (0.13), residues: 1454 sheet: -0.03 (0.38), residues: 166 loop : -1.29 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2101 TYR 0.014 0.001 TYR A 754 PHE 0.020 0.001 PHE A 546 TRP 0.010 0.001 TRP A1189 HIS 0.007 0.001 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00324 (20302) covalent geometry : angle 0.60769 (27441) hydrogen bonds : bond 0.04689 ( 1126) hydrogen bonds : angle 4.00254 ( 3295) *********************** 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 409 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 362 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7830 (mt) cc_final: 0.7589 (mp) REVERT: A 263 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7815 (mtpp) REVERT: A 351 SER cc_start: 0.7695 (t) cc_final: 0.7193 (m) REVERT: A 401 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7146 (mtp85) REVERT: A 411 LEU cc_start: 0.7991 (pp) cc_final: 0.7695 (pp) REVERT: A 467 LYS cc_start: 0.7269 (mtmm) cc_final: 0.6877 (mtmm) REVERT: A 515 MET cc_start: 0.8069 (tpp) cc_final: 0.7834 (tpp) REVERT: A 545 LEU cc_start: 0.7102 (mp) cc_final: 0.6767 (mt) REVERT: A 553 MET cc_start: 0.7769 (tpt) cc_final: 0.7374 (mmm) REVERT: A 650 MET cc_start: 0.5997 (tpt) cc_final: 0.5700 (tpt) REVERT: A 765 ARG cc_start: 0.6749 (mmm-85) cc_final: 0.6538 (mmm-85) REVERT: A 768 SER cc_start: 0.7400 (t) cc_final: 0.6992 (p) REVERT: A 852 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6862 (mtt180) REVERT: A 877 LYS cc_start: 0.8275 (tptt) cc_final: 0.7998 (tptt) REVERT: A 880 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: A 912 MET cc_start: 0.7768 (mmm) cc_final: 0.7444 (tpp) REVERT: A 1023 ILE cc_start: 0.8439 (tp) cc_final: 0.8165 (tt) REVERT: A 1107 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 1275 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6748 (ttm-80) REVERT: A 1345 GLU cc_start: 0.6964 (tt0) cc_final: 0.6714 (tt0) REVERT: A 1385 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7283 (mmmm) REVERT: A 1444 MET cc_start: 0.8098 (tpp) cc_final: 0.7866 (tpp) REVERT: A 1608 GLN cc_start: 0.8224 (mm-40) cc_final: 0.8021 (mm-40) REVERT: A 1729 LEU cc_start: 0.6842 (mm) cc_final: 0.6552 (mt) REVERT: A 1750 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7117 (tp30) REVERT: A 1924 ASP cc_start: 0.7289 (m-30) cc_final: 0.6900 (m-30) REVERT: A 1959 MET cc_start: 0.7786 (mtm) cc_final: 0.7394 (mtm) REVERT: A 2001 ILE cc_start: 0.7622 (tp) cc_final: 0.7357 (tp) REVERT: A 2125 LYS cc_start: 0.8243 (mttt) cc_final: 0.7916 (mmmm) REVERT: A 2136 ASN cc_start: 0.6409 (t0) cc_final: 0.5919 (m110) REVERT: A 2181 ILE cc_start: 0.3679 (OUTLIER) cc_final: 0.3434 (mt) REVERT: C 371 MET cc_start: 0.4040 (mmt) cc_final: 0.3618 (mmm) REVERT: C 447 SER cc_start: 0.7658 (t) cc_final: 0.7412 (p) REVERT: F 106 MET cc_start: 0.7057 (tpp) cc_final: 0.6709 (tpp) REVERT: F 118 MET cc_start: 0.7292 (mmt) cc_final: 0.7014 (mmt) REVERT: F 159 LEU cc_start: 0.7724 (mt) cc_final: 0.7389 (mt) REVERT: G 77 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6646 (tm-30) REVERT: G 118 MET cc_start: 0.5330 (tpt) cc_final: 0.5024 (tpt) REVERT: G 128 LEU cc_start: 0.8469 (mt) cc_final: 0.8182 (mt) REVERT: G 129 MET cc_start: 0.7523 (mmt) cc_final: 0.7244 (mmt) outliers start: 47 outliers final: 34 residues processed: 392 average time/residue: 0.1623 time to fit residues: 95.5493 Evaluate side-chains 396 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER 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 245 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 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 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 1107 ASP Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1613 CYS 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 1993 LEU 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 F residue 71 SER 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 169 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 151 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 A1186 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134030 restraints weight = 48012.146| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.84 r_work: 0.3479 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20302 Z= 0.144 Angle : 0.618 27.408 27441 Z= 0.300 Chirality : 0.041 0.193 3159 Planarity : 0.005 0.072 3436 Dihedral : 4.408 36.361 2696 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.79 % Allowed : 13.04 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2449 helix: 2.23 (0.13), residues: 1454 sheet: 0.04 (0.38), residues: 166 loop : -1.32 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2101 TYR 0.014 0.001 TYR A 754 PHE 0.020 0.001 PHE A 546 TRP 0.009 0.001 TRP A 168 HIS 0.010 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00329 (20302) covalent geometry : angle 0.61843 (27441) hydrogen bonds : bond 0.04673 ( 1126) hydrogen bonds : angle 4.00985 ( 3295) ********************** 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 404 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 364 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7810 (mt) cc_final: 0.7562 (mp) REVERT: A 263 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7802 (mtpp) REVERT: A 350 PHE cc_start: 0.7778 (m-10) cc_final: 0.7559 (m-80) REVERT: A 411 LEU cc_start: 0.8004 (pp) cc_final: 0.7720 (pp) REVERT: A 467 LYS cc_start: 0.7259 (mtmm) cc_final: 0.6854 (mtmm) REVERT: A 515 MET cc_start: 0.8064 (tpp) cc_final: 0.7856 (tpp) REVERT: A 545 LEU cc_start: 0.7112 (mp) cc_final: 0.6823 (mt) REVERT: A 553 MET cc_start: 0.7786 (tpt) cc_final: 0.7388 (mmm) REVERT: A 650 MET cc_start: 0.6007 (tpt) cc_final: 0.5707 (tpt) REVERT: A 765 ARG cc_start: 0.6781 (mmm-85) cc_final: 0.6560 (mmm-85) REVERT: A 768 SER cc_start: 0.7411 (t) cc_final: 0.7005 (p) REVERT: A 852 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6891 (mtt180) REVERT: A 877 LYS cc_start: 0.8282 (tptt) cc_final: 0.7974 (tptt) REVERT: A 880 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: A 912 MET cc_start: 0.7764 (mmm) cc_final: 0.7452 (tpp) REVERT: A 1023 ILE cc_start: 0.8409 (tp) cc_final: 0.8143 (tt) REVERT: A 1121 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7431 (mtm110) REVERT: A 1158 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7019 (mp0) REVERT: A 1176 THR cc_start: 0.5503 (m) cc_final: 0.4232 (p) REVERT: A 1275 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6738 (ttm-80) REVERT: A 1345 GLU cc_start: 0.6978 (tt0) cc_final: 0.6704 (tt0) REVERT: A 1385 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7273 (mmmm) REVERT: A 1424 PHE cc_start: 0.7864 (m-80) cc_final: 0.6446 (m-80) REVERT: A 1444 MET cc_start: 0.8140 (tpp) cc_final: 0.7868 (tpp) REVERT: A 1729 LEU cc_start: 0.6779 (mm) cc_final: 0.6502 (mt) REVERT: A 1924 ASP cc_start: 0.7252 (m-30) cc_final: 0.6822 (m-30) REVERT: A 1959 MET cc_start: 0.7833 (mtm) cc_final: 0.7428 (mtm) REVERT: A 2001 ILE cc_start: 0.7614 (tp) cc_final: 0.7369 (tp) REVERT: A 2123 ASN cc_start: 0.7716 (m-40) cc_final: 0.7507 (m-40) REVERT: A 2125 LYS cc_start: 0.8249 (mttt) cc_final: 0.7930 (mmmm) REVERT: A 2136 ASN cc_start: 0.6414 (t0) cc_final: 0.5907 (m110) REVERT: A 2181 ILE cc_start: 0.3692 (OUTLIER) cc_final: 0.3455 (mt) REVERT: C 371 MET cc_start: 0.4005 (mmt) cc_final: 0.3678 (mmm) REVERT: C 447 SER cc_start: 0.7667 (t) cc_final: 0.7442 (p) REVERT: F 104 MET cc_start: 0.7161 (mmt) cc_final: 0.6931 (mmt) REVERT: F 106 MET cc_start: 0.7009 (tpp) cc_final: 0.6662 (tpp) REVERT: F 118 MET cc_start: 0.7225 (mmt) cc_final: 0.6969 (mmt) REVERT: F 159 LEU cc_start: 0.7714 (mt) cc_final: 0.7368 (mt) REVERT: G 77 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6659 (tm-30) REVERT: G 128 LEU cc_start: 0.8472 (mt) cc_final: 0.8190 (mt) REVERT: G 129 MET cc_start: 0.7548 (mmt) cc_final: 0.7312 (mmt) outliers start: 40 outliers final: 35 residues processed: 386 average time/residue: 0.1615 time to fit residues: 93.8594 Evaluate side-chains 398 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 361 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 655 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 764 VAL 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 1192 VAL Chi-restraints excluded: chain A residue 1613 CYS 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 1993 LEU 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 C residue 494 LEU Chi-restraints excluded: chain F residue 71 SER 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 17 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 219 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 A1317 ASN A1377 HIS ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.165357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133266 restraints weight = 55792.668| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.53 r_work: 0.3415 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 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 = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20302 Z= 0.183 Angle : 0.653 26.885 27441 Z= 0.320 Chirality : 0.043 0.203 3159 Planarity : 0.005 0.073 3436 Dihedral : 4.549 39.762 2696 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.97 % Allowed : 12.82 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.17), residues: 2449 helix: 2.03 (0.13), residues: 1466 sheet: 0.00 (0.38), residues: 166 loop : -1.42 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1058 TYR 0.016 0.002 TYR A 832 PHE 0.022 0.002 PHE A 546 TRP 0.011 0.001 TRP A 476 HIS 0.008 0.001 HIS A1722 Details of bonding type rmsd covalent geometry : bond 0.00430 (20302) covalent geometry : angle 0.65309 (27441) hydrogen bonds : bond 0.05168 ( 1126) hydrogen bonds : angle 4.11175 ( 3295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.41 seconds wall clock time: 92 minutes 2.50 seconds (5522.50 seconds total)