Starting phenix.real_space_refine on Sat Aug 23 13:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdg_29011/08_2025/8fdg_29011.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 7707 2.51 5 N 2064 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12163 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1505, 12163 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 76, 'TRANS': 1428} Time building chain proxies: 2.36, per 1000 atoms: 0.19 Number of scatterers: 12163 At special positions: 0 Unit cell: (92.7, 110.7, 142.2, 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 55 16.00 O 2337 8.00 N 2064 7.00 C 7707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.05 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A 994 " - pdb=" SG CYS A1020 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1330 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1490 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 416.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 21 sheets defined 5.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.686A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.786A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.667A pdb=" N GLU A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.516A pdb=" N SER A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.545A pdb=" N ASN A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N CYS A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 760 through 764 removed outlier: 4.281A pdb=" N SER A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.877A pdb=" N ALA A1206 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A1207 " --> pdb=" O ARG A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing helix chain 'A' and resid 1501 through 1505 removed outlier: 3.889A pdb=" N LYS A1505 " --> pdb=" O ILE A1502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.163A pdb=" N ARG A 4 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 40 removed outlier: 3.759A pdb=" N LYS A 75 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 10 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 185 removed outlier: 3.725A pdb=" N LYS A 181 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 269 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 249 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.178A pdb=" N ILE A 217 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 276 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 370 removed outlier: 3.650A pdb=" N LYS A 408 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 328 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 410 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU A 330 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 401 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.696A pdb=" N ILE A 395 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS A 498 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 397 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 478 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 515 removed outlier: 7.221A pdb=" N THR A 579 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 513 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 581 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 515 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 583 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 520 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 511 through 515 removed outlier: 7.221A pdb=" N THR A 579 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 513 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 581 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 515 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 583 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 575 removed outlier: 6.675A pdb=" N LEU A 572 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 654 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 574 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 594 through 596 removed outlier: 3.680A pdb=" N LEU A 594 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 883 through 891 removed outlier: 6.194A pdb=" N ARG A 849 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG A 928 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 851 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LYS A 930 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 853 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 973 " --> pdb=" O ASN A 931 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.322A pdb=" N ILE A 917 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N CYS A1020 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 919 " --> pdb=" O CYS A1020 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1019 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 995 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 4.456A pdb=" N ARG A1036 " --> pdb=" O TRP A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 3.750A pdb=" N MET A1089 " --> pdb=" O LEU A1170 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A1154 " --> pdb=" O HIS A1112 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A1131 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1178 through 1179 removed outlier: 3.677A pdb=" N MET A1178 " --> pdb=" O GLY A1329 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU A1326 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A1245 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN A1328 " --> pdb=" O THR A1243 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN A1233 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1311 " --> pdb=" O GLN A1233 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A1235 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A1309 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A1237 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ALA A1307 " --> pdb=" O GLN A1237 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLU A1239 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A1305 " --> pdb=" O GLU A1239 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N ILE A1241 " --> pdb=" O PRO A1303 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A1243 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1245 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A1310 " --> pdb=" O TYR A1266 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1266 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1312 " --> pdb=" O VAL A1264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1264 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A1262 " --> pdb=" O PRO A1314 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A1316 " --> pdb=" O THR A1260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1192 through 1193 removed outlier: 7.022A pdb=" N GLN A1233 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1311 " --> pdb=" O GLN A1233 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A1235 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A1309 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A1237 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ALA A1307 " --> pdb=" O GLN A1237 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLU A1239 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N ILE A1305 " --> pdb=" O GLU A1239 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N ILE A1241 " --> pdb=" O PRO A1303 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A1243 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1245 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A1310 " --> pdb=" O TYR A1266 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1266 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1312 " --> pdb=" O VAL A1264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A1264 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A1262 " --> pdb=" O PRO A1314 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A1316 " --> pdb=" O THR A1260 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1266 " --> pdb=" O GLN A1274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1217 through 1218 removed outlier: 3.820A pdb=" N TRP A1217 " --> pdb=" O LEU A1323 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1323 " --> pdb=" O TRP A1217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1434 through 1435 removed outlier: 3.730A pdb=" N TYR A1426 " --> pdb=" O LYS A1434 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A1419 " --> pdb=" O TRP A1477 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP A1477 " --> pdb=" O VAL A1419 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A1421 " --> pdb=" O LYS A1475 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A1427 " --> pdb=" O PHE A1469 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A1469 " --> pdb=" O SER A1427 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1461 " --> pdb=" O THR A1403 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR A1403 " --> pdb=" O PHE A1461 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N LYS A1401 " --> pdb=" O PRO A1463 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N ILE A1465 " --> pdb=" O ILE A1399 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ILE A1399 " --> pdb=" O ILE A1465 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER A1467 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A1397 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A1469 " --> pdb=" O ASP A1395 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A1395 " --> pdb=" O PHE A1469 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG A1471 " --> pdb=" O GLU A1393 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A1393 " --> pdb=" O ARG A1471 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A1488 " --> pdb=" O THR A1403 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE A1405 " --> pdb=" O GLU A1486 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU A1486 " --> pdb=" O ILE A1405 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3967 1.34 - 1.47: 3113 1.47 - 1.60: 5305 1.60 - 1.72: 0 1.72 - 1.85: 92 Bond restraints: 12477 Sorted by residual: bond pdb=" C ILE A 339 " pdb=" N PRO A 340 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.22e-02 6.72e+03 7.96e+00 bond pdb=" CA GLU A 907 " pdb=" CB GLU A 907 " ideal model delta sigma weight residual 1.526 1.562 -0.035 1.76e-02 3.23e+03 4.05e+00 bond pdb=" N GLU A1494 " pdb=" CA GLU A1494 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.10e-02 8.26e+03 3.17e+00 bond pdb=" CB CYS A 498 " pdb=" SG CYS A 498 " ideal model delta sigma weight residual 1.808 1.848 -0.040 3.30e-02 9.18e+02 1.47e+00 bond pdb=" C PRO A 670 " pdb=" N PRO A 671 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 ... (remaining 12472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 16598 2.19 - 4.38: 287 4.38 - 6.58: 23 6.58 - 8.77: 4 8.77 - 10.96: 2 Bond angle restraints: 16914 Sorted by residual: angle pdb=" C ARG A1282 " pdb=" N ASN A1283 " pdb=" CA ASN A1283 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" N VAL A1033 " pdb=" CA VAL A1033 " pdb=" C VAL A1033 " ideal model delta sigma weight residual 113.53 110.14 3.39 9.80e-01 1.04e+00 1.20e+01 angle pdb=" CA ILE A 878 " pdb=" C ILE A 878 " pdb=" N PRO A 879 " ideal model delta sigma weight residual 116.57 119.65 -3.08 9.80e-01 1.04e+00 9.85e+00 angle pdb=" C VAL A1332 " pdb=" N ASN A1333 " pdb=" CA ASN A1333 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 121.35 -6.95 2.30e+00 1.89e-01 9.12e+00 ... (remaining 16909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6776 17.70 - 35.41: 600 35.41 - 53.11: 82 53.11 - 70.81: 26 70.81 - 88.52: 17 Dihedral angle restraints: 7501 sinusoidal: 3085 harmonic: 4416 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 656 " pdb=" CB CYS A 656 " ideal model delta sinusoidal sigma weight residual 93.00 145.34 -52.34 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS A 994 " pdb=" SG CYS A 994 " pdb=" SG CYS A1020 " pdb=" CB CYS A1020 " ideal model delta sinusoidal sigma weight residual 93.00 46.99 46.01 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 498 " pdb=" CB CYS A 498 " ideal model delta sinusoidal sigma weight residual 93.00 47.59 45.41 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1174 0.038 - 0.075: 403 0.075 - 0.112: 156 0.112 - 0.150: 50 0.150 - 0.187: 6 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CB ILE A 604 " pdb=" CA ILE A 604 " pdb=" CG1 ILE A 604 " pdb=" CG2 ILE A 604 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE A1019 " pdb=" CA ILE A1019 " pdb=" CG1 ILE A1019 " pdb=" CG2 ILE A1019 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA PHE A1368 " pdb=" N PHE A1368 " pdb=" C PHE A1368 " pdb=" CB PHE A1368 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 1786 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1493 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR A1493 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A1493 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A1494 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 20 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 21 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1337 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A1338 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1338 " -0.030 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 501 2.71 - 3.26: 11655 3.26 - 3.81: 17400 3.81 - 4.35: 21212 4.35 - 4.90: 37298 Nonbonded interactions: 88066 Sorted by model distance: nonbonded pdb=" OG SER A1267 " pdb=" O ASN A1269 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLU A 372 " pdb=" OG1 THR A 380 " model vdw 2.181 3.040 nonbonded pdb=" OG SER A 92 " pdb=" OE2 GLU A1494 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN A1215 " pdb=" NE2 HIS A1252 " model vdw 2.229 3.120 nonbonded pdb=" O ASN A 432 " pdb=" OG1 THR A 436 " model vdw 2.233 3.040 ... (remaining 88061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12484 Z= 0.131 Angle : 0.683 10.961 16928 Z= 0.371 Chirality : 0.047 0.187 1789 Planarity : 0.005 0.055 2194 Dihedral : 13.998 88.518 4642 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -2.81 (0.20), residues: 1503 helix: -2.47 (0.65), residues: 42 sheet: -0.11 (0.25), residues: 440 loop : -2.88 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 935 TYR 0.017 0.001 TYR A 840 PHE 0.017 0.001 PHE A1368 TRP 0.026 0.001 TRP A1391 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00268 (12477) covalent geometry : angle 0.68170 (16914) SS BOND : bond 0.00731 ( 7) SS BOND : angle 1.54684 ( 14) hydrogen bonds : bond 0.13092 ( 186) hydrogen bonds : angle 6.65075 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.8051 (m) cc_final: 0.7701 (p) REVERT: A 382 ASN cc_start: 0.7130 (m-40) cc_final: 0.6680 (m110) REVERT: A 400 ARG cc_start: 0.8266 (mtm110) cc_final: 0.7739 (ptm-80) REVERT: A 610 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 759 MET cc_start: 0.2996 (mmm) cc_final: 0.0835 (ttt) REVERT: A 847 ASN cc_start: 0.7647 (m-40) cc_final: 0.7419 (m-40) REVERT: A 1031 MET cc_start: 0.7629 (mmt) cc_final: 0.7410 (mmt) REVERT: A 1366 GLU cc_start: 0.7895 (tt0) cc_final: 0.7558 (tt0) REVERT: A 1381 TRP cc_start: 0.6620 (p90) cc_final: 0.6326 (p90) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0972 time to fit residues: 23.9295 Evaluate side-chains 106 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 211 ASN A 222 HIS ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.198179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.154327 restraints weight = 17038.172| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.66 r_work: 0.3914 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12484 Z= 0.131 Angle : 0.678 8.123 16928 Z= 0.357 Chirality : 0.048 0.248 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.815 26.872 1648 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.89 % Allowed : 6.98 % Favored : 92.13 % 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: -2.72 (0.20), residues: 1503 helix: -2.01 (0.73), residues: 42 sheet: -0.01 (0.25), residues: 437 loop : -2.85 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 935 TYR 0.023 0.001 TYR A 840 PHE 0.014 0.002 PHE A 771 TRP 0.020 0.001 TRP A1391 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00296 (12477) covalent geometry : angle 0.67338 (16914) SS BOND : bond 0.00900 ( 7) SS BOND : angle 2.90166 ( 14) hydrogen bonds : bond 0.03899 ( 186) hydrogen bonds : angle 6.11236 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.7633 (m) cc_final: 0.7431 (p) REVERT: A 400 ARG cc_start: 0.8502 (mtm110) cc_final: 0.7942 (ptm-80) REVERT: A 681 MET cc_start: 0.0408 (pmm) cc_final: -0.1755 (mtt) REVERT: A 847 ASN cc_start: 0.7653 (m-40) cc_final: 0.7321 (m-40) REVERT: A 857 GLU cc_start: 0.7355 (tt0) cc_final: 0.7137 (tt0) REVERT: A 1031 MET cc_start: 0.7877 (mmt) cc_final: 0.7589 (mmt) REVERT: A 1341 MET cc_start: 0.5684 (tpt) cc_final: 0.5395 (tpt) REVERT: A 1365 TRP cc_start: 0.7181 (m100) cc_final: 0.6883 (m100) REVERT: A 1366 GLU cc_start: 0.8134 (tt0) cc_final: 0.7443 (tp30) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.0858 time to fit residues: 15.6713 Evaluate side-chains 108 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 1 optimal weight: 0.0030 chunk 129 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1496 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.192895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148353 restraints weight = 17258.651| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.85 r_work: 0.3835 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 12484 Z= 0.175 Angle : 0.732 12.363 16928 Z= 0.386 Chirality : 0.049 0.271 1789 Planarity : 0.005 0.063 2194 Dihedral : 6.114 33.929 1648 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 1.93 % Allowed : 9.73 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.88 (0.20), residues: 1503 helix: -1.94 (0.72), residues: 42 sheet: -0.12 (0.26), residues: 405 loop : -2.89 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1096 TYR 0.021 0.002 TYR A1200 PHE 0.017 0.002 PHE A 651 TRP 0.015 0.001 TRP A 15 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00418 (12477) covalent geometry : angle 0.72315 (16914) SS BOND : bond 0.01205 ( 7) SS BOND : angle 4.09485 ( 14) hydrogen bonds : bond 0.04410 ( 186) hydrogen bonds : angle 6.12430 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.7787 (m) cc_final: 0.7513 (p) REVERT: A 385 MET cc_start: 0.7011 (mpp) cc_final: 0.6435 (mpp) REVERT: A 400 ARG cc_start: 0.8534 (mtm110) cc_final: 0.7916 (ptm-80) REVERT: A 847 ASN cc_start: 0.7856 (m-40) cc_final: 0.7600 (m-40) REVERT: A 857 GLU cc_start: 0.7434 (tt0) cc_final: 0.7142 (tt0) REVERT: A 1143 MET cc_start: 0.8466 (ttp) cc_final: 0.8224 (ttp) REVERT: A 1366 GLU cc_start: 0.8210 (tt0) cc_final: 0.7562 (tp30) outliers start: 26 outliers final: 18 residues processed: 128 average time/residue: 0.0883 time to fit residues: 17.0933 Evaluate side-chains 117 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1407 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 148 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN A1215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.196606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.149028 restraints weight = 17138.155| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.33 r_work: 0.3896 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 12484 Z= 0.119 Angle : 0.662 14.702 16928 Z= 0.348 Chirality : 0.047 0.277 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.798 30.792 1648 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 1.93 % Allowed : 11.21 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.84 (0.20), residues: 1503 helix: -1.85 (0.75), residues: 42 sheet: 0.00 (0.26), residues: 398 loop : -2.90 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 935 TYR 0.018 0.001 TYR A 840 PHE 0.012 0.001 PHE A 771 TRP 0.015 0.001 TRP A1361 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00278 (12477) covalent geometry : angle 0.65248 (16914) SS BOND : bond 0.01100 ( 7) SS BOND : angle 3.89753 ( 14) hydrogen bonds : bond 0.03542 ( 186) hydrogen bonds : angle 5.92124 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.7784 (m) cc_final: 0.7521 (p) REVERT: A 400 ARG cc_start: 0.8509 (mtm110) cc_final: 0.7943 (ptm-80) REVERT: A 759 MET cc_start: 0.2866 (mmm) cc_final: 0.0022 (ttt) REVERT: A 847 ASN cc_start: 0.7620 (m-40) cc_final: 0.7396 (m-40) REVERT: A 857 GLU cc_start: 0.7369 (tt0) cc_final: 0.7131 (tt0) REVERT: A 1200 TYR cc_start: 0.7282 (t80) cc_final: 0.7062 (t80) REVERT: A 1341 MET cc_start: 0.5672 (tpt) cc_final: 0.5327 (tpt) REVERT: A 1366 GLU cc_start: 0.8249 (tt0) cc_final: 0.7595 (tp30) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.0802 time to fit residues: 15.6542 Evaluate side-chains 118 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1407 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 105 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 149 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A1161 GLN A1252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.189831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141872 restraints weight = 17283.014| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.31 r_work: 0.3808 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12484 Z= 0.206 Angle : 0.758 13.052 16928 Z= 0.401 Chirality : 0.050 0.247 1789 Planarity : 0.005 0.070 2194 Dihedral : 6.247 27.508 1648 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.91 % Favored : 87.03 % Rotamer: Outliers : 2.75 % Allowed : 13.36 % Favored : 83.89 % 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: -2.99 (0.20), residues: 1503 helix: -1.85 (0.73), residues: 48 sheet: -0.20 (0.26), residues: 402 loop : -2.97 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1096 TYR 0.019 0.002 TYR A 840 PHE 0.018 0.002 PHE A 651 TRP 0.016 0.002 TRP A 529 HIS 0.006 0.002 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00488 (12477) covalent geometry : angle 0.75004 (16914) SS BOND : bond 0.01076 ( 7) SS BOND : angle 3.85815 ( 14) hydrogen bonds : bond 0.04735 ( 186) hydrogen bonds : angle 6.14746 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4290 (m-30) cc_final: 0.3610 (t0) REVERT: A 367 MET cc_start: 0.7196 (ptm) cc_final: 0.6980 (ptt) REVERT: A 373 ASP cc_start: 0.8007 (p0) cc_final: 0.7691 (p0) REVERT: A 400 ARG cc_start: 0.8566 (mtm110) cc_final: 0.7955 (ptm-80) REVERT: A 480 ASP cc_start: 0.8495 (t0) cc_final: 0.8098 (t0) REVERT: A 847 ASN cc_start: 0.7797 (m-40) cc_final: 0.7285 (m-40) REVERT: A 857 GLU cc_start: 0.7437 (tt0) cc_final: 0.7144 (tt0) REVERT: A 1143 MET cc_start: 0.8441 (ttp) cc_final: 0.8210 (ttp) REVERT: A 1200 TYR cc_start: 0.7218 (t80) cc_final: 0.6902 (t80) REVERT: A 1341 MET cc_start: 0.5917 (tpt) cc_final: 0.5608 (tpt) REVERT: A 1366 GLU cc_start: 0.8326 (tt0) cc_final: 0.7648 (tp30) outliers start: 37 outliers final: 22 residues processed: 140 average time/residue: 0.0777 time to fit residues: 16.6233 Evaluate side-chains 125 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 GLN Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 42 optimal weight: 0.0470 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.194987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147458 restraints weight = 17133.583| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.32 r_work: 0.3881 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12484 Z= 0.117 Angle : 0.660 13.462 16928 Z= 0.349 Chirality : 0.047 0.187 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.876 30.364 1648 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.00 % Allowed : 14.77 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.89 (0.20), residues: 1503 helix: -1.94 (0.73), residues: 42 sheet: -0.04 (0.26), residues: 397 loop : -2.92 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1162 TYR 0.016 0.001 TYR A 840 PHE 0.012 0.001 PHE A 603 TRP 0.009 0.001 TRP A1217 HIS 0.007 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00268 (12477) covalent geometry : angle 0.65278 (16914) SS BOND : bond 0.01129 ( 7) SS BOND : angle 3.37563 ( 14) hydrogen bonds : bond 0.03472 ( 186) hydrogen bonds : angle 5.92092 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4095 (m-30) cc_final: 0.3564 (t0) REVERT: A 367 MET cc_start: 0.7028 (ptm) cc_final: 0.6804 (ptt) REVERT: A 373 ASP cc_start: 0.7968 (p0) cc_final: 0.7659 (p0) REVERT: A 400 ARG cc_start: 0.8530 (mtm110) cc_final: 0.7979 (ptm-80) REVERT: A 480 ASP cc_start: 0.8516 (t0) cc_final: 0.8123 (t0) REVERT: A 759 MET cc_start: 0.2425 (mmm) cc_final: -0.0299 (ttt) REVERT: A 857 GLU cc_start: 0.7359 (tt0) cc_final: 0.7022 (tt0) REVERT: A 1200 TYR cc_start: 0.7105 (t80) cc_final: 0.6682 (t80) REVERT: A 1341 MET cc_start: 0.5689 (tpt) cc_final: 0.5425 (tpt) REVERT: A 1366 GLU cc_start: 0.8286 (tt0) cc_final: 0.7622 (tp30) outliers start: 27 outliers final: 23 residues processed: 123 average time/residue: 0.0860 time to fit residues: 16.0103 Evaluate side-chains 119 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1406 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.0370 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.194597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147143 restraints weight = 17047.444| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.30 r_work: 0.3874 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12484 Z= 0.120 Angle : 0.652 11.582 16928 Z= 0.344 Chirality : 0.047 0.197 1789 Planarity : 0.005 0.060 2194 Dihedral : 5.770 28.299 1648 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 2.38 % Allowed : 14.70 % Favored : 82.93 % 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: -2.82 (0.20), residues: 1503 helix: -1.69 (0.82), residues: 36 sheet: 0.03 (0.26), residues: 407 loop : -2.91 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1308 TYR 0.016 0.001 TYR A 840 PHE 0.015 0.001 PHE A 603 TRP 0.011 0.001 TRP A1217 HIS 0.007 0.001 HIS A1252 Details of bonding type rmsd covalent geometry : bond 0.00278 (12477) covalent geometry : angle 0.64643 (16914) SS BOND : bond 0.00949 ( 7) SS BOND : angle 3.07591 ( 14) hydrogen bonds : bond 0.03492 ( 186) hydrogen bonds : angle 5.81007 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4049 (m-30) cc_final: 0.3274 (t0) REVERT: A 373 ASP cc_start: 0.8012 (p0) cc_final: 0.7706 (p0) REVERT: A 400 ARG cc_start: 0.8529 (mtm110) cc_final: 0.7991 (ptm-80) REVERT: A 480 ASP cc_start: 0.8517 (t0) cc_final: 0.8147 (t0) REVERT: A 491 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7504 (pp) REVERT: A 645 LYS cc_start: 0.7415 (mttm) cc_final: 0.7198 (mmtt) REVERT: A 759 MET cc_start: 0.2486 (mmm) cc_final: -0.0131 (ttt) REVERT: A 857 GLU cc_start: 0.7326 (tt0) cc_final: 0.6966 (tt0) REVERT: A 1200 TYR cc_start: 0.7124 (t80) cc_final: 0.6659 (t80) REVERT: A 1366 GLU cc_start: 0.8335 (tt0) cc_final: 0.7655 (tp30) outliers start: 32 outliers final: 24 residues processed: 129 average time/residue: 0.0822 time to fit residues: 16.5620 Evaluate side-chains 123 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.191081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143451 restraints weight = 17083.080| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.27 r_work: 0.3828 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12484 Z= 0.165 Angle : 0.708 11.266 16928 Z= 0.375 Chirality : 0.049 0.205 1789 Planarity : 0.005 0.063 2194 Dihedral : 6.036 30.380 1648 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.11 % Favored : 86.83 % Rotamer: Outliers : 2.60 % Allowed : 14.25 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.91 (0.20), residues: 1503 helix: -1.73 (0.79), residues: 42 sheet: -0.14 (0.26), residues: 398 loop : -2.91 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.016 0.002 TYR A 840 PHE 0.017 0.002 PHE A 651 TRP 0.013 0.001 TRP A 15 HIS 0.008 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00388 (12477) covalent geometry : angle 0.70187 (16914) SS BOND : bond 0.01028 ( 7) SS BOND : angle 3.38440 ( 14) hydrogen bonds : bond 0.04125 ( 186) hydrogen bonds : angle 5.93328 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6818 (OUTLIER) cc_final: 0.5407 (t) REVERT: A 135 ASP cc_start: 0.4669 (m-30) cc_final: 0.3577 (p0) REVERT: A 367 MET cc_start: 0.7180 (ptm) cc_final: 0.6975 (ptt) REVERT: A 373 ASP cc_start: 0.8111 (p0) cc_final: 0.7830 (p0) REVERT: A 400 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8002 (ptm-80) REVERT: A 480 ASP cc_start: 0.8504 (t0) cc_final: 0.8202 (t0) REVERT: A 759 MET cc_start: 0.2719 (mmm) cc_final: 0.0135 (ttt) REVERT: A 857 GLU cc_start: 0.7381 (tt0) cc_final: 0.7015 (tt0) REVERT: A 1200 TYR cc_start: 0.7142 (t80) cc_final: 0.6624 (t80) REVERT: A 1366 GLU cc_start: 0.8384 (tt0) cc_final: 0.7820 (tp30) outliers start: 35 outliers final: 27 residues processed: 131 average time/residue: 0.0801 time to fit residues: 16.4029 Evaluate side-chains 129 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 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 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.193189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145689 restraints weight = 17012.350| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.28 r_work: 0.3854 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12484 Z= 0.127 Angle : 0.674 10.239 16928 Z= 0.354 Chirality : 0.048 0.212 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.893 36.466 1648 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.78 % Favored : 88.16 % Rotamer: Outliers : 2.15 % Allowed : 14.48 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.92 (0.20), residues: 1503 helix: -1.74 (0.80), residues: 42 sheet: -0.13 (0.26), residues: 397 loop : -2.92 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.016 0.001 TYR A 840 PHE 0.015 0.001 PHE A 603 TRP 0.014 0.001 TRP A1365 HIS 0.008 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00295 (12477) covalent geometry : angle 0.66600 (16914) SS BOND : bond 0.01058 ( 7) SS BOND : angle 3.61871 ( 14) hydrogen bonds : bond 0.03579 ( 186) hydrogen bonds : angle 5.84520 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6726 (OUTLIER) cc_final: 0.5480 (p) REVERT: A 89 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 135 ASP cc_start: 0.4414 (m-30) cc_final: 0.3423 (p0) REVERT: A 367 MET cc_start: 0.7140 (ptm) cc_final: 0.6933 (ptt) REVERT: A 373 ASP cc_start: 0.8123 (p0) cc_final: 0.7816 (p0) REVERT: A 400 ARG cc_start: 0.8529 (mtm110) cc_final: 0.7998 (ptm-80) REVERT: A 480 ASP cc_start: 0.8526 (t0) cc_final: 0.8227 (t0) REVERT: A 608 ARG cc_start: 0.6891 (ptp-110) cc_final: 0.6529 (ptp-110) REVERT: A 759 MET cc_start: 0.2458 (mmm) cc_final: 0.0075 (ttt) REVERT: A 857 GLU cc_start: 0.7321 (tt0) cc_final: 0.6973 (tt0) REVERT: A 1200 TYR cc_start: 0.7106 (t80) cc_final: 0.6620 (t80) REVERT: A 1366 GLU cc_start: 0.8337 (tt0) cc_final: 0.7803 (tp30) outliers start: 29 outliers final: 25 residues processed: 127 average time/residue: 0.0744 time to fit residues: 14.8398 Evaluate side-chains 128 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 0.0470 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 HIS A1248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.194041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.146955 restraints weight = 16707.875| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.21 r_work: 0.3855 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12484 Z= 0.116 Angle : 0.653 9.523 16928 Z= 0.344 Chirality : 0.047 0.214 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.738 35.096 1648 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 2.00 % Allowed : 14.85 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.84 (0.20), residues: 1503 helix: -1.68 (0.81), residues: 42 sheet: -0.04 (0.26), residues: 407 loop : -2.91 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 935 TYR 0.015 0.001 TYR A 840 PHE 0.016 0.001 PHE A 603 TRP 0.017 0.001 TRP A1365 HIS 0.007 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00268 (12477) covalent geometry : angle 0.64625 (16914) SS BOND : bond 0.00876 ( 7) SS BOND : angle 3.39773 ( 14) hydrogen bonds : bond 0.03352 ( 186) hydrogen bonds : angle 5.73465 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6668 (OUTLIER) cc_final: 0.5416 (p) REVERT: A 89 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8463 (mm) REVERT: A 135 ASP cc_start: 0.4367 (m-30) cc_final: 0.3834 (m-30) REVERT: A 373 ASP cc_start: 0.8163 (p0) cc_final: 0.7846 (p0) REVERT: A 376 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6592 (t80) REVERT: A 400 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8050 (ptm-80) REVERT: A 480 ASP cc_start: 0.8500 (t0) cc_final: 0.8127 (t0) REVERT: A 608 ARG cc_start: 0.6906 (ptp-110) cc_final: 0.6505 (ptp-110) REVERT: A 759 MET cc_start: 0.2690 (mmm) cc_final: 0.0280 (ttt) REVERT: A 1200 TYR cc_start: 0.7125 (t80) cc_final: 0.6626 (t80) REVERT: A 1366 GLU cc_start: 0.8331 (tt0) cc_final: 0.7773 (tp30) outliers start: 27 outliers final: 24 residues processed: 131 average time/residue: 0.0773 time to fit residues: 15.4624 Evaluate side-chains 129 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 143 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.193553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146153 restraints weight = 16602.994| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.24 r_work: 0.3861 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12484 Z= 0.125 Angle : 0.664 9.648 16928 Z= 0.349 Chirality : 0.047 0.216 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.755 34.654 1648 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.38 % Favored : 87.56 % Rotamer: Outliers : 2.45 % Allowed : 14.55 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.81 (0.20), residues: 1503 helix: -1.73 (0.81), residues: 42 sheet: -0.03 (0.26), residues: 414 loop : -2.90 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 935 TYR 0.015 0.001 TYR A 840 PHE 0.016 0.001 PHE A 603 TRP 0.020 0.001 TRP A1365 HIS 0.007 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00289 (12477) covalent geometry : angle 0.65758 (16914) SS BOND : bond 0.00896 ( 7) SS BOND : angle 3.38410 ( 14) hydrogen bonds : bond 0.03455 ( 186) hydrogen bonds : angle 5.74061 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.33 seconds wall clock time: 44 minutes 2.11 seconds (2642.11 seconds total)