Starting phenix.real_space_refine on Mon Dec 30 05:44:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_29011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_29011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_29011.map" model { file = "/net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_29011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdg_29011/12_2024/8fdg_29011.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.46, per 1000 atoms: 0.61 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: 2.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.41 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: 4.78 Time building geometry restraints manager: 3.22 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: 2.040 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.730 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- 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 12477 Z= 0.178 Angle : 0.682 10.961 16914 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.001 TRP A1391 HIS 0.004 0.001 HIS A 318 PHE 0.017 0.001 PHE A1368 TYR 0.017 0.001 TYR A 840 ARG 0.006 0.000 ARG A 935 *********************** 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 : 1.211 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: 0.2541 time to fit residues: 62.7202 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 : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 40.0000 chunk 136 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A1026 HIS ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1215 ASN A1237 GLN A1496 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 12477 Z= 0.450 Angle : 0.878 11.801 16914 Z= 0.465 Chirality : 0.054 0.328 1789 Planarity : 0.007 0.085 2194 Dihedral : 6.755 28.382 1648 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.37 % Favored : 85.50 % Rotamer: Outliers : 1.34 % Allowed : 9.58 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1503 helix: -2.07 (0.71), residues: 48 sheet: -0.32 (0.25), residues: 416 loop : -3.09 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1391 HIS 0.010 0.002 HIS A 420 PHE 0.024 0.003 PHE A 651 TYR 0.026 0.003 TYR A 840 ARG 0.006 0.001 ARG A 918 *********************** 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 133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4237 (m-30) cc_final: 0.3675 (t0) REVERT: A 375 SER cc_start: 0.7751 (m) cc_final: 0.7531 (p) REVERT: A 400 ARG cc_start: 0.8393 (mtm110) cc_final: 0.7742 (ptm-80) REVERT: A 480 ASP cc_start: 0.8382 (t0) cc_final: 0.8177 (t0) REVERT: A 847 ASN cc_start: 0.7946 (m-40) cc_final: 0.7715 (m-40) REVERT: A 857 GLU cc_start: 0.7400 (tt0) cc_final: 0.7149 (tt0) REVERT: A 890 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7353 (mmp80) REVERT: A 1031 MET cc_start: 0.7882 (mmt) cc_final: 0.7637 (mmt) REVERT: A 1143 MET cc_start: 0.8557 (ttp) cc_final: 0.8335 (ttp) REVERT: A 1221 LYS cc_start: 0.7883 (tppt) cc_final: 0.7505 (tptt) REVERT: A 1318 TYR cc_start: 0.7612 (t80) cc_final: 0.7382 (t80) REVERT: A 1326 GLU cc_start: 0.7959 (tp30) cc_final: 0.7735 (tp30) REVERT: A 1341 MET cc_start: 0.5712 (tpt) cc_final: 0.5479 (tpt) REVERT: A 1366 GLU cc_start: 0.8315 (tt0) cc_final: 0.7599 (tp30) REVERT: A 1381 TRP cc_start: 0.7029 (p90) cc_final: 0.6676 (p90) REVERT: A 1457 VAL cc_start: 0.8330 (t) cc_final: 0.8060 (p) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2567 time to fit residues: 48.4008 Evaluate side-chains 116 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 266 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 1137 SER 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 75 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 136 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN A1215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 12477 Z= 0.212 Angle : 0.689 12.171 16914 Z= 0.365 Chirality : 0.048 0.284 1789 Planarity : 0.005 0.066 2194 Dihedral : 6.225 27.541 1648 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.91 % Favored : 88.02 % Rotamer: Outliers : 1.86 % Allowed : 11.66 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1503 helix: -2.11 (0.72), residues: 42 sheet: -0.25 (0.26), residues: 407 loop : -2.97 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1361 HIS 0.006 0.001 HIS A 318 PHE 0.013 0.001 PHE A 771 TYR 0.019 0.001 TYR A 840 ARG 0.004 0.000 ARG A 935 *********************** 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 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4012 (m-30) cc_final: 0.3464 (t0) REVERT: A 400 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7761 (ptm-80) REVERT: A 480 ASP cc_start: 0.8276 (t0) cc_final: 0.8015 (t0) REVERT: A 491 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7768 (pp) REVERT: A 759 MET cc_start: 0.3114 (mmm) cc_final: 0.0505 (ttt) REVERT: A 847 ASN cc_start: 0.7734 (m-40) cc_final: 0.7476 (m-40) REVERT: A 857 GLU cc_start: 0.7245 (tt0) cc_final: 0.6909 (tt0) REVERT: A 1200 TYR cc_start: 0.6974 (t80) cc_final: 0.6619 (t80) REVERT: A 1366 GLU cc_start: 0.8175 (tt0) cc_final: 0.7521 (tp30) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 0.2175 time to fit residues: 44.7278 Evaluate side-chains 114 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 266 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 388 ASP 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 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 1161 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 12477 Z= 0.295 Angle : 0.732 15.621 16914 Z= 0.388 Chirality : 0.049 0.252 1789 Planarity : 0.005 0.071 2194 Dihedral : 6.312 27.592 1648 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.91 % Favored : 86.03 % Rotamer: Outliers : 2.45 % Allowed : 13.44 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1503 helix: -2.01 (0.72), residues: 48 sheet: -0.24 (0.26), residues: 404 loop : -3.02 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 15 HIS 0.005 0.001 HIS A1010 PHE 0.018 0.002 PHE A 651 TYR 0.019 0.002 TYR A 840 ARG 0.003 0.000 ARG A1162 *********************** 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 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6760 (OUTLIER) cc_final: 0.5549 (p) REVERT: A 135 ASP cc_start: 0.4178 (m-30) cc_final: 0.3571 (t0) REVERT: A 373 ASP cc_start: 0.8016 (p0) cc_final: 0.7450 (p0) REVERT: A 400 ARG cc_start: 0.8395 (mtm110) cc_final: 0.7771 (ptm-80) REVERT: A 480 ASP cc_start: 0.8428 (t0) cc_final: 0.7977 (t0) REVERT: A 847 ASN cc_start: 0.7821 (m-40) cc_final: 0.7237 (m-40) REVERT: A 857 GLU cc_start: 0.7334 (tt0) cc_final: 0.6935 (tt0) REVERT: A 1143 MET cc_start: 0.8538 (ttp) cc_final: 0.8309 (ttp) REVERT: A 1200 TYR cc_start: 0.6999 (t80) cc_final: 0.6511 (t80) REVERT: A 1221 LYS cc_start: 0.7770 (tppt) cc_final: 0.7431 (tptt) REVERT: A 1366 GLU cc_start: 0.8264 (tt0) cc_final: 0.7568 (tp30) outliers start: 33 outliers final: 20 residues processed: 128 average time/residue: 0.2386 time to fit residues: 46.2783 Evaluate side-chains 122 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 332 ILE 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 638 MET Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1157 VAL 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 1451 THR Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0050 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12477 Z= 0.246 Angle : 0.703 13.771 16914 Z= 0.373 Chirality : 0.048 0.224 1789 Planarity : 0.005 0.068 2194 Dihedral : 6.253 28.613 1648 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.57 % Favored : 87.36 % Rotamer: Outliers : 2.97 % Allowed : 14.55 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.20), residues: 1503 helix: -2.02 (0.72), residues: 48 sheet: -0.24 (0.26), residues: 405 loop : -3.00 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 15 HIS 0.007 0.001 HIS A 318 PHE 0.014 0.002 PHE A 651 TYR 0.018 0.001 TYR A 840 ARG 0.003 0.000 ARG A 935 *********************** 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6680 (OUTLIER) cc_final: 0.5438 (p) REVERT: A 135 ASP cc_start: 0.4156 (m-30) cc_final: 0.3450 (m-30) REVERT: A 373 ASP cc_start: 0.8014 (p0) cc_final: 0.7680 (p0) REVERT: A 400 ARG cc_start: 0.8403 (mtm110) cc_final: 0.7816 (ptm-80) REVERT: A 480 ASP cc_start: 0.8478 (t0) cc_final: 0.8108 (t0) REVERT: A 759 MET cc_start: 0.2863 (mmm) cc_final: 0.0241 (ttt) REVERT: A 847 ASN cc_start: 0.7814 (m-40) cc_final: 0.7195 (m-40) REVERT: A 857 GLU cc_start: 0.7349 (tt0) cc_final: 0.7013 (tt0) REVERT: A 1200 TYR cc_start: 0.6999 (t80) cc_final: 0.6478 (t80) REVERT: A 1221 LYS cc_start: 0.7751 (tppt) cc_final: 0.7422 (tptt) REVERT: A 1341 MET cc_start: 0.5460 (tpt) cc_final: 0.5217 (tpt) REVERT: A 1361 TRP cc_start: 0.5238 (t60) cc_final: 0.5019 (t60) REVERT: A 1366 GLU cc_start: 0.8201 (tt0) cc_final: 0.7490 (tp30) outliers start: 40 outliers final: 26 residues processed: 137 average time/residue: 0.2238 time to fit residues: 47.0821 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 : 1.412 ------------------------------------------------------------------------------- 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 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 638 MET Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1157 VAL 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 1451 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12477 Z= 0.256 Angle : 0.715 13.108 16914 Z= 0.378 Chirality : 0.049 0.208 1789 Planarity : 0.005 0.071 2194 Dihedral : 6.246 27.591 1648 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.71 % Favored : 86.23 % Rotamer: Outliers : 2.82 % Allowed : 15.52 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.20), residues: 1503 helix: -2.14 (0.71), residues: 48 sheet: -0.25 (0.26), residues: 405 loop : -3.03 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 15 HIS 0.007 0.001 HIS A 318 PHE 0.016 0.002 PHE A 651 TYR 0.017 0.002 TYR A 840 ARG 0.002 0.000 ARG A 995 *********************** 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.5546 (p) REVERT: A 89 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 135 ASP cc_start: 0.4174 (m-30) cc_final: 0.3279 (p0) REVERT: A 373 ASP cc_start: 0.8006 (p0) cc_final: 0.7655 (p0) REVERT: A 400 ARG cc_start: 0.8410 (mtm110) cc_final: 0.7818 (ptm-80) REVERT: A 480 ASP cc_start: 0.8464 (t0) cc_final: 0.8137 (t0) REVERT: A 759 MET cc_start: 0.2664 (mmm) cc_final: 0.0161 (ttt) REVERT: A 847 ASN cc_start: 0.7833 (m-40) cc_final: 0.7259 (m-40) REVERT: A 857 GLU cc_start: 0.7369 (tt0) cc_final: 0.7000 (tt0) REVERT: A 1143 MET cc_start: 0.8481 (ttp) cc_final: 0.8264 (ttp) REVERT: A 1200 TYR cc_start: 0.7048 (t80) cc_final: 0.6498 (t80) REVERT: A 1221 LYS cc_start: 0.7761 (tppt) cc_final: 0.7425 (tptt) REVERT: A 1366 GLU cc_start: 0.8182 (tt0) cc_final: 0.7489 (tp30) outliers start: 38 outliers final: 29 residues processed: 139 average time/residue: 0.2324 time to fit residues: 49.0381 Evaluate side-chains 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 638 MET 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 1119 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1172 MET 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 1451 THR Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12477 Z= 0.208 Angle : 0.686 12.441 16914 Z= 0.363 Chirality : 0.048 0.191 1789 Planarity : 0.005 0.063 2194 Dihedral : 6.124 32.288 1648 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.64 % Favored : 87.29 % Rotamer: Outliers : 3.12 % Allowed : 15.89 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.20), residues: 1503 helix: -2.16 (0.71), residues: 48 sheet: -0.19 (0.26), residues: 415 loop : -3.01 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1361 HIS 0.007 0.001 HIS A 318 PHE 0.014 0.001 PHE A 651 TYR 0.017 0.001 TYR A 840 ARG 0.004 0.000 ARG A 306 *********************** 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 152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6703 (OUTLIER) cc_final: 0.5491 (p) REVERT: A 89 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 135 ASP cc_start: 0.4199 (m-30) cc_final: 0.3533 (m-30) REVERT: A 372 GLU cc_start: 0.7102 (tp30) cc_final: 0.6516 (tp30) REVERT: A 373 ASP cc_start: 0.7974 (p0) cc_final: 0.7583 (p0) REVERT: A 400 ARG cc_start: 0.8404 (mtm110) cc_final: 0.7842 (ptm-80) REVERT: A 480 ASP cc_start: 0.8473 (t0) cc_final: 0.8168 (t0) REVERT: A 759 MET cc_start: 0.2703 (mmm) cc_final: 0.0394 (ttt) REVERT: A 847 ASN cc_start: 0.7743 (m-40) cc_final: 0.7167 (m-40) REVERT: A 857 GLU cc_start: 0.7318 (tt0) cc_final: 0.6948 (tt0) REVERT: A 1200 TYR cc_start: 0.7084 (t80) cc_final: 0.6495 (t80) REVERT: A 1221 LYS cc_start: 0.7726 (tppt) cc_final: 0.7374 (tptt) REVERT: A 1341 MET cc_start: 0.5498 (tpt) cc_final: 0.5258 (tpt) REVERT: A 1366 GLU cc_start: 0.8134 (tt0) cc_final: 0.7450 (tp30) outliers start: 42 outliers final: 31 residues processed: 142 average time/residue: 0.2360 time to fit residues: 50.6859 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 266 THR 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 638 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1451 THR Chi-restraints excluded: chain A residue 1452 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12477 Z= 0.187 Angle : 0.668 11.616 16914 Z= 0.353 Chirality : 0.047 0.171 1789 Planarity : 0.005 0.061 2194 Dihedral : 5.979 30.225 1648 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 2.97 % Allowed : 15.96 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.20), residues: 1503 helix: -2.30 (0.72), residues: 42 sheet: -0.10 (0.26), residues: 406 loop : -2.98 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1365 HIS 0.008 0.001 HIS A 318 PHE 0.012 0.001 PHE A 651 TYR 0.016 0.001 TYR A 840 ARG 0.002 0.000 ARG A 306 *********************** 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 153 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6709 (OUTLIER) cc_final: 0.5456 (t) REVERT: A 89 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 135 ASP cc_start: 0.4228 (m-30) cc_final: 0.3417 (t0) REVERT: A 372 GLU cc_start: 0.7107 (tp30) cc_final: 0.6547 (tp30) REVERT: A 373 ASP cc_start: 0.7913 (p0) cc_final: 0.7569 (p0) REVERT: A 400 ARG cc_start: 0.8451 (mtm110) cc_final: 0.7929 (ptm-80) REVERT: A 480 ASP cc_start: 0.8425 (t0) cc_final: 0.8044 (t0) REVERT: A 608 ARG cc_start: 0.6943 (ptp-110) cc_final: 0.6446 (ptp-110) REVERT: A 759 MET cc_start: 0.2581 (mmm) cc_final: 0.0411 (ttt) REVERT: A 847 ASN cc_start: 0.7707 (m-40) cc_final: 0.7130 (m-40) REVERT: A 857 GLU cc_start: 0.7280 (tt0) cc_final: 0.6897 (tt0) REVERT: A 1173 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: A 1200 TYR cc_start: 0.7090 (t80) cc_final: 0.6481 (t80) REVERT: A 1221 LYS cc_start: 0.7585 (tppt) cc_final: 0.7229 (tptt) REVERT: A 1341 MET cc_start: 0.5570 (tpt) cc_final: 0.5248 (tpt) REVERT: A 1366 GLU cc_start: 0.8153 (tt0) cc_final: 0.7470 (tp30) REVERT: A 1461 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.4995 (p90) outliers start: 40 outliers final: 31 residues processed: 145 average time/residue: 0.2401 time to fit residues: 52.0746 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 312 THR Chi-restraints excluded: chain A residue 332 ILE 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 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 845 ASN 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 1119 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1451 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1461 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 105 optimal weight: 0.0050 chunk 41 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12477 Z= 0.167 Angle : 0.642 10.658 16914 Z= 0.336 Chirality : 0.046 0.168 1789 Planarity : 0.005 0.061 2194 Dihedral : 5.704 28.522 1648 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.15 % Allowed : 16.85 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1503 helix: -1.41 (0.94), residues: 30 sheet: -0.01 (0.26), residues: 407 loop : -2.90 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1365 HIS 0.008 0.001 HIS A 318 PHE 0.014 0.001 PHE A 603 TYR 0.015 0.001 TYR A 840 ARG 0.002 0.000 ARG A1308 *********************** 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 139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6467 (OUTLIER) cc_final: 0.5280 (p) REVERT: A 89 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (mm) REVERT: A 135 ASP cc_start: 0.4328 (m-30) cc_final: 0.3576 (p0) REVERT: A 373 ASP cc_start: 0.7850 (p0) cc_final: 0.7554 (p0) REVERT: A 400 ARG cc_start: 0.8432 (mtm110) cc_final: 0.7944 (ptm-80) REVERT: A 480 ASP cc_start: 0.8425 (t0) cc_final: 0.8039 (t0) REVERT: A 608 ARG cc_start: 0.6897 (ptp-110) cc_final: 0.6468 (ptp-110) REVERT: A 759 MET cc_start: 0.2556 (mmm) cc_final: 0.0446 (ttt) REVERT: A 847 ASN cc_start: 0.7669 (m-40) cc_final: 0.7140 (m-40) REVERT: A 1026 HIS cc_start: 0.8245 (t-90) cc_final: 0.8019 (t-90) REVERT: A 1124 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6943 (mmtt) REVERT: A 1173 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: A 1200 TYR cc_start: 0.7044 (t80) cc_final: 0.6442 (t80) REVERT: A 1341 MET cc_start: 0.5617 (tpt) cc_final: 0.5224 (tpp) REVERT: A 1366 GLU cc_start: 0.8095 (tt0) cc_final: 0.7733 (mp0) outliers start: 29 outliers final: 23 residues processed: 132 average time/residue: 0.2348 time to fit residues: 46.8048 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 : 1.464 ------------------------------------------------------------------------------- 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 312 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 529 TRP 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 638 MET Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Chi-restraints excluded: chain A residue 1339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 448 GLN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12477 Z= 0.161 Angle : 0.624 9.646 16914 Z= 0.326 Chirality : 0.046 0.168 1789 Planarity : 0.005 0.061 2194 Dihedral : 5.453 26.196 1648 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 2.38 % Allowed : 16.63 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1503 helix: -1.31 (0.96), residues: 30 sheet: 0.08 (0.26), residues: 410 loop : -2.84 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1365 HIS 0.006 0.001 HIS A 318 PHE 0.013 0.001 PHE A 603 TYR 0.015 0.001 TYR A 840 ARG 0.004 0.000 ARG A 643 ********************** 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6380 (OUTLIER) cc_final: 0.5269 (p) REVERT: A 89 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8307 (mm) REVERT: A 135 ASP cc_start: 0.4076 (m-30) cc_final: 0.3740 (t0) REVERT: A 373 ASP cc_start: 0.7821 (p0) cc_final: 0.7520 (p0) REVERT: A 400 ARG cc_start: 0.8407 (mtm110) cc_final: 0.7956 (ptm-80) REVERT: A 480 ASP cc_start: 0.8403 (t0) cc_final: 0.8046 (t0) REVERT: A 608 ARG cc_start: 0.6917 (ptp-110) cc_final: 0.6486 (ptp-110) REVERT: A 759 MET cc_start: 0.2524 (mmm) cc_final: 0.0443 (ttt) REVERT: A 847 ASN cc_start: 0.7624 (m-40) cc_final: 0.7334 (m110) REVERT: A 1173 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6958 (m-30) REVERT: A 1200 TYR cc_start: 0.7008 (t80) cc_final: 0.6391 (t80) REVERT: A 1237 GLN cc_start: 0.8101 (mt0) cc_final: 0.7886 (mt0) REVERT: A 1318 TYR cc_start: 0.7227 (t80) cc_final: 0.6960 (t80) REVERT: A 1366 GLU cc_start: 0.8162 (tt0) cc_final: 0.7480 (tp30) REVERT: A 1408 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7269 (pp30) outliers start: 32 outliers final: 25 residues processed: 138 average time/residue: 0.2293 time to fit residues: 48.5687 Evaluate side-chains 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 312 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 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 529 TRP 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 638 MET Chi-restraints excluded: chain A residue 845 ASN 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 1172 MET Chi-restraints excluded: chain A residue 1173 ASP Chi-restraints excluded: chain A residue 1215 ASN Chi-restraints excluded: chain A residue 1231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 21 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 448 GLN A1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.196336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.148981 restraints weight = 16986.649| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.29 r_work: 0.3896 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12477 Z= 0.167 Angle : 0.629 9.694 16914 Z= 0.328 Chirality : 0.046 0.168 1789 Planarity : 0.005 0.060 2194 Dihedral : 5.432 26.173 1648 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.24 % Favored : 88.69 % Rotamer: Outliers : 2.60 % Allowed : 16.85 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1503 helix: -1.22 (0.96), residues: 30 sheet: 0.07 (0.26), residues: 418 loop : -2.86 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1365 HIS 0.006 0.001 HIS A 318 PHE 0.012 0.001 PHE A 603 TYR 0.023 0.001 TYR A 324 ARG 0.002 0.000 ARG A 935 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.46 seconds wall clock time: 49 minutes 54.43 seconds (2994.43 seconds total)