Starting phenix.real_space_refine on Wed Jul 30 12:15:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdg_29011/07_2025/8fdg_29011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdg_29011/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fdg_29011/07_2025/8fdg_29011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdg_29011/07_2025/8fdg_29011.map" model { file = "/net/cci-nas-00/data/ceres_data/8fdg_29011/07_2025/8fdg_29011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdg_29011/07_2025/8fdg_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-5711/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: 7.75, per 1000 atoms: 0.64 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 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: 1.67 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: 5.23 Time building geometry restraints manager: 2.96 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: 2.320 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.610 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13092 ( 186) hydrogen bonds : angle 6.65075 ( 483) SS BOND : bond 0.00731 ( 7) SS BOND : angle 1.54684 ( 14) covalent geometry : bond 0.00268 (12477) covalent geometry : angle 0.68170 (16914) *********************** 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 : 1.419 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: 0.2669 time to fit residues: 66.7972 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 : 1.226 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.187624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.139900 restraints weight = 17064.767| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.26 r_work: 0.3780 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 12484 Z= 0.286 Angle : 0.883 11.801 16928 Z= 0.467 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 Details of bonding type rmsd hydrogen bonds : bond 0.05717 ( 186) hydrogen bonds : angle 6.60879 ( 483) SS BOND : bond 0.01517 ( 7) SS BOND : angle 3.50184 ( 14) covalent geometry : bond 0.00677 (12477) covalent geometry : angle 0.87777 (16914) *********************** 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 : 1.361 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4478 (m-30) cc_final: 0.3704 (t0) REVERT: A 400 ARG cc_start: 0.8566 (mtm110) cc_final: 0.7951 (ptm-80) REVERT: A 480 ASP cc_start: 0.8436 (t0) cc_final: 0.8198 (t0) REVERT: A 847 ASN cc_start: 0.7989 (m-40) cc_final: 0.7772 (m-40) REVERT: A 857 GLU cc_start: 0.7401 (tt0) cc_final: 0.7160 (tt0) REVERT: A 1031 MET cc_start: 0.8051 (mmt) cc_final: 0.7794 (mmt) REVERT: A 1221 LYS cc_start: 0.7968 (tppt) cc_final: 0.7608 (tptt) REVERT: A 1326 GLU cc_start: 0.7970 (tp30) cc_final: 0.7769 (tp30) REVERT: A 1366 GLU cc_start: 0.8369 (tt0) cc_final: 0.7761 (tp30) REVERT: A 1381 TRP cc_start: 0.7301 (p90) cc_final: 0.6989 (p90) REVERT: A 1457 VAL cc_start: 0.8281 (t) cc_final: 0.8001 (p) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2380 time to fit residues: 44.7862 Evaluate side-chains 114 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 39 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.192494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144961 restraints weight = 17262.071| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.32 r_work: 0.3848 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12484 Z= 0.140 Angle : 0.708 12.611 16928 Z= 0.374 Chirality : 0.048 0.270 1789 Planarity : 0.005 0.068 2194 Dihedral : 6.278 27.665 1648 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.11 % Favored : 87.82 % Rotamer: Outliers : 2.00 % Allowed : 11.43 % Favored : 86.56 % 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: -3.04 (0.20), residues: 1503 helix: -2.13 (0.71), residues: 42 sheet: -0.26 (0.26), residues: 405 loop : -2.99 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.003 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 186) hydrogen bonds : angle 6.23096 ( 483) SS BOND : bond 0.01030 ( 7) SS BOND : angle 3.77844 ( 14) covalent geometry : bond 0.00328 (12477) covalent geometry : angle 0.69941 (16914) *********************** 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 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: 0.4293 (m-30) cc_final: 0.3468 (t0) REVERT: A 373 ASP cc_start: 0.8062 (p0) cc_final: 0.7743 (p0) REVERT: A 400 ARG cc_start: 0.8556 (mtm110) cc_final: 0.7938 (ptm-80) REVERT: A 480 ASP cc_start: 0.8400 (t0) cc_final: 0.8127 (t0) REVERT: A 491 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7692 (pp) REVERT: A 759 MET cc_start: 0.2703 (mmm) cc_final: 0.0149 (ttt) REVERT: A 847 ASN cc_start: 0.7734 (m-40) cc_final: 0.7533 (m-40) REVERT: A 857 GLU cc_start: 0.7320 (tt0) cc_final: 0.7004 (tt0) REVERT: A 1200 TYR cc_start: 0.7122 (t80) cc_final: 0.6788 (t80) REVERT: A 1366 GLU cc_start: 0.8274 (tt0) cc_final: 0.7682 (tp30) outliers start: 27 outliers final: 15 residues processed: 132 average time/residue: 0.2449 time to fit residues: 50.5448 Evaluate side-chains 115 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 1161 GLN Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.148266 restraints weight = 16996.431| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.76 r_work: 0.3824 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 12484 Z= 0.136 Angle : 0.692 15.377 16928 Z= 0.365 Chirality : 0.048 0.236 1789 Planarity : 0.005 0.062 2194 Dihedral : 6.093 27.119 1648 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.44 % Favored : 86.49 % Rotamer: Outliers : 2.38 % Allowed : 12.84 % Favored : 84.78 % 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: -2.99 (0.20), residues: 1503 helix: -2.06 (0.73), residues: 42 sheet: -0.23 (0.26), residues: 406 loop : -2.96 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1361 HIS 0.006 0.001 HIS A 318 PHE 0.015 0.001 PHE A 651 TYR 0.018 0.001 TYR A 840 ARG 0.002 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 186) hydrogen bonds : angle 6.08761 ( 483) SS BOND : bond 0.01144 ( 7) SS BOND : angle 3.58021 ( 14) covalent geometry : bond 0.00319 (12477) covalent geometry : angle 0.68415 (16914) *********************** 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 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6759 (OUTLIER) cc_final: 0.5359 (t) REVERT: A 135 ASP cc_start: 0.4382 (m-30) cc_final: 0.3550 (t0) REVERT: A 373 ASP cc_start: 0.8062 (p0) cc_final: 0.7525 (p0) REVERT: A 400 ARG cc_start: 0.8579 (mtm110) cc_final: 0.7962 (ptm-80) REVERT: A 480 ASP cc_start: 0.8516 (t0) cc_final: 0.8253 (t0) REVERT: A 491 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7624 (pp) REVERT: A 857 GLU cc_start: 0.7386 (tt0) cc_final: 0.7118 (tt0) REVERT: A 1200 TYR cc_start: 0.7069 (t80) cc_final: 0.6599 (t80) REVERT: A 1341 MET cc_start: 0.5545 (tpt) cc_final: 0.5216 (tpt) REVERT: A 1361 TRP cc_start: 0.5563 (t60) cc_final: 0.5357 (t60) REVERT: A 1366 GLU cc_start: 0.8306 (tt0) cc_final: 0.7707 (tp30) outliers start: 32 outliers final: 21 residues processed: 127 average time/residue: 0.2045 time to fit residues: 40.4368 Evaluate side-chains 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 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 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 1452 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 79 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 0.0060 chunk 147 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.195365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148123 restraints weight = 17074.535| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.30 r_work: 0.3889 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12484 Z= 0.111 Angle : 0.646 12.960 16928 Z= 0.341 Chirality : 0.047 0.201 1789 Planarity : 0.005 0.060 2194 Dihedral : 5.823 28.643 1648 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 2.60 % Allowed : 14.11 % Favored : 83.30 % 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: -2.85 (0.20), residues: 1503 helix: -2.00 (0.75), residues: 42 sheet: 0.04 (0.26), residues: 405 loop : -2.94 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1361 HIS 0.007 0.001 HIS A 318 PHE 0.012 0.001 PHE A 771 TYR 0.016 0.001 TYR A 840 ARG 0.003 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 186) hydrogen bonds : angle 5.84687 ( 483) SS BOND : bond 0.01124 ( 7) SS BOND : angle 3.20163 ( 14) covalent geometry : bond 0.00254 (12477) covalent geometry : angle 0.63995 (16914) *********************** 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 148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6495 (OUTLIER) cc_final: 0.5275 (p) REVERT: A 135 ASP cc_start: 0.4012 (m-30) cc_final: 0.3493 (t0) REVERT: A 306 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.5052 (mtp180) REVERT: A 373 ASP cc_start: 0.8055 (p0) cc_final: 0.7622 (p0) REVERT: A 400 ARG cc_start: 0.8527 (mtm110) cc_final: 0.7995 (ptm-80) REVERT: A 480 ASP cc_start: 0.8540 (t0) cc_final: 0.8094 (t0) REVERT: A 491 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7372 (pp) REVERT: A 608 ARG cc_start: 0.6965 (ptp-110) cc_final: 0.6465 (ptp-110) REVERT: A 759 MET cc_start: 0.2517 (mmm) cc_final: 0.0026 (ttt) REVERT: A 857 GLU cc_start: 0.7321 (tt0) cc_final: 0.6993 (tt0) REVERT: A 1200 TYR cc_start: 0.7034 (t80) cc_final: 0.6541 (t80) REVERT: A 1366 GLU cc_start: 0.8201 (tt0) cc_final: 0.7670 (tp30) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.2379 time to fit residues: 49.2549 Evaluate side-chains 129 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 306 ARG 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 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 1157 VAL 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 1466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.192197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144734 restraints weight = 17206.121| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.30 r_work: 0.3846 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12484 Z= 0.140 Angle : 0.682 12.458 16928 Z= 0.360 Chirality : 0.047 0.196 1789 Planarity : 0.005 0.061 2194 Dihedral : 5.902 28.036 1648 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 2.45 % Allowed : 15.37 % Favored : 82.18 % 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: -2.88 (0.20), residues: 1503 helix: -2.13 (0.72), residues: 42 sheet: -0.05 (0.26), residues: 402 loop : -2.91 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 0.002 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 186) hydrogen bonds : angle 5.84378 ( 483) SS BOND : bond 0.00960 ( 7) SS BOND : angle 3.23211 ( 14) covalent geometry : bond 0.00328 (12477) covalent geometry : angle 0.67546 (16914) *********************** 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 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6751 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 135 ASP cc_start: 0.4168 (m-30) cc_final: 0.3326 (t0) REVERT: A 373 ASP cc_start: 0.7961 (p0) cc_final: 0.7607 (p0) REVERT: A 400 ARG cc_start: 0.8542 (mtm110) cc_final: 0.7995 (ptm-80) REVERT: A 480 ASP cc_start: 0.8564 (t0) cc_final: 0.8183 (t0) REVERT: A 491 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7541 (pp) REVERT: A 759 MET cc_start: 0.2473 (mmm) cc_final: -0.0095 (ttt) REVERT: A 857 GLU cc_start: 0.7360 (tt0) cc_final: 0.6997 (tt0) REVERT: A 1200 TYR cc_start: 0.7147 (t80) cc_final: 0.6607 (t80) REVERT: A 1366 GLU cc_start: 0.8244 (tt0) cc_final: 0.7667 (tp30) outliers start: 33 outliers final: 26 residues processed: 128 average time/residue: 0.2374 time to fit residues: 47.9533 Evaluate side-chains 126 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 261 VAL 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 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 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 1407 THR 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 90 optimal weight: 3.9990 chunk 136 optimal weight: 0.0040 chunk 11 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.191989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144518 restraints weight = 17145.695| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.28 r_work: 0.3840 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2222 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= 0.144 Angle : 0.686 11.910 16928 Z= 0.362 Chirality : 0.048 0.190 1789 Planarity : 0.005 0.059 2194 Dihedral : 5.957 33.695 1648 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 3.04 % Allowed : 15.37 % Favored : 81.59 % 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: -2.90 (0.20), residues: 1503 helix: -1.81 (0.81), residues: 36 sheet: -0.16 (0.25), residues: 410 loop : -2.92 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 15 HIS 0.007 0.001 HIS A 318 PHE 0.014 0.001 PHE A 651 TYR 0.016 0.001 TYR A 840 ARG 0.002 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 186) hydrogen bonds : angle 5.86421 ( 483) SS BOND : bond 0.00990 ( 7) SS BOND : angle 3.80327 ( 14) covalent geometry : bond 0.00338 (12477) covalent geometry : angle 0.67729 (16914) *********************** 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 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.6796 (OUTLIER) cc_final: 0.5442 (t) REVERT: A 89 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8467 (mm) REVERT: A 135 ASP cc_start: 0.4639 (m-30) cc_final: 0.3501 (p0) REVERT: A 373 ASP cc_start: 0.8046 (p0) cc_final: 0.7696 (p0) REVERT: A 400 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8031 (ptm-80) REVERT: A 480 ASP cc_start: 0.8577 (t0) cc_final: 0.8239 (t0) REVERT: A 491 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7563 (pp) REVERT: A 645 LYS cc_start: 0.7469 (mttm) cc_final: 0.7234 (mmtt) REVERT: A 759 MET cc_start: 0.2483 (mmm) cc_final: 0.0073 (ttt) REVERT: A 857 GLU cc_start: 0.7363 (tt0) cc_final: 0.7009 (tt0) REVERT: A 1124 LYS cc_start: 0.7353 (mmtt) cc_final: 0.7027 (mmtt) REVERT: A 1200 TYR cc_start: 0.7195 (t80) cc_final: 0.6642 (t80) REVERT: A 1366 GLU cc_start: 0.8223 (tt0) cc_final: 0.7628 (tp30) outliers start: 41 outliers final: 32 residues processed: 135 average time/residue: 0.2151 time to fit residues: 45.2040 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 : 1.392 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain A residue 264 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 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 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 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 1407 THR 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 127 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.188138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140236 restraints weight = 17300.980| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.29 r_work: 0.3789 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12484 Z= 0.203 Angle : 0.764 12.392 16928 Z= 0.404 Chirality : 0.050 0.212 1789 Planarity : 0.005 0.072 2194 Dihedral : 6.290 31.811 1648 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.77 % Favored : 86.16 % Rotamer: Outliers : 2.90 % Allowed : 15.44 % Favored : 81.66 % 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: -3.04 (0.20), residues: 1503 helix: -1.90 (0.78), residues: 42 sheet: -0.27 (0.26), residues: 404 loop : -2.99 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 15 HIS 0.009 0.002 HIS A 318 PHE 0.019 0.002 PHE A 651 TYR 0.017 0.002 TYR A1082 ARG 0.003 0.000 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 186) hydrogen bonds : angle 6.07710 ( 483) SS BOND : bond 0.01107 ( 7) SS BOND : angle 3.90009 ( 14) covalent geometry : bond 0.00481 (12477) covalent geometry : angle 0.75647 (16914) *********************** 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 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6908 (OUTLIER) cc_final: 0.5614 (p) REVERT: A 89 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 91 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 135 ASP cc_start: 0.5160 (m-30) cc_final: 0.4693 (m-30) REVERT: A 372 GLU cc_start: 0.7482 (tp30) cc_final: 0.6882 (tp30) REVERT: A 373 ASP cc_start: 0.8082 (p0) cc_final: 0.7710 (p0) REVERT: A 400 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8010 (ptm-80) REVERT: A 480 ASP cc_start: 0.8586 (t0) cc_final: 0.8213 (t0) REVERT: A 491 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7716 (pp) REVERT: A 630 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 857 GLU cc_start: 0.7448 (tt0) cc_final: 0.7058 (tt0) REVERT: A 1200 TYR cc_start: 0.7285 (t80) cc_final: 0.6616 (t80) REVERT: A 1221 LYS cc_start: 0.7817 (tppt) cc_final: 0.7454 (tptt) REVERT: A 1366 GLU cc_start: 0.8337 (tt0) cc_final: 0.7651 (tp30) outliers start: 39 outliers final: 28 residues processed: 141 average time/residue: 0.2645 time to fit residues: 57.4864 Evaluate side-chains 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 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 491 LEU 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 630 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.189199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.141521 restraints weight = 17108.976| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.27 r_work: 0.3805 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12484 Z= 0.168 Angle : 0.727 12.150 16928 Z= 0.383 Chirality : 0.049 0.198 1789 Planarity : 0.005 0.068 2194 Dihedral : 6.224 31.095 1648 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.71 % Favored : 87.23 % Rotamer: Outliers : 3.12 % Allowed : 15.14 % Favored : 81.74 % 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: -3.10 (0.20), residues: 1503 helix: -2.18 (0.70), residues: 48 sheet: -0.34 (0.26), residues: 387 loop : -2.98 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 15 HIS 0.009 0.001 HIS A 318 PHE 0.019 0.002 PHE A 651 TYR 0.017 0.002 TYR A1082 ARG 0.002 0.000 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 186) hydrogen bonds : angle 6.06382 ( 483) SS BOND : bond 0.01032 ( 7) SS BOND : angle 3.62229 ( 14) covalent geometry : bond 0.00395 (12477) covalent geometry : angle 0.71989 (16914) *********************** 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 147 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6843 (OUTLIER) cc_final: 0.5534 (p) REVERT: A 89 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 135 ASP cc_start: 0.4959 (m-30) cc_final: 0.3799 (p0) REVERT: A 372 GLU cc_start: 0.7540 (tp30) cc_final: 0.6951 (tp30) REVERT: A 373 ASP cc_start: 0.8128 (p0) cc_final: 0.7745 (p0) REVERT: A 400 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8038 (ptm-80) REVERT: A 480 ASP cc_start: 0.8517 (t0) cc_final: 0.8168 (t0) REVERT: A 491 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 857 GLU cc_start: 0.7368 (tt0) cc_final: 0.6994 (tt0) REVERT: A 1173 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 1200 TYR cc_start: 0.7245 (t80) cc_final: 0.6642 (t80) REVERT: A 1221 LYS cc_start: 0.7744 (tppt) cc_final: 0.7393 (tptt) REVERT: A 1366 GLU cc_start: 0.8261 (tt0) cc_final: 0.7727 (tp30) REVERT: A 1461 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5346 (p90) outliers start: 42 outliers final: 31 residues processed: 140 average time/residue: 0.2210 time to fit residues: 47.9049 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 261 VAL 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 491 LEU 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 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 1161 GLN Chi-restraints excluded: chain A residue 1172 MET Chi-restraints excluded: chain A residue 1173 ASP 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 Chi-restraints excluded: chain A residue 1461 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 583 HIS A1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.187290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140214 restraints weight = 16777.205| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.20 r_work: 0.3786 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12484 Z= 0.198 Angle : 0.771 12.344 16928 Z= 0.406 Chirality : 0.050 0.203 1789 Planarity : 0.005 0.073 2194 Dihedral : 6.350 30.562 1648 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.17 % Favored : 85.76 % Rotamer: Outliers : 2.67 % Allowed : 15.81 % Favored : 81.51 % 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: -3.16 (0.20), residues: 1503 helix: -2.12 (0.71), residues: 48 sheet: -0.36 (0.26), residues: 386 loop : -3.03 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 15 HIS 0.009 0.001 HIS A 318 PHE 0.019 0.002 PHE A 651 TYR 0.018 0.002 TYR A 819 ARG 0.003 0.000 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 186) hydrogen bonds : angle 6.17120 ( 483) SS BOND : bond 0.01090 ( 7) SS BOND : angle 3.89789 ( 14) covalent geometry : bond 0.00467 (12477) covalent geometry : angle 0.76311 (16914) ********************** 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 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 SER cc_start: 0.6989 (OUTLIER) cc_final: 0.5655 (p) REVERT: A 89 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 91 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: A 135 ASP cc_start: 0.5239 (m-30) cc_final: 0.4724 (m-30) REVERT: A 372 GLU cc_start: 0.7602 (tp30) cc_final: 0.6963 (tp30) REVERT: A 373 ASP cc_start: 0.8092 (p0) cc_final: 0.7560 (p0) REVERT: A 400 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8009 (ptm-80) REVERT: A 480 ASP cc_start: 0.8484 (t0) cc_final: 0.8170 (t0) REVERT: A 491 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7738 (pp) REVERT: A 759 MET cc_start: 0.2022 (mmm) cc_final: -0.0542 (ttp) REVERT: A 857 GLU cc_start: 0.7398 (tt0) cc_final: 0.7002 (tt0) REVERT: A 1173 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 1200 TYR cc_start: 0.7269 (t80) cc_final: 0.6645 (t80) REVERT: A 1221 LYS cc_start: 0.7797 (tppt) cc_final: 0.7465 (tptt) REVERT: A 1366 GLU cc_start: 0.8288 (tt0) cc_final: 0.7760 (tp30) REVERT: A 1408 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 1461 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5390 (p90) outliers start: 36 outliers final: 26 residues processed: 135 average time/residue: 0.2202 time to fit residues: 45.8066 Evaluate side-chains 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 491 LEU Chi-restraints excluded: chain A residue 529 TRP 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 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 1173 ASP 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 1461 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.189446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141930 restraints weight = 17107.297| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.27 r_work: 0.3811 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12484 Z= 0.150 Angle : 0.721 11.945 16928 Z= 0.379 Chirality : 0.048 0.188 1789 Planarity : 0.005 0.065 2194 Dihedral : 6.210 29.775 1648 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.57 % Favored : 87.36 % Rotamer: Outliers : 2.52 % Allowed : 15.96 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.20), residues: 1503 helix: -2.01 (0.72), residues: 48 sheet: -0.34 (0.26), residues: 392 loop : -3.01 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 582 HIS 0.009 0.001 HIS A 318 PHE 0.016 0.001 PHE A 651 TYR 0.016 0.001 TYR A1082 ARG 0.002 0.000 ARG A 935 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 186) hydrogen bonds : angle 6.10101 ( 483) SS BOND : bond 0.00997 ( 7) SS BOND : angle 3.75625 ( 14) covalent geometry : bond 0.00349 (12477) covalent geometry : angle 0.71313 (16914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6628.80 seconds wall clock time: 115 minutes 4.29 seconds (6904.29 seconds total)