Starting phenix.real_space_refine on Fri Jul 3 05:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2026/7dsh_30833.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7764 2.51 5 N 2004 2.21 5 O 2242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12071 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9066 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 35, 'TRANS': 1102} Chain breaks: 1 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.02, per 1000 atoms: 0.25 Number of scatterers: 12071 At special positions: 0 Unit cell: (148.755, 108.665, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 3 15.00 Mg 1 11.99 O 2242 8.00 N 2004 7.00 C 7764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 614.3 milliseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 34.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.874A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.671A pdb=" N SER A 243 " --> pdb=" O PRO A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 268 removed outlier: 4.255A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.534A pdb=" N ARG A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 549 through 571 removed outlier: 3.807A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.745A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.528A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 634 removed outlier: 3.657A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 4.120A pdb=" N ILE A 654 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 655 " --> pdb=" O TRP A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 656 through 659 Processing helix chain 'A' and resid 696 through 700 removed outlier: 4.278A pdb=" N GLY A 699 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 726 removed outlier: 3.614A pdb=" N GLU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 725 " --> pdb=" O LYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 775 removed outlier: 3.605A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.807A pdb=" N ALA A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 903 Processing helix chain 'A' and resid 922 through 936 removed outlier: 3.791A pdb=" N TRP A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.723A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 951' Processing helix chain 'A' and resid 971 through 977 removed outlier: 3.968A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1001 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.539A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1107 through 1120 removed outlier: 3.560A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1197 removed outlier: 3.548A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.567A pdb=" N PHE A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1239 removed outlier: 3.847A pdb=" N ILE A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.578A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 removed outlier: 4.046A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.784A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1329 removed outlier: 3.653A pdb=" N ILE A1318 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1347 removed outlier: 3.601A pdb=" N ALA A1343 " --> pdb=" O GLY A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 3.536A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1374 removed outlier: 3.861A pdb=" N ARG A1371 " --> pdb=" O LYS A1367 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 4.161A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1404 Proline residue: A1392 - end of helix removed outlier: 4.033A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1416 removed outlier: 3.566A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.618A pdb=" N VAL B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 191' Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 372 through 395 removed outlier: 3.920A pdb=" N TYR B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.631A pdb=" N GLY A 520 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 521 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 removed outlier: 4.102A pdb=" N TYR A 432 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.146A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 487 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 496 " --> pdb=" O TRP A 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1099 through 1100 removed outlier: 6.939A pdb=" N LEU A 985 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 662 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TRP A 986 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.883A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.555A pdb=" N ASP A 793 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 813 through 818 removed outlier: 3.655A pdb=" N SER A 814 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 839 through 840 removed outlier: 3.782A pdb=" N SER A 850 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 851 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 129 removed outlier: 6.512A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 144 removed outlier: 3.557A pdb=" N ARG B 143 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.794A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 247 327 hydrogen bonds defined for protein. 912 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: 1.90 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1984 1.32 - 1.44: 3402 1.44 - 1.57: 6875 1.57 - 1.69: 6 1.69 - 1.82: 86 Bond restraints: 12353 Sorted by residual: bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.10e-02 8.26e+03 2.40e+01 bond pdb=" C GLU A1028 " pdb=" N PRO A1029 " ideal model delta sigma weight residual 1.337 1.391 -0.054 1.24e-02 6.50e+03 1.92e+01 bond pdb=" C ILE B 214 " pdb=" O ILE B 214 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.03e-02 9.43e+03 1.81e+01 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 16289 2.75 - 5.49: 382 5.49 - 8.24: 64 8.24 - 10.98: 22 10.98 - 13.73: 4 Bond angle restraints: 16761 Sorted by residual: angle pdb=" C ILE B 214 " pdb=" CA ILE B 214 " pdb=" CB ILE B 214 " ideal model delta sigma weight residual 111.08 103.81 7.27 1.17e+00 7.31e-01 3.86e+01 angle pdb=" N VAL A1311 " pdb=" CA VAL A1311 " pdb=" C VAL A1311 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" C MET A1187 " pdb=" N ILE A1188 " pdb=" CA ILE A1188 " ideal model delta sigma weight residual 120.24 123.75 -3.51 6.30e-01 2.52e+00 3.10e+01 angle pdb=" C LYS A 668 " pdb=" N THR A 669 " pdb=" CA THR A 669 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C CYS A1102 " pdb=" N CYS A1103 " pdb=" CA CYS A1103 " ideal model delta sigma weight residual 123.47 131.75 -8.28 1.53e+00 4.27e-01 2.93e+01 ... (remaining 16756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 7225 35.24 - 70.48: 57 70.48 - 105.72: 3 105.72 - 140.96: 0 140.96 - 176.20: 1 Dihedral angle restraints: 7286 sinusoidal: 2913 harmonic: 4373 Sorted by residual: dihedral pdb=" CA LEU A1101 " pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -136.42 -43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -28.45 -57.55 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA PHE B 398 " pdb=" C PHE B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 148.68 31.32 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 7283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1399 0.064 - 0.128: 390 0.128 - 0.192: 52 0.192 - 0.256: 18 0.256 - 0.320: 6 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN A 675 " pdb=" N ASN A 675 " pdb=" C ASN A 675 " pdb=" CB ASN A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A1072 " pdb=" CA ILE A1072 " pdb=" CG1 ILE A1072 " pdb=" CG2 ILE A1072 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1862 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.031 2.00e-02 2.50e+03 5.98e-02 3.58e+01 pdb=" C VAL A1408 " -0.104 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C PHE B 398 " -0.099 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 986 " -0.023 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 986 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 986 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 986 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 986 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 986 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 986 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 986 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 986 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 986 " -0.006 2.00e-02 2.50e+03 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 223 2.66 - 3.22: 10909 3.22 - 3.78: 18638 3.78 - 4.34: 25981 4.34 - 4.90: 41468 Nonbonded interactions: 97219 Sorted by model distance: nonbonded pdb=" NE2 HIS B 209 " pdb=" OG SER B 220 " model vdw 2.099 3.120 nonbonded pdb=" N ASP B 210 " pdb=" OD1 ASP B 210 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.243 3.040 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.250 3.040 nonbonded pdb=" O3G ACP A1601 " pdb="MG MG A1602 " model vdw 2.254 2.170 ... (remaining 97214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 : 0.007 0.099 12360 Z= 0.322 Angle : 1.099 16.034 16774 Z= 0.588 Chirality : 0.063 0.320 1865 Planarity : 0.007 0.070 2123 Dihedral : 11.353 176.197 4476 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.50 % Favored : 90.36 % Rotamer: Outliers : 0.46 % Allowed : 3.61 % Favored : 95.93 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.04 (0.14), residues: 1494 helix: -4.69 (0.09), residues: 536 sheet: -3.88 (0.36), residues: 128 loop : -3.64 (0.16), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 272 TYR 0.030 0.003 TYR A1217 PHE 0.030 0.003 PHE A1287 TRP 0.054 0.004 TRP B 308 HIS 0.013 0.002 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.32 (12353) covalent geometry : angle 1.08499 / 0.59 (16761) SS BOND : bond 0.00394 / 0.28 ( 2) SS BOND : angle 1.11105 / 0.82 ( 4) hydrogen bonds : bond 0.30506 / 19.70 ( 327) hydrogen bonds : angle 11.93959 / 8.19 ( 912) Misc. bond : bond 0.00348 / 0.24 ( 2) link_BETA1-4 : bond 0.01280 / 0.86 ( 2) link_BETA1-4 : angle 7.08138 / 4.85 ( 6) link_NAG-ASN : bond 0.00867 / 0.58 ( 1) link_NAG-ASN : angle 8.40935 / 6.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASN cc_start: 0.7842 (t0) cc_final: 0.7468 (t0) REVERT: A 740 TYR cc_start: 0.6855 (p90) cc_final: 0.6138 (p90) REVERT: A 945 GLU cc_start: 0.7323 (tt0) cc_final: 0.6957 (tt0) REVERT: A 1097 CYS cc_start: 0.7329 (p) cc_final: 0.7069 (p) REVERT: A 1139 GLN cc_start: 0.6897 (mt0) cc_final: 0.6677 (pt0) REVERT: A 1296 MET cc_start: 0.8377 (mmm) cc_final: 0.8060 (mmt) REVERT: A 1306 ASP cc_start: 0.7188 (p0) cc_final: 0.6944 (t0) REVERT: A 1321 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7448 (mp) outliers start: 6 outliers final: 3 residues processed: 197 average time/residue: 0.1128 time to fit residues: 31.8291 Evaluate side-chains 110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 216 HIS A 475 HIS A 484 ASN A 550 ASN A 704 GLN A 736 ASN A 778 HIS A 831 GLN A1176 HIS A1307 HIS B 155 GLN B 172 ASN B 256 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097599 restraints weight = 20304.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095667 restraints weight = 18660.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096773 restraints weight = 15689.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.097308 restraints weight = 12160.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097803 restraints weight = 10575.075| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12360 Z= 0.189 Angle : 0.738 10.047 16774 Z= 0.384 Chirality : 0.047 0.205 1865 Planarity : 0.005 0.045 2123 Dihedral : 8.233 175.349 1649 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.23 % Allowed : 7.37 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.17), residues: 1494 helix: -3.10 (0.17), residues: 536 sheet: -3.59 (0.35), residues: 150 loop : -3.23 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 765 TYR 0.021 0.002 TYR A1040 PHE 0.033 0.002 PHE A 679 TRP 0.033 0.002 TRP B 308 HIS 0.005 0.001 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (12353) covalent geometry : angle 0.73114 / 0.38 (16761) SS BOND : bond 0.00301 / 0.21 ( 2) SS BOND : angle 1.14869 / 0.68 ( 4) hydrogen bonds : bond 0.03932 / 2.56 ( 327) hydrogen bonds : angle 6.40724 / 4.38 ( 912) Misc. bond : bond 0.00190 / 0.14 ( 2) link_BETA1-4 : bond 0.00737 / 0.52 ( 2) link_BETA1-4 : angle 3.84114 / 2.73 ( 6) link_NAG-ASN : bond 0.00974 / 0.65 ( 1) link_NAG-ASN : angle 5.07323 / 3.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4819 (pttm) cc_final: 0.4514 (mtpt) REVERT: A 267 VAL cc_start: 0.7100 (OUTLIER) cc_final: 0.6855 (t) REVERT: A 477 ASN cc_start: 0.7640 (t0) cc_final: 0.7007 (t0) REVERT: A 827 MET cc_start: 0.8438 (ppp) cc_final: 0.8130 (ppp) REVERT: A 942 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8088 (t0) REVERT: A 1006 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8149 (pp) outliers start: 29 outliers final: 16 residues processed: 129 average time/residue: 0.0859 time to fit residues: 16.6850 Evaluate side-chains 110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 7 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 GLN A 927 ASN A 998 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100462 restraints weight = 20091.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099789 restraints weight = 16206.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101009 restraints weight = 16639.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101211 restraints weight = 10774.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101384 restraints weight = 11047.190| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12360 Z= 0.117 Angle : 0.636 7.722 16774 Z= 0.331 Chirality : 0.044 0.174 1865 Planarity : 0.004 0.041 2123 Dihedral : 7.667 176.107 1646 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.07 % Allowed : 9.37 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.19), residues: 1494 helix: -2.11 (0.20), residues: 528 sheet: -3.18 (0.38), residues: 145 loop : -3.03 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.026 0.002 TYR A1040 PHE 0.017 0.001 PHE A 679 TRP 0.015 0.002 TRP B 308 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12353) covalent geometry : angle 0.62929 / 0.33 (16761) SS BOND : bond 0.00306 / 0.21 ( 2) SS BOND : angle 1.10119 / 0.67 ( 4) hydrogen bonds : bond 0.03403 / 2.20 ( 327) hydrogen bonds : angle 5.72489 / 3.91 ( 912) Misc. bond : bond 0.00144 / 0.10 ( 2) link_BETA1-4 : bond 0.00445 / 0.32 ( 2) link_BETA1-4 : angle 3.39955 / 2.35 ( 6) link_NAG-ASN : bond 0.00471 / 0.31 ( 1) link_NAG-ASN : angle 5.26281 / 4.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (tp) REVERT: A 477 ASN cc_start: 0.7681 (t0) cc_final: 0.7147 (t0) REVERT: A 482 GLN cc_start: 0.6520 (pm20) cc_final: 0.6180 (mp10) REVERT: A 485 MET cc_start: 0.4986 (tpt) cc_final: 0.4416 (tmm) REVERT: A 804 LEU cc_start: 0.7887 (mm) cc_final: 0.7540 (mm) REVERT: A 827 MET cc_start: 0.8390 (ppp) cc_final: 0.8099 (ppp) REVERT: A 852 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6792 (mt) REVERT: A 942 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 1263 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7795 (tmtt) outliers start: 27 outliers final: 16 residues processed: 126 average time/residue: 0.0890 time to fit residues: 16.7261 Evaluate side-chains 106 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.0670 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.131209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097734 restraints weight = 20228.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097688 restraints weight = 17139.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098580 restraints weight = 16367.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098808 restraints weight = 11326.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099136 restraints weight = 10123.388| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12360 Z= 0.153 Angle : 0.645 8.923 16774 Z= 0.332 Chirality : 0.045 0.179 1865 Planarity : 0.004 0.040 2123 Dihedral : 7.520 176.400 1646 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.15 % Allowed : 9.68 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.20), residues: 1494 helix: -1.72 (0.21), residues: 528 sheet: -2.85 (0.41), residues: 142 loop : -2.94 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 703 TYR 0.023 0.002 TYR A1040 PHE 0.019 0.002 PHE A1399 TRP 0.016 0.002 TRP A 986 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12353) covalent geometry : angle 0.63804 / 0.33 (16761) SS BOND : bond 0.00403 / 0.27 ( 2) SS BOND : angle 1.51528 / 0.96 ( 4) hydrogen bonds : bond 0.03077 / 1.96 ( 327) hydrogen bonds : angle 5.38376 / 3.66 ( 912) Misc. bond : bond 0.00165 / 0.12 ( 2) link_BETA1-4 : bond 0.00359 / 0.25 ( 2) link_BETA1-4 : angle 3.54860 / 2.50 ( 6) link_NAG-ASN : bond 0.00851 / 0.57 ( 1) link_NAG-ASN : angle 4.79840 / 3.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7114 (t) REVERT: A 477 ASN cc_start: 0.7641 (t0) cc_final: 0.7058 (t0) REVERT: A 482 GLN cc_start: 0.6558 (pm20) cc_final: 0.6257 (mp10) REVERT: A 486 LYS cc_start: 0.6145 (tptt) cc_final: 0.5765 (tptt) REVERT: A 827 MET cc_start: 0.8358 (ppp) cc_final: 0.8034 (ppp) REVERT: A 852 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6830 (mt) REVERT: A 1196 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6750 (ppp) REVERT: A 1263 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7890 (tmtt) REVERT: A 1306 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6387 (p0) outliers start: 41 outliers final: 29 residues processed: 124 average time/residue: 0.0809 time to fit residues: 15.8386 Evaluate side-chains 120 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099824 restraints weight = 20281.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099688 restraints weight = 16324.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100575 restraints weight = 15296.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101132 restraints weight = 10641.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101241 restraints weight = 10036.473| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.002 0.034 12360 Z= 0.112 Angle : 0.603 7.526 16774 Z= 0.310 Chirality : 0.044 0.170 1865 Planarity : 0.003 0.041 2123 Dihedral : 7.284 176.270 1646 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.30 % Allowed : 10.83 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.20), residues: 1494 helix: -1.33 (0.22), residues: 527 sheet: -2.72 (0.41), residues: 144 loop : -2.78 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.023 0.001 TYR A1040 PHE 0.020 0.001 PHE A1399 TRP 0.013 0.001 TRP A 517 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12353) covalent geometry : angle 0.59633 / 0.31 (16761) SS BOND : bond 0.00287 / 0.19 ( 2) SS BOND : angle 1.52965 / 0.96 ( 4) hydrogen bonds : bond 0.02807 / 1.80 ( 327) hydrogen bonds : angle 5.16042 / 3.49 ( 912) Misc. bond : bond 0.00137 / 0.10 ( 2) link_BETA1-4 : bond 0.00319 / 0.23 ( 2) link_BETA1-4 : angle 3.33543 / 2.32 ( 6) link_NAG-ASN : bond 0.00515 / 0.34 ( 1) link_NAG-ASN : angle 4.67757 / 3.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 267 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7143 (t) REVERT: A 477 ASN cc_start: 0.7589 (t0) cc_final: 0.6964 (t0) REVERT: A 482 GLN cc_start: 0.6370 (pm20) cc_final: 0.6032 (mp10) REVERT: A 771 MET cc_start: 0.7929 (mmt) cc_final: 0.7561 (mmt) REVERT: A 827 MET cc_start: 0.8212 (ppp) cc_final: 0.7935 (ppp) REVERT: A 852 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6905 (mt) REVERT: A 1196 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6770 (ppp) REVERT: A 1263 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7935 (tmtt) REVERT: A 1306 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6224 (p0) outliers start: 43 outliers final: 27 residues processed: 130 average time/residue: 0.0830 time to fit residues: 16.6696 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 82 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094975 restraints weight = 20767.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094399 restraints weight = 17630.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095460 restraints weight = 17960.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095677 restraints weight = 12033.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095812 restraints weight = 11505.397| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12360 Z= 0.217 Angle : 0.687 9.520 16774 Z= 0.351 Chirality : 0.047 0.198 1865 Planarity : 0.004 0.040 2123 Dihedral : 7.469 175.840 1646 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.92 % Allowed : 11.52 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.20), residues: 1494 helix: -1.42 (0.22), residues: 544 sheet: -2.76 (0.42), residues: 147 loop : -2.82 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.020 0.002 TYR A1040 PHE 0.018 0.002 PHE A1366 TRP 0.020 0.002 TRP A 986 HIS 0.004 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (12353) covalent geometry : angle 0.68093 / 0.35 (16761) SS BOND : bond 0.00290 / 0.20 ( 2) SS BOND : angle 1.26596 / 0.79 ( 4) hydrogen bonds : bond 0.03096 / 1.95 ( 327) hydrogen bonds : angle 5.18108 / 3.49 ( 912) Misc. bond : bond 0.00178 / 0.13 ( 2) link_BETA1-4 : bond 0.00580 / 0.39 ( 2) link_BETA1-4 : angle 3.79326 / 2.69 ( 6) link_NAG-ASN : bond 0.01202 / 0.80 ( 1) link_NAG-ASN : angle 4.57864 / 3.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7196 (t) REVERT: A 477 ASN cc_start: 0.7577 (t0) cc_final: 0.6935 (t0) REVERT: A 482 GLN cc_start: 0.6415 (pm20) cc_final: 0.6124 (mp10) REVERT: A 827 MET cc_start: 0.8288 (ppp) cc_final: 0.7948 (ppp) REVERT: A 852 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6931 (mt) REVERT: A 1196 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6820 (ppp) REVERT: B 127 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7083 (mp10) outliers start: 51 outliers final: 42 residues processed: 138 average time/residue: 0.0852 time to fit residues: 18.2571 Evaluate side-chains 133 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096519 restraints weight = 20446.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096608 restraints weight = 16511.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097488 restraints weight = 15599.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097805 restraints weight = 10693.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097938 restraints weight = 10127.277| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12360 Z= 0.142 Angle : 0.635 10.317 16774 Z= 0.323 Chirality : 0.045 0.172 1865 Planarity : 0.003 0.040 2123 Dihedral : 7.145 176.122 1644 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.84 % Allowed : 11.52 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.21), residues: 1494 helix: -1.14 (0.22), residues: 534 sheet: -2.67 (0.43), residues: 146 loop : -2.70 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 703 TYR 0.022 0.002 TYR A1040 PHE 0.021 0.002 PHE A1399 TRP 0.012 0.001 TRP A 986 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (12353) covalent geometry : angle 0.62884 / 0.32 (16761) SS BOND : bond 0.00389 / 0.27 ( 2) SS BOND : angle 1.50416 / 0.91 ( 4) hydrogen bonds : bond 0.02827 / 1.81 ( 327) hydrogen bonds : angle 5.04371 / 3.40 ( 912) Misc. bond : bond 0.00219 / 0.16 ( 2) link_BETA1-4 : bond 0.00301 / 0.21 ( 2) link_BETA1-4 : angle 3.45136 / 2.41 ( 6) link_NAG-ASN : bond 0.00656 / 0.44 ( 1) link_NAG-ASN : angle 4.55148 / 3.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7882 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7223 (t) REVERT: A 477 ASN cc_start: 0.7562 (t0) cc_final: 0.6907 (t0) REVERT: A 482 GLN cc_start: 0.6422 (pm20) cc_final: 0.6157 (mp10) REVERT: A 679 PHE cc_start: 0.7060 (t80) cc_final: 0.6853 (t80) REVERT: A 827 MET cc_start: 0.8285 (ppp) cc_final: 0.7922 (ppp) REVERT: A 849 MET cc_start: 0.5413 (tpt) cc_final: 0.5171 (tpt) REVERT: A 852 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6888 (mt) REVERT: A 1196 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6680 (ppp) REVERT: A 1306 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 127 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6982 (mp10) outliers start: 50 outliers final: 35 residues processed: 135 average time/residue: 0.0824 time to fit residues: 17.2547 Evaluate side-chains 131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 126 optimal weight: 0.4980 chunk 113 optimal weight: 0.0470 chunk 117 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097060 restraints weight = 20523.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097237 restraints weight = 17122.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098163 restraints weight = 16057.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098290 restraints weight = 10794.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098429 restraints weight = 10667.321| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12360 Z= 0.139 Angle : 0.634 9.024 16774 Z= 0.320 Chirality : 0.045 0.169 1865 Planarity : 0.003 0.041 2123 Dihedral : 7.042 175.779 1644 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.92 % Allowed : 11.90 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.21), residues: 1494 helix: -0.97 (0.23), residues: 527 sheet: -2.69 (0.42), residues: 146 loop : -2.67 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.021 0.002 TYR A1040 PHE 0.021 0.002 PHE A1399 TRP 0.011 0.001 TRP A 986 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12353) covalent geometry : angle 0.62768 / 0.32 (16761) SS BOND : bond 0.00340 / 0.23 ( 2) SS BOND : angle 1.36870 / 0.84 ( 4) hydrogen bonds : bond 0.02730 / 1.75 ( 327) hydrogen bonds : angle 4.92323 / 3.31 ( 912) Misc. bond : bond 0.00228 / 0.16 ( 2) link_BETA1-4 : bond 0.00314 / 0.22 ( 2) link_BETA1-4 : angle 3.42676 / 2.40 ( 6) link_NAG-ASN : bond 0.00748 / 0.50 ( 1) link_NAG-ASN : angle 4.49289 / 3.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 246 PRO cc_start: 0.8158 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7209 (t) REVERT: A 477 ASN cc_start: 0.7548 (t0) cc_final: 0.6904 (t0) REVERT: A 482 GLN cc_start: 0.6368 (pm20) cc_final: 0.6105 (mp10) REVERT: A 827 MET cc_start: 0.8211 (ppp) cc_final: 0.7854 (ppp) REVERT: A 849 MET cc_start: 0.5407 (tpt) cc_final: 0.5161 (tpt) REVERT: A 852 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6887 (mt) REVERT: A 964 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: A 1306 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6251 (p0) REVERT: B 127 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7003 (mp10) outliers start: 51 outliers final: 39 residues processed: 132 average time/residue: 0.0950 time to fit residues: 18.9129 Evaluate side-chains 132 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 106 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.127725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094318 restraints weight = 20568.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093498 restraints weight = 17624.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094483 restraints weight = 18102.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094827 restraints weight = 12208.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094939 restraints weight = 11705.176| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12360 Z= 0.229 Angle : 0.716 11.418 16774 Z= 0.361 Chirality : 0.048 0.183 1865 Planarity : 0.004 0.039 2123 Dihedral : 7.292 175.585 1644 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 3.38 % Allowed : 12.75 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.20), residues: 1494 helix: -1.19 (0.22), residues: 541 sheet: -2.80 (0.42), residues: 147 loop : -2.72 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 703 TYR 0.018 0.002 TYR A1040 PHE 0.019 0.002 PHE A1399 TRP 0.020 0.002 TRP A 986 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (12353) covalent geometry : angle 0.71042 / 0.36 (16761) SS BOND : bond 0.00211 / 0.14 ( 2) SS BOND : angle 1.22372 / 0.78 ( 4) hydrogen bonds : bond 0.03106 / 1.97 ( 327) hydrogen bonds : angle 5.05182 / 3.40 ( 912) Misc. bond : bond 0.00240 / 0.17 ( 2) link_BETA1-4 : bond 0.00466 / 0.32 ( 2) link_BETA1-4 : angle 3.77691 / 2.69 ( 6) link_NAG-ASN : bond 0.01233 / 0.82 ( 1) link_NAG-ASN : angle 4.47785 / 3.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7443 (t) REVERT: A 477 ASN cc_start: 0.7574 (t0) cc_final: 0.6905 (t0) REVERT: A 482 GLN cc_start: 0.6376 (pm20) cc_final: 0.6058 (mp10) REVERT: A 827 MET cc_start: 0.8234 (ppp) cc_final: 0.7984 (ppp) REVERT: A 852 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6954 (mt) REVERT: A 964 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7882 (pp20) REVERT: A 1306 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6262 (p0) REVERT: B 127 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6976 (mp10) outliers start: 44 outliers final: 36 residues processed: 121 average time/residue: 0.0855 time to fit residues: 16.3860 Evaluate side-chains 123 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 89 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 105 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.0010 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.132328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098606 restraints weight = 20326.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096425 restraints weight = 19356.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097623 restraints weight = 16836.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098301 restraints weight = 12423.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098481 restraints weight = 11395.236| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12360 Z= 0.111 Angle : 0.621 9.120 16774 Z= 0.313 Chirality : 0.044 0.156 1865 Planarity : 0.003 0.042 2123 Dihedral : 6.995 175.283 1644 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.69 % Allowed : 13.52 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.21), residues: 1494 helix: -0.83 (0.23), residues: 532 sheet: -2.61 (0.43), residues: 147 loop : -2.57 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1104 TYR 0.024 0.001 TYR A1040 PHE 0.023 0.001 PHE A1399 TRP 0.012 0.001 TRP A 517 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (12353) covalent geometry : angle 0.61432 / 0.31 (16761) SS BOND : bond 0.00369 / 0.25 ( 2) SS BOND : angle 1.65369 / 1.01 ( 4) hydrogen bonds : bond 0.02643 / 1.69 ( 327) hydrogen bonds : angle 4.88950 / 3.30 ( 912) Misc. bond : bond 0.00178 / 0.13 ( 2) link_BETA1-4 : bond 0.00282 / 0.20 ( 2) link_BETA1-4 : angle 3.18867 / 2.21 ( 6) link_NAG-ASN : bond 0.00415 / 0.28 ( 1) link_NAG-ASN : angle 4.50538 / 3.44 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7328 (t) REVERT: A 477 ASN cc_start: 0.7492 (t0) cc_final: 0.6804 (t0) REVERT: A 482 GLN cc_start: 0.6363 (pm20) cc_final: 0.6127 (mp10) REVERT: A 771 MET cc_start: 0.7900 (mmt) cc_final: 0.7562 (mmt) REVERT: A 827 MET cc_start: 0.8264 (ppp) cc_final: 0.7854 (ppp) REVERT: A 849 MET cc_start: 0.5444 (tpt) cc_final: 0.5225 (tpt) REVERT: A 964 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7910 (pp20) REVERT: B 127 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7095 (mp10) outliers start: 35 outliers final: 28 residues processed: 123 average time/residue: 0.1122 time to fit residues: 20.8294 Evaluate side-chains 119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.0060 chunk 114 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097666 restraints weight = 20549.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095710 restraints weight = 20536.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097034 restraints weight = 17686.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097565 restraints weight = 12645.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.097696 restraints weight = 11878.441| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12360 Z= 0.133 Angle : 0.638 9.627 16774 Z= 0.324 Chirality : 0.045 0.178 1865 Planarity : 0.003 0.041 2123 Dihedral : 6.954 173.845 1644 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.46 % Allowed : 14.29 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1494 helix: -0.83 (0.22), residues: 541 sheet: -2.64 (0.45), residues: 137 loop : -2.55 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 488 TYR 0.021 0.001 TYR A1040 PHE 0.039 0.002 PHE A 679 TRP 0.012 0.001 TRP A 517 HIS 0.004 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (12353) covalent geometry : angle 0.63146 / 0.32 (16761) SS BOND : bond 0.00292 / 0.20 ( 2) SS BOND : angle 1.39608 / 0.88 ( 4) hydrogen bonds : bond 0.02737 / 1.75 ( 327) hydrogen bonds : angle 4.85969 / 3.27 ( 912) Misc. bond : bond 0.00179 / 0.13 ( 2) link_BETA1-4 : bond 0.00332 / 0.23 ( 2) link_BETA1-4 : angle 3.36626 / 2.36 ( 6) link_NAG-ASN : bond 0.00710 / 0.47 ( 1) link_NAG-ASN : angle 4.41583 / 3.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.52 seconds wall clock time: 30 minutes 52.20 seconds (1852.20 seconds total)