Starting phenix.real_space_refine on Wed Jul 30 13:25:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_30833.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_30833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_30833.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_30833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsh_30833/07_2025/7dsh_30833.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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: 7.56, per 1000 atoms: 0.63 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.35 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: 3.67 Time building geometry restraints manager: 3.67 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: 7279 35.24 - 70.48: 82 70.48 - 105.72: 13 105.72 - 140.96: 0 140.96 - 176.20: 1 Dihedral angle restraints: 7375 sinusoidal: 3002 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 7372 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 12.541 176.197 4565 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.054 0.004 TRP B 308 HIS 0.013 0.002 HIS A 216 PHE 0.030 0.003 PHE A1287 TYR 0.030 0.003 TYR A1217 ARG 0.006 0.001 ARG B 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00867 ( 1) link_NAG-ASN : angle 8.40935 ( 3) link_BETA1-4 : bond 0.01280 ( 2) link_BETA1-4 : angle 7.08138 ( 6) hydrogen bonds : bond 0.30506 ( 327) hydrogen bonds : angle 11.93959 ( 912) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.11105 ( 4) covalent geometry : bond 0.00662 (12353) covalent geometry : angle 1.08499 (16761) Misc. bond : bond 0.00348 ( 2) *********************** 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 : 1.367 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: 0.2574 time to fit residues: 71.8455 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 : 1.274 ------------------------------------------------------------------------------- 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 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 475 HIS A 484 ASN A 550 ASN A 736 ASN A 778 HIS A 831 GLN A1139 GLN A1307 HIS B 155 GLN B 172 ASN B 256 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.132226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099581 restraints weight = 19908.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097841 restraints weight = 17654.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099138 restraints weight = 15396.188| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12360 Z= 0.150 Angle : 0.714 10.285 16774 Z= 0.371 Chirality : 0.047 0.207 1865 Planarity : 0.005 0.046 2123 Dihedral : 10.516 174.332 1738 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.92 % Allowed : 7.14 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.17), residues: 1494 helix: -3.13 (0.17), residues: 541 sheet: -3.46 (0.36), residues: 144 loop : -3.28 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 308 HIS 0.004 0.001 HIS A 899 PHE 0.038 0.002 PHE A 679 TYR 0.022 0.002 TYR A1040 ARG 0.008 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 1) link_NAG-ASN : angle 5.82587 ( 3) link_BETA1-4 : bond 0.00567 ( 2) link_BETA1-4 : angle 4.18097 ( 6) hydrogen bonds : bond 0.04128 ( 327) hydrogen bonds : angle 6.49117 ( 912) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.11944 ( 4) covalent geometry : bond 0.00333 (12353) covalent geometry : angle 0.70566 (16761) Misc. bond : bond 0.00181 ( 2) *********************** 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: 25 poor density : 114 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4715 (pttm) cc_final: 0.4433 (mtpt) REVERT: A 477 ASN cc_start: 0.7651 (t0) cc_final: 0.7045 (t0) REVERT: A 482 GLN cc_start: 0.6545 (pm20) cc_final: 0.6167 (mp10) REVERT: A 740 TYR cc_start: 0.6740 (p90) cc_final: 0.6396 (p90) REVERT: A 827 MET cc_start: 0.8405 (ppp) cc_final: 0.8125 (ppp) REVERT: A 942 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 1006 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 84 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8414 (p) outliers start: 25 outliers final: 14 residues processed: 130 average time/residue: 0.2319 time to fit residues: 45.3289 Evaluate side-chains 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU 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 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 84 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 103 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 42 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 141 optimal weight: 0.0030 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 660 GLN A 704 GLN A 927 ASN A 998 ASN A1139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101490 restraints weight = 20015.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100575 restraints weight = 15716.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101738 restraints weight = 15539.027| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2209 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= 0.112 Angle : 0.633 7.858 16774 Z= 0.329 Chirality : 0.045 0.211 1865 Planarity : 0.004 0.042 2123 Dihedral : 9.196 174.770 1735 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.07 % Allowed : 10.06 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.19), residues: 1494 helix: -2.08 (0.20), residues: 529 sheet: -3.17 (0.38), residues: 145 loop : -3.03 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 308 HIS 0.005 0.001 HIS A 899 PHE 0.018 0.001 PHE A 815 TYR 0.027 0.002 TYR A1040 ARG 0.004 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 1) link_NAG-ASN : angle 5.86680 ( 3) link_BETA1-4 : bond 0.00643 ( 2) link_BETA1-4 : angle 3.96793 ( 6) hydrogen bonds : bond 0.03359 ( 327) hydrogen bonds : angle 5.64781 ( 912) SS BOND : bond 0.00067 ( 2) SS BOND : angle 1.63554 ( 4) covalent geometry : bond 0.00240 (12353) covalent geometry : angle 0.62368 (16761) Misc. bond : bond 0.00137 ( 2) *********************** 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 : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4793 (pttm) cc_final: 0.4556 (mtpt) REVERT: A 224 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7439 (tp) REVERT: A 267 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6980 (t) REVERT: A 477 ASN cc_start: 0.7647 (t0) cc_final: 0.7076 (t0) REVERT: A 482 GLN cc_start: 0.6499 (pm20) cc_final: 0.6224 (mp10) REVERT: A 804 LEU cc_start: 0.7944 (mm) cc_final: 0.7626 (mm) REVERT: A 827 MET cc_start: 0.8410 (ppp) cc_final: 0.8107 (ppp) REVERT: A 852 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6835 (mt) REVERT: A 942 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 1124 MET cc_start: 0.6954 (mmt) cc_final: 0.6741 (mmt) REVERT: B 257 TYR cc_start: 0.8010 (t80) cc_final: 0.7803 (t80) outliers start: 27 outliers final: 15 residues processed: 126 average time/residue: 0.2450 time to fit residues: 48.0222 Evaluate side-chains 107 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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 730 LEU 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 1013 LEU Chi-restraints excluded: chain A residue 1077 LEU 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 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097601 restraints weight = 20200.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097143 restraints weight = 16465.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098376 restraints weight = 16089.413| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12360 Z= 0.160 Angle : 0.648 7.750 16774 Z= 0.334 Chirality : 0.046 0.190 1865 Planarity : 0.004 0.041 2123 Dihedral : 8.846 174.760 1735 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.38 % Allowed : 9.68 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.20), residues: 1494 helix: -1.67 (0.21), residues: 527 sheet: -2.88 (0.40), residues: 142 loop : -2.93 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 986 HIS 0.005 0.001 HIS A 899 PHE 0.019 0.002 PHE A1399 TYR 0.024 0.002 TYR A1040 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 1) link_NAG-ASN : angle 5.42698 ( 3) link_BETA1-4 : bond 0.00511 ( 2) link_BETA1-4 : angle 4.01956 ( 6) hydrogen bonds : bond 0.03096 ( 327) hydrogen bonds : angle 5.33058 ( 912) SS BOND : bond 0.00232 ( 2) SS BOND : angle 1.24797 ( 4) covalent geometry : bond 0.00370 (12353) covalent geometry : angle 0.63927 (16761) Misc. bond : bond 0.00150 ( 2) *********************** 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 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4880 (pttm) cc_final: 0.4530 (mtpt) REVERT: A 267 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7091 (t) REVERT: A 477 ASN cc_start: 0.7631 (t0) cc_final: 0.6979 (t0) REVERT: A 482 GLN cc_start: 0.6409 (pm20) cc_final: 0.6139 (mp10) REVERT: A 827 MET cc_start: 0.8383 (ppp) cc_final: 0.8045 (ppp) REVERT: A 852 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6935 (mt) REVERT: A 1109 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7245 (mp-120) REVERT: A 1196 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6744 (ppp) REVERT: A 1306 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6369 (p0) outliers start: 44 outliers final: 31 residues processed: 127 average time/residue: 0.1992 time to fit residues: 39.9489 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 913 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 1109 GLN Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1360 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 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 24 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.0030 chunk 126 optimal weight: 0.0670 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099440 restraints weight = 20141.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098886 restraints weight = 16344.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100183 restraints weight = 15721.354| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12360 Z= 0.111 Angle : 0.607 7.916 16774 Z= 0.311 Chirality : 0.044 0.179 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.425 174.984 1733 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.15 % Allowed : 10.75 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.20), residues: 1494 helix: -1.34 (0.22), residues: 527 sheet: -2.77 (0.40), residues: 144 loop : -2.79 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 517 HIS 0.005 0.001 HIS A 899 PHE 0.019 0.001 PHE A1399 TYR 0.023 0.001 TYR A1040 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 1) link_NAG-ASN : angle 5.38203 ( 3) link_BETA1-4 : bond 0.00397 ( 2) link_BETA1-4 : angle 3.69097 ( 6) hydrogen bonds : bond 0.02830 ( 327) hydrogen bonds : angle 5.13761 ( 912) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.42676 ( 4) covalent geometry : bond 0.00247 (12353) covalent geometry : angle 0.59847 (16761) Misc. bond : bond 0.00226 ( 2) *********************** 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 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4854 (pttm) cc_final: 0.4600 (mtpt) REVERT: A 224 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7611 (tp) REVERT: A 267 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7117 (t) REVERT: A 477 ASN cc_start: 0.7578 (t0) cc_final: 0.6920 (t0) REVERT: A 482 GLN cc_start: 0.6285 (pm20) cc_final: 0.5963 (mp10) REVERT: A 771 MET cc_start: 0.7889 (mmt) cc_final: 0.7488 (mmt) REVERT: A 827 MET cc_start: 0.8242 (ppp) cc_final: 0.7939 (ppp) REVERT: A 852 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6924 (mt) REVERT: A 1109 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7168 (mp-120) REVERT: A 1196 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6805 (ppp) REVERT: A 1306 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6187 (p0) REVERT: B 56 ASP cc_start: 0.6973 (t70) cc_final: 0.6723 (t0) outliers start: 41 outliers final: 23 residues processed: 126 average time/residue: 0.2468 time to fit residues: 47.9674 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 913 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 1109 GLN Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 84 VAL 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 51 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094388 restraints weight = 21085.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092222 restraints weight = 24797.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093512 restraints weight = 27415.796| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 12360 Z= 0.323 Angle : 0.817 10.286 16774 Z= 0.415 Chirality : 0.052 0.224 1865 Planarity : 0.005 0.040 2123 Dihedral : 9.037 176.755 1733 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 4.15 % Allowed : 11.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.19), residues: 1494 helix: -1.76 (0.20), residues: 553 sheet: -2.82 (0.41), residues: 145 loop : -3.02 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 986 HIS 0.006 0.002 HIS A1061 PHE 0.026 0.003 PHE A1366 TYR 0.026 0.003 TYR A1217 ARG 0.004 0.001 ARG A1393 Details of bonding type rmsd link_NAG-ASN : bond 0.01794 ( 1) link_NAG-ASN : angle 5.04090 ( 3) link_BETA1-4 : bond 0.01017 ( 2) link_BETA1-4 : angle 4.46075 ( 6) hydrogen bonds : bond 0.03591 ( 327) hydrogen bonds : angle 5.44980 ( 912) SS BOND : bond 0.00267 ( 2) SS BOND : angle 1.10926 ( 4) covalent geometry : bond 0.00753 (12353) covalent geometry : angle 0.81026 (16761) Misc. bond : bond 0.00281 ( 2) *********************** 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 145 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 91 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7274 (t) REVERT: A 477 ASN cc_start: 0.7536 (t0) cc_final: 0.6887 (t0) REVERT: A 852 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6922 (mt) REVERT: A 1109 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7270 (mp-120) outliers start: 54 outliers final: 45 residues processed: 132 average time/residue: 0.2111 time to fit residues: 43.4636 Evaluate side-chains 131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 83 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 913 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 1077 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1113 VAL 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 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 133 TYR 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 58 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095466 restraints weight = 20505.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095553 restraints weight = 16414.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096447 restraints weight = 15538.971| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12360 Z= 0.149 Angle : 0.656 9.639 16774 Z= 0.333 Chirality : 0.045 0.190 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.599 179.322 1733 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.00 % Allowed : 12.75 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.20), residues: 1494 helix: -1.26 (0.22), residues: 539 sheet: -2.70 (0.42), residues: 146 loop : -2.79 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.005 0.001 HIS A 899 PHE 0.021 0.002 PHE A1399 TYR 0.023 0.002 TYR A1040 ARG 0.006 0.000 ARG A 703 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 1) link_NAG-ASN : angle 5.26840 ( 3) link_BETA1-4 : bond 0.00479 ( 2) link_BETA1-4 : angle 3.79496 ( 6) hydrogen bonds : bond 0.02943 ( 327) hydrogen bonds : angle 5.16757 ( 912) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.51465 ( 4) covalent geometry : bond 0.00346 (12353) covalent geometry : angle 0.64789 (16761) Misc. bond : bond 0.00142 ( 2) *********************** 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 128 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7293 (t) REVERT: A 477 ASN cc_start: 0.7564 (t0) cc_final: 0.6897 (t0) REVERT: A 482 GLN cc_start: 0.6581 (pm20) cc_final: 0.6112 (mp10) REVERT: A 827 MET cc_start: 0.8407 (ppp) cc_final: 0.8088 (ppp) REVERT: A 849 MET cc_start: 0.5475 (tpt) cc_final: 0.5248 (tpt) REVERT: A 852 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6985 (mt) REVERT: A 1109 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7244 (mp-120) REVERT: A 1196 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6742 (ppp) REVERT: A 1306 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6457 (p0) REVERT: B 127 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7072 (mp10) outliers start: 39 outliers final: 28 residues processed: 119 average time/residue: 0.2282 time to fit residues: 41.6657 Evaluate side-chains 117 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 523 MET 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 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 1109 GLN Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 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 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 280 TYR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094915 restraints weight = 20681.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095001 restraints weight = 17785.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095811 restraints weight = 16753.659| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12360 Z= 0.177 Angle : 0.668 9.577 16774 Z= 0.339 Chirality : 0.046 0.190 1865 Planarity : 0.004 0.040 2123 Dihedral : 8.558 179.511 1733 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.30 % Allowed : 12.98 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1494 helix: -1.21 (0.22), residues: 546 sheet: -2.67 (0.42), residues: 147 loop : -2.76 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 986 HIS 0.005 0.001 HIS A 899 PHE 0.020 0.002 PHE A1399 TYR 0.021 0.002 TYR A1040 ARG 0.007 0.000 ARG A 703 Details of bonding type rmsd link_NAG-ASN : bond 0.01030 ( 1) link_NAG-ASN : angle 5.10681 ( 3) link_BETA1-4 : bond 0.00545 ( 2) link_BETA1-4 : angle 3.87027 ( 6) hydrogen bonds : bond 0.02919 ( 327) hydrogen bonds : angle 5.09614 ( 912) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.28454 ( 4) covalent geometry : bond 0.00414 (12353) covalent geometry : angle 0.65995 (16761) Misc. bond : bond 0.00157 ( 2) *********************** 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 127 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (t) REVERT: A 477 ASN cc_start: 0.7554 (t0) cc_final: 0.6902 (t0) REVERT: A 482 GLN cc_start: 0.6547 (pm20) cc_final: 0.6085 (mp10) REVERT: A 827 MET cc_start: 0.8395 (ppp) cc_final: 0.8116 (ppp) REVERT: A 849 MET cc_start: 0.5484 (tpt) cc_final: 0.5246 (tpt) REVERT: A 852 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6933 (mt) REVERT: A 1109 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7141 (mp-120) REVERT: A 1196 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6713 (ppp) REVERT: A 1306 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6410 (p0) REVERT: B 127 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7096 (mp10) outliers start: 43 outliers final: 32 residues processed: 117 average time/residue: 0.2330 time to fit residues: 41.9361 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 523 MET 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 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 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 1360 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 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096010 restraints weight = 20407.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096022 restraints weight = 17042.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096956 restraints weight = 16358.425| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12360 Z= 0.147 Angle : 0.643 9.577 16774 Z= 0.326 Chirality : 0.045 0.185 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.419 179.753 1733 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.38 % Allowed : 13.06 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.21), residues: 1494 helix: -1.03 (0.22), residues: 540 sheet: -2.55 (0.46), residues: 126 loop : -2.69 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.005 0.001 HIS A 899 PHE 0.023 0.002 PHE A1399 TYR 0.021 0.002 TYR A1040 ARG 0.003 0.000 ARG A 846 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 1) link_NAG-ASN : angle 5.10828 ( 3) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 3.70886 ( 6) hydrogen bonds : bond 0.02770 ( 327) hydrogen bonds : angle 4.99652 ( 912) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.39367 ( 4) covalent geometry : bond 0.00342 (12353) covalent geometry : angle 0.63583 (16761) Misc. bond : bond 0.00134 ( 2) *********************** 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 133 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7379 (t) REVERT: A 477 ASN cc_start: 0.7526 (t0) cc_final: 0.6893 (t0) REVERT: A 482 GLN cc_start: 0.6511 (pm20) cc_final: 0.6058 (mp10) REVERT: A 827 MET cc_start: 0.8376 (ppp) cc_final: 0.8082 (ppp) REVERT: A 849 MET cc_start: 0.5481 (tpt) cc_final: 0.5244 (tpt) REVERT: A 852 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6940 (mt) REVERT: A 1109 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7180 (mp-120) REVERT: A 1306 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6364 (p0) REVERT: B 127 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7020 (mp10) outliers start: 44 outliers final: 34 residues processed: 123 average time/residue: 0.2293 time to fit residues: 43.8534 Evaluate side-chains 123 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 523 MET 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 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE 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 1360 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 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 28 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.130034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096198 restraints weight = 20552.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096139 restraints weight = 16929.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097031 restraints weight = 16661.423| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12360 Z= 0.147 Angle : 0.648 9.488 16774 Z= 0.328 Chirality : 0.045 0.180 1865 Planarity : 0.003 0.041 2123 Dihedral : 8.355 178.785 1733 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.15 % Allowed : 13.29 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.21), residues: 1494 helix: -0.95 (0.22), residues: 542 sheet: -2.54 (0.46), residues: 126 loop : -2.65 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 986 HIS 0.004 0.001 HIS A 899 PHE 0.022 0.002 PHE A1399 TYR 0.024 0.002 TYR A 693 ARG 0.003 0.000 ARG A 703 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 1) link_NAG-ASN : angle 5.06830 ( 3) link_BETA1-4 : bond 0.00471 ( 2) link_BETA1-4 : angle 3.68731 ( 6) hydrogen bonds : bond 0.02791 ( 327) hydrogen bonds : angle 4.95255 ( 912) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.36133 ( 4) covalent geometry : bond 0.00340 (12353) covalent geometry : angle 0.64067 (16761) Misc. bond : bond 0.00261 ( 2) ********************** 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 128 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7375 (t) REVERT: A 477 ASN cc_start: 0.7508 (t0) cc_final: 0.6854 (t0) REVERT: A 482 GLN cc_start: 0.6463 (pm20) cc_final: 0.6013 (mp10) REVERT: A 827 MET cc_start: 0.8375 (ppp) cc_final: 0.8073 (ppp) REVERT: A 852 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6875 (mt) REVERT: A 1109 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7200 (mp-120) REVERT: A 1306 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6288 (p0) REVERT: B 127 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7111 (mp10) outliers start: 41 outliers final: 33 residues processed: 119 average time/residue: 0.2317 time to fit residues: 42.4735 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 523 MET 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 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE 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 1360 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 110 CYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 141 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097679 restraints weight = 20402.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096926 restraints weight = 16985.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098367 restraints weight = 16504.811| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12360 Z= 0.124 Angle : 0.620 9.206 16774 Z= 0.315 Chirality : 0.044 0.173 1865 Planarity : 0.003 0.042 2123 Dihedral : 8.192 178.264 1733 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.15 % Allowed : 13.21 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1494 helix: -0.72 (0.23), residues: 528 sheet: -2.49 (0.44), residues: 136 loop : -2.57 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 517 HIS 0.004 0.001 HIS A 899 PHE 0.022 0.001 PHE A1399 TYR 0.022 0.001 TYR A1040 ARG 0.003 0.000 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 1) link_NAG-ASN : angle 5.07835 ( 3) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 3.56074 ( 6) hydrogen bonds : bond 0.02693 ( 327) hydrogen bonds : angle 4.85934 ( 912) SS BOND : bond 0.00346 ( 2) SS BOND : angle 1.43641 ( 4) covalent geometry : bond 0.00285 (12353) covalent geometry : angle 0.61276 (16761) Misc. bond : bond 0.00174 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.75 seconds wall clock time: 65 minutes 8.78 seconds (3908.78 seconds total)