Starting phenix.real_space_refine on Fri Jul 3 05:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f7f_31487/07_2026/7f7f_31487.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 60 5.16 5 C 7766 2.51 5 N 1996 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 9046 Classifications: {'peptide': 1135} Link IDs: {'CIS': 2, 'PTRANS': 36, 'TRANS': 1096} Chain breaks: 3 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.22 Number of scatterers: 12076 At special positions: 0 Unit cell: (148.755, 109.72, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 1 11.99 O 2253 8.00 N 1996 7.00 C 7766 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 584.4 milliseconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 32.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 221 through 232 removed outlier: 4.596A pdb=" N PHE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.958A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.512A pdb=" N ASP A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.937A pdb=" N GLY A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.510A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.799A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.760A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.509A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.685A pdb=" N LEU A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.004A pdb=" N PHE A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.663A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.849A pdb=" N TYR A 903 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 removed outlier: 4.226A pdb=" N LYS A 925 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.500A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.717A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.997A pdb=" N ALA A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1038 " --> pdb=" O ASP A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.754A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.693A pdb=" N LEU A1092 " --> pdb=" O ARG A1088 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1121 removed outlier: 3.614A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.672A pdb=" N MET A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' 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 1173 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.590A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.628A pdb=" N PHE A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 4.192A pdb=" N LEU A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1255 removed outlier: 3.756A pdb=" N LEU A1255 " --> pdb=" O VAL A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1252 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.666A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1266 through 1287 removed outlier: 3.567A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1275 " --> pdb=" O LEU A1271 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A1276 " --> pdb=" O TRP A1272 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1285 " --> pdb=" O SER A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.738A pdb=" N ILE A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 3.507A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.604A pdb=" N VAL A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1395 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 3.528A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1418 removed outlier: 3.550A pdb=" N ARG A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 97 removed outlier: 4.126A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.673A pdb=" N ASP B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.660A pdb=" N ASP B 269 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.713A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.667A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.610A pdb=" N ILE A 409 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 8.227A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 683 removed outlier: 7.829A pdb=" N MET A 677 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 966 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE A 679 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU A 964 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 681 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 960 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 836 through 839 removed outlier: 3.851A pdb=" N ILE A 852 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.769A pdb=" N VAL B 173 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.021A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.612A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 247 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3684 1.34 - 1.46: 2798 1.46 - 1.58: 5781 1.58 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 12353 Sorted by residual: bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.64e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.488 -0.039 1.45e-02 4.76e+03 7.26e+00 bond pdb=" C VAL A1408 " pdb=" N GLU A1409 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.50e-02 4.44e+03 5.88e+00 bond pdb=" CD LYS A 542 " pdb=" CE LYS A 542 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.30e+00 bond pdb=" CG LYS A 542 " pdb=" CD LYS A 542 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.79e+00 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15956 2.37 - 4.74: 658 4.74 - 7.11: 100 7.11 - 9.48: 31 9.48 - 11.84: 7 Bond angle restraints: 16752 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 112.29 105.99 6.30 9.40e-01 1.13e+00 4.49e+01 angle pdb=" N PHE A1366 " pdb=" CA PHE A1366 " pdb=" C PHE A1366 " ideal model delta sigma weight residual 114.56 107.61 6.95 1.27e+00 6.20e-01 3.00e+01 angle pdb=" C TYR A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C CYS A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 16747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 6575 14.98 - 29.96: 554 29.96 - 44.94: 131 44.94 - 59.92: 10 59.92 - 74.91: 2 Dihedral angle restraints: 7272 sinusoidal: 2908 harmonic: 4364 Sorted by residual: dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual -180.00 -137.75 -42.25 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N LYS A 542 " pdb=" CA LYS A 542 " ideal model delta harmonic sigma weight residual -180.00 -138.58 -41.42 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLN A 233 " pdb=" C GLN A 233 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " ideal model delta harmonic sigma weight residual 180.00 -138.98 -41.02 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 7269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1246 0.058 - 0.116: 482 0.116 - 0.174: 121 0.174 - 0.231: 18 0.231 - 0.289: 6 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CB VAL A 245 " pdb=" CA VAL A 245 " pdb=" CG1 VAL A 245 " pdb=" CG2 VAL A 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1870 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C PHE B 398 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C VAL A1408 " -0.100 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1287 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1288 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1288 " -0.047 5.00e-02 4.00e+02 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 292 2.68 - 3.23: 11016 3.23 - 3.79: 18973 3.79 - 4.34: 25164 4.34 - 4.90: 40361 Nonbonded interactions: 95806 Sorted by model distance: nonbonded pdb=" O THR A 669 " pdb="MG MG A1601 " model vdw 2.121 2.170 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.184 3.040 nonbonded pdb=" O ASP A 667 " pdb=" OG1 THR A 671 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A1221 " pdb=" OG1 THR A1353 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.262 2.170 ... (remaining 95801 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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: 2.310 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.008 0.102 12364 Z= 0.326 Angle : 1.136 12.979 16777 Z= 0.596 Chirality : 0.064 0.289 1873 Planarity : 0.008 0.084 2123 Dihedral : 11.796 74.905 4468 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.60 (0.16), residues: 1487 helix: -4.70 (0.10), residues: 493 sheet: -3.22 (0.37), residues: 128 loop : -3.29 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1412 TYR 0.045 0.003 TYR A1273 PHE 0.036 0.004 PHE A1287 TRP 0.043 0.003 TRP A1415 HIS 0.012 0.002 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.33 (12353) covalent geometry : angle 1.12455 / 0.59 (16752) SS BOND : bond 0.00380 / 0.20 ( 2) SS BOND : angle 1.48052 / 0.66 ( 4) hydrogen bonds : bond 0.31708 / 20.15 ( 243) hydrogen bonds : angle 11.62823 / 7.95 ( 690) Misc. bond : bond 0.00220 / 0.11 ( 2) link_BETA1-4 : bond 0.00820 / 0.41 ( 3) link_BETA1-4 : angle 4.56100 / 2.34 ( 9) link_BETA1-6 : bond 0.00567 / 0.30 ( 1) link_BETA1-6 : angle 2.47684 / 1.21 ( 3) link_NAG-ASN : bond 0.00847 / 0.43 ( 3) link_NAG-ASN : angle 5.11886 / 2.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.5546 (mpm) cc_final: 0.4399 (mtt) REVERT: A 519 MET cc_start: -0.0530 (mtt) cc_final: -0.0964 (ttm) REVERT: A 633 TYR cc_start: 0.8188 (t80) cc_final: 0.7971 (t80) REVERT: A 652 TRP cc_start: 0.7261 (m100) cc_final: 0.7015 (m-10) REVERT: A 848 ARG cc_start: 0.4870 (mtt90) cc_final: 0.3017 (mtm110) REVERT: A 992 LYS cc_start: 0.6964 (pptt) cc_final: 0.6753 (ptmm) REVERT: B 123 SER cc_start: 0.8729 (m) cc_final: 0.8036 (p) REVERT: B 142 TRP cc_start: 0.7858 (m-10) cc_final: 0.7143 (m-10) REVERT: B 370 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7934 (ttt90) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.1134 time to fit residues: 29.7507 Evaluate side-chains 115 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN A 484 ASN A 556 ASN A 674 GLN A1067 ASN A1209 ASN A1226 ASN A1301 ASN A1307 HIS A1330 HIS B 125 HIS B 171 ASN B 209 HIS B 330 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.196572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174810 restraints weight = 14554.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.168293 restraints weight = 24022.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166183 restraints weight = 36297.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166447 restraints weight = 28482.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166541 restraints weight = 23891.353| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12364 Z= 0.130 Angle : 0.698 8.356 16777 Z= 0.366 Chirality : 0.046 0.350 1873 Planarity : 0.005 0.061 2123 Dihedral : 7.045 37.906 1635 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 2.08 % Allowed : 9.46 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.17), residues: 1487 helix: -3.86 (0.15), residues: 498 sheet: -2.83 (0.40), residues: 133 loop : -2.84 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 187 TYR 0.017 0.001 TYR A1256 PHE 0.028 0.002 PHE A 565 TRP 0.013 0.001 TRP A1415 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12353) covalent geometry : angle 0.68999 / 0.36 (16752) SS BOND : bond 0.00006 / 0.00 ( 2) SS BOND : angle 0.42429 / 0.16 ( 4) hydrogen bonds : bond 0.05242 / 3.38 ( 243) hydrogen bonds : angle 6.91350 / 4.75 ( 690) Misc. bond : bond 0.00066 / 0.03 ( 2) link_BETA1-4 : bond 0.00884 / 0.44 ( 3) link_BETA1-4 : angle 3.15779 / 1.61 ( 9) link_BETA1-6 : bond 0.00640 / 0.34 ( 1) link_BETA1-6 : angle 1.60263 / 0.74 ( 3) link_NAG-ASN : bond 0.00720 / 0.37 ( 3) link_NAG-ASN : angle 3.48766 / 1.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1735 (OUTLIER) cc_final: 0.1476 (mp) REVERT: A 189 MET cc_start: 0.5328 (mpm) cc_final: 0.4639 (mtt) REVERT: A 519 MET cc_start: -0.0013 (mtt) cc_final: -0.0807 (ttm) REVERT: A 633 TYR cc_start: 0.8043 (t80) cc_final: 0.7826 (t80) REVERT: A 643 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6924 (tt) REVERT: A 652 TRP cc_start: 0.7358 (m100) cc_final: 0.7005 (m-10) REVERT: A 677 MET cc_start: 0.5215 (mmm) cc_final: 0.4609 (mtt) REVERT: A 1039 LYS cc_start: 0.7374 (ttpt) cc_final: 0.7102 (ttpt) REVERT: A 1137 MET cc_start: 0.7533 (ttp) cc_final: 0.7302 (ttp) REVERT: A 1330 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6501 (m-70) REVERT: B 123 SER cc_start: 0.8461 (m) cc_final: 0.7919 (p) REVERT: B 238 MET cc_start: 0.7305 (ttt) cc_final: 0.7064 (ttt) REVERT: B 321 ASP cc_start: 0.7108 (t0) cc_final: 0.6844 (t70) REVERT: B 359 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 370 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.8039 (ttt180) outliers start: 27 outliers final: 11 residues processed: 165 average time/residue: 0.1042 time to fit residues: 24.9480 Evaluate side-chains 135 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 148 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN A 763 GLN A1061 HIS A1330 HIS B 341 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155698 restraints weight = 14858.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149424 restraints weight = 16464.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149334 restraints weight = 20418.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149522 restraints weight = 19605.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149888 restraints weight = 16029.423| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12364 Z= 0.177 Angle : 0.703 12.833 16777 Z= 0.362 Chirality : 0.047 0.404 1873 Planarity : 0.005 0.063 2123 Dihedral : 6.741 34.823 1635 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.15 % Allowed : 10.54 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.19), residues: 1487 helix: -3.31 (0.18), residues: 499 sheet: -2.81 (0.41), residues: 127 loop : -2.63 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 916 TYR 0.013 0.002 TYR A 585 PHE 0.028 0.002 PHE A 565 TRP 0.016 0.002 TRP A1415 HIS 0.008 0.001 HIS A1330 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (12353) covalent geometry : angle 0.69435 / 0.36 (16752) SS BOND : bond 0.00145 / 0.08 ( 2) SS BOND : angle 0.76153 / 0.32 ( 4) hydrogen bonds : bond 0.04460 / 2.95 ( 243) hydrogen bonds : angle 6.31524 / 4.34 ( 690) Misc. bond : bond 0.00055 / 0.03 ( 2) link_BETA1-4 : bond 0.00523 / 0.26 ( 3) link_BETA1-4 : angle 3.17138 / 1.58 ( 9) link_BETA1-6 : bond 0.00605 / 0.32 ( 1) link_BETA1-6 : angle 1.49573 / 0.67 ( 3) link_NAG-ASN : bond 0.00686 / 0.35 ( 3) link_NAG-ASN : angle 3.50560 / 1.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2342 (OUTLIER) cc_final: 0.1600 (mp) REVERT: A 189 MET cc_start: 0.5853 (mpm) cc_final: 0.4319 (mtt) REVERT: A 519 MET cc_start: -0.1545 (mtt) cc_final: -0.1757 (ttm) REVERT: A 643 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6964 (tt) REVERT: A 677 MET cc_start: 0.5916 (mmm) cc_final: 0.5001 (mtt) REVERT: A 684 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.5062 (pt) REVERT: A 706 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6249 (pp) REVERT: A 1039 LYS cc_start: 0.7358 (ttpt) cc_final: 0.7144 (ttpt) REVERT: A 1072 ILE cc_start: 0.7670 (tp) cc_final: 0.7417 (tp) REVERT: A 1108 SER cc_start: 0.7944 (p) cc_final: 0.7482 (t) REVERT: B 66 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6916 (pt) REVERT: B 123 SER cc_start: 0.8547 (m) cc_final: 0.8164 (p) REVERT: B 238 MET cc_start: 0.7539 (ttt) cc_final: 0.7281 (ttt) outliers start: 41 outliers final: 22 residues processed: 162 average time/residue: 0.0977 time to fit residues: 23.8019 Evaluate side-chains 151 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 124 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 113 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 685 ASN A 778 HIS A1417 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.194264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180005 restraints weight = 14770.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.177468 restraints weight = 24384.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173411 restraints weight = 26718.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171875 restraints weight = 33830.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170624 restraints weight = 27828.912| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12364 Z= 0.135 Angle : 0.661 9.328 16777 Z= 0.339 Chirality : 0.046 0.380 1873 Planarity : 0.004 0.057 2123 Dihedral : 6.335 33.934 1635 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.92 % Allowed : 11.69 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.19), residues: 1487 helix: -2.99 (0.19), residues: 501 sheet: -2.65 (0.41), residues: 135 loop : -2.46 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.014 0.001 TYR A1040 PHE 0.022 0.001 PHE A 565 TRP 0.011 0.001 TRP A1415 HIS 0.003 0.001 HIS A1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12353) covalent geometry : angle 0.65369 / 0.34 (16752) SS BOND : bond 0.00111 / 0.06 ( 2) SS BOND : angle 0.75806 / 0.32 ( 4) hydrogen bonds : bond 0.03758 / 2.46 ( 243) hydrogen bonds : angle 5.85031 / 4.05 ( 690) Misc. bond : bond 0.00052 / 0.03 ( 2) link_BETA1-4 : bond 0.00574 / 0.29 ( 3) link_BETA1-4 : angle 2.97337 / 1.49 ( 9) link_BETA1-6 : bond 0.00595 / 0.31 ( 1) link_BETA1-6 : angle 1.39199 / 0.63 ( 3) link_NAG-ASN : bond 0.00705 / 0.37 ( 3) link_NAG-ASN : angle 3.17806 / 1.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.1706 (OUTLIER) cc_final: 0.1488 (mp) REVERT: A 189 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.4311 (mtt) REVERT: A 224 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.2926 (pp) REVERT: A 229 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4001 (mm) REVERT: A 519 MET cc_start: 0.0394 (mtt) cc_final: -0.0777 (ttm) REVERT: A 643 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7025 (tt) REVERT: A 677 MET cc_start: 0.5148 (mmm) cc_final: 0.4672 (mtt) REVERT: A 706 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6435 (pp) REVERT: A 1040 TYR cc_start: 0.3849 (t80) cc_final: 0.2829 (t80) REVERT: A 1108 SER cc_start: 0.7780 (p) cc_final: 0.7368 (t) REVERT: A 1414 MET cc_start: 0.8243 (ptp) cc_final: 0.8026 (ptm) REVERT: B 123 SER cc_start: 0.8141 (m) cc_final: 0.7871 (p) REVERT: B 238 MET cc_start: 0.7397 (ttt) cc_final: 0.7193 (ttt) REVERT: B 351 LEU cc_start: 0.8695 (mt) cc_final: 0.8494 (mt) outliers start: 38 outliers final: 21 residues processed: 157 average time/residue: 0.0948 time to fit residues: 22.5368 Evaluate side-chains 145 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 130 optimal weight: 0.0060 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.188371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164251 restraints weight = 15045.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161347 restraints weight = 29664.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159951 restraints weight = 30101.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157973 restraints weight = 25721.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158523 restraints weight = 23165.608| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12364 Z= 0.237 Angle : 0.737 9.411 16777 Z= 0.378 Chirality : 0.050 0.441 1873 Planarity : 0.005 0.069 2123 Dihedral : 6.591 32.978 1635 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.08 % Allowed : 12.23 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.19), residues: 1487 helix: -2.92 (0.19), residues: 505 sheet: -2.66 (0.42), residues: 120 loop : -2.50 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1393 TYR 0.023 0.002 TYR A1040 PHE 0.025 0.002 PHE A 565 TRP 0.018 0.002 TRP A1336 HIS 0.006 0.001 HIS A1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (12353) covalent geometry : angle 0.72866 / 0.38 (16752) SS BOND : bond 0.00275 / 0.14 ( 2) SS BOND : angle 0.97846 / 0.39 ( 4) hydrogen bonds : bond 0.04082 / 2.71 ( 243) hydrogen bonds : angle 5.92228 / 4.13 ( 690) Misc. bond : bond 0.00103 / 0.05 ( 2) link_BETA1-4 : bond 0.00402 / 0.20 ( 3) link_BETA1-4 : angle 3.15025 / 1.56 ( 9) link_BETA1-6 : bond 0.00487 / 0.26 ( 1) link_BETA1-6 : angle 1.62696 / 0.76 ( 3) link_NAG-ASN : bond 0.00593 / 0.30 ( 3) link_NAG-ASN : angle 3.50859 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2234 (OUTLIER) cc_final: 0.1841 (mp) REVERT: A 189 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4440 (mtp) REVERT: A 196 ILE cc_start: 0.1081 (OUTLIER) cc_final: 0.0353 (tp) REVERT: A 224 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.3053 (pp) REVERT: A 229 LEU cc_start: 0.4135 (OUTLIER) cc_final: 0.3818 (mm) REVERT: A 519 MET cc_start: 0.0099 (mtt) cc_final: -0.1007 (ttm) REVERT: A 643 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7017 (tt) REVERT: A 677 MET cc_start: 0.5272 (mmm) cc_final: 0.4730 (mtt) REVERT: A 706 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6433 (pp) REVERT: A 1037 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5977 (pt) REVERT: A 1040 TYR cc_start: 0.4109 (t80) cc_final: 0.2603 (t80) REVERT: A 1108 SER cc_start: 0.7894 (p) cc_final: 0.7516 (t) REVERT: B 123 SER cc_start: 0.8427 (m) cc_final: 0.8122 (p) REVERT: B 238 MET cc_start: 0.7536 (ttt) cc_final: 0.7235 (ttt) REVERT: B 348 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8558 (t60) outliers start: 53 outliers final: 30 residues processed: 165 average time/residue: 0.0884 time to fit residues: 22.1730 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 123 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.191156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166983 restraints weight = 14872.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.164967 restraints weight = 28623.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162334 restraints weight = 26336.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160457 restraints weight = 26554.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161102 restraints weight = 22630.841| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12364 Z= 0.157 Angle : 0.674 9.310 16777 Z= 0.345 Chirality : 0.046 0.403 1873 Planarity : 0.004 0.064 2123 Dihedral : 6.224 32.711 1635 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.54 % Allowed : 14.38 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.20), residues: 1487 helix: -2.70 (0.20), residues: 500 sheet: -2.69 (0.40), residues: 128 loop : -2.36 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.018 0.002 TYR A1040 PHE 0.016 0.002 PHE B 128 TRP 0.010 0.001 TRP A1415 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12353) covalent geometry : angle 0.66659 / 0.34 (16752) SS BOND : bond 0.00132 / 0.07 ( 2) SS BOND : angle 0.74137 / 0.30 ( 4) hydrogen bonds : bond 0.03521 / 2.34 ( 243) hydrogen bonds : angle 5.67278 / 3.95 ( 690) Misc. bond : bond 0.00064 / 0.03 ( 2) link_BETA1-4 : bond 0.00501 / 0.25 ( 3) link_BETA1-4 : angle 2.98437 / 1.50 ( 9) link_BETA1-6 : bond 0.00412 / 0.22 ( 1) link_BETA1-6 : angle 1.39594 / 0.63 ( 3) link_NAG-ASN : bond 0.00757 / 0.39 ( 3) link_NAG-ASN : angle 3.19046 / 1.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2227 (OUTLIER) cc_final: 0.1826 (mp) REVERT: A 189 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4397 (mtp) REVERT: A 224 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.3048 (pp) REVERT: A 229 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3912 (mm) REVERT: A 519 MET cc_start: 0.0020 (mtt) cc_final: -0.0999 (ttm) REVERT: A 643 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6952 (tt) REVERT: A 677 MET cc_start: 0.5454 (mmm) cc_final: 0.4847 (mtt) REVERT: A 706 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6331 (pp) REVERT: A 1040 TYR cc_start: 0.4318 (t80) cc_final: 0.2993 (t80) REVERT: A 1058 LYS cc_start: 0.3338 (OUTLIER) cc_final: 0.2522 (tmtt) REVERT: A 1108 SER cc_start: 0.7924 (p) cc_final: 0.7492 (t) REVERT: A 1186 GLU cc_start: 0.7471 (tp30) cc_final: 0.7135 (tp30) REVERT: A 1270 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7951 (t80) REVERT: B 123 SER cc_start: 0.8242 (m) cc_final: 0.8021 (p) REVERT: B 348 TRP cc_start: 0.9233 (OUTLIER) cc_final: 0.8636 (t60) outliers start: 46 outliers final: 28 residues processed: 157 average time/residue: 0.0966 time to fit residues: 23.1916 Evaluate side-chains 152 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 674 GLN A 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.194973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.180587 restraints weight = 14649.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176607 restraints weight = 25494.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173514 restraints weight = 30896.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.171046 restraints weight = 32110.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.167436 restraints weight = 33240.897| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12364 Z= 0.148 Angle : 0.655 9.112 16777 Z= 0.337 Chirality : 0.046 0.378 1873 Planarity : 0.004 0.064 2123 Dihedral : 6.055 31.963 1635 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.38 % Allowed : 13.69 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.20), residues: 1487 helix: -2.50 (0.21), residues: 501 sheet: -2.54 (0.41), residues: 120 loop : -2.33 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.032 0.001 TYR A1256 PHE 0.021 0.002 PHE B 128 TRP 0.013 0.001 TRP A 652 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12353) covalent geometry : angle 0.64832 / 0.34 (16752) SS BOND : bond 0.00087 / 0.04 ( 2) SS BOND : angle 0.69279 / 0.32 ( 4) hydrogen bonds : bond 0.03383 / 2.25 ( 243) hydrogen bonds : angle 5.47940 / 3.82 ( 690) Misc. bond : bond 0.00045 / 0.02 ( 2) link_BETA1-4 : bond 0.00493 / 0.25 ( 3) link_BETA1-4 : angle 2.90470 / 1.45 ( 9) link_BETA1-6 : bond 0.00530 / 0.28 ( 1) link_BETA1-6 : angle 1.44066 / 0.65 ( 3) link_NAG-ASN : bond 0.00643 / 0.33 ( 3) link_NAG-ASN : angle 2.98013 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2334 (OUTLIER) cc_final: 0.1983 (mp) REVERT: A 189 MET cc_start: 0.5240 (OUTLIER) cc_final: 0.4378 (mtp) REVERT: A 196 ILE cc_start: 0.1049 (OUTLIER) cc_final: 0.0276 (tp) REVERT: A 224 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.2982 (pp) REVERT: A 229 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3785 (mm) REVERT: A 519 MET cc_start: 0.0138 (mtt) cc_final: -0.0902 (ttm) REVERT: A 643 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7064 (tt) REVERT: A 706 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6206 (pp) REVERT: A 965 ASP cc_start: 0.7544 (t0) cc_final: 0.7038 (m-30) REVERT: A 1040 TYR cc_start: 0.4303 (t80) cc_final: 0.2985 (t80) REVERT: A 1058 LYS cc_start: 0.3199 (OUTLIER) cc_final: 0.2518 (tmtt) REVERT: A 1108 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7441 (t) REVERT: A 1186 GLU cc_start: 0.7606 (tp30) cc_final: 0.7298 (tp30) REVERT: A 1270 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7748 (t80) REVERT: B 238 MET cc_start: 0.7235 (ttt) cc_final: 0.6915 (ttt) REVERT: B 343 ASP cc_start: 0.7172 (m-30) cc_final: 0.6623 (p0) REVERT: B 348 TRP cc_start: 0.9229 (OUTLIER) cc_final: 0.8631 (t60) outliers start: 57 outliers final: 33 residues processed: 155 average time/residue: 0.0895 time to fit residues: 21.1477 Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 19 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 102 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.194405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171157 restraints weight = 14594.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167467 restraints weight = 27343.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164133 restraints weight = 29914.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162334 restraints weight = 32689.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162504 restraints weight = 28370.968| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12364 Z= 0.116 Angle : 0.637 9.543 16777 Z= 0.325 Chirality : 0.045 0.364 1873 Planarity : 0.004 0.067 2123 Dihedral : 5.783 31.557 1635 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.69 % Allowed : 14.92 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.20), residues: 1487 helix: -2.28 (0.21), residues: 504 sheet: -2.37 (0.40), residues: 128 loop : -2.27 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.015 0.001 TYR A1040 PHE 0.023 0.001 PHE B 128 TRP 0.014 0.001 TRP B 126 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12353) covalent geometry : angle 0.63050 / 0.32 (16752) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 0.66635 / 0.31 ( 4) hydrogen bonds : bond 0.03151 / 2.10 ( 243) hydrogen bonds : angle 5.31612 / 3.70 ( 690) Misc. bond : bond 0.00045 / 0.02 ( 2) link_BETA1-4 : bond 0.00489 / 0.24 ( 3) link_BETA1-4 : angle 2.72555 / 1.36 ( 9) link_BETA1-6 : bond 0.00448 / 0.24 ( 1) link_BETA1-6 : angle 1.32111 / 0.59 ( 3) link_NAG-ASN : bond 0.00713 / 0.37 ( 3) link_NAG-ASN : angle 2.82108 / 1.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2364 (OUTLIER) cc_final: 0.2011 (mp) REVERT: A 189 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4401 (mtp) REVERT: A 196 ILE cc_start: 0.1024 (OUTLIER) cc_final: 0.0255 (tp) REVERT: A 224 LEU cc_start: 0.4305 (OUTLIER) cc_final: 0.3154 (pp) REVERT: A 229 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3789 (mm) REVERT: A 519 MET cc_start: -0.0224 (mtt) cc_final: -0.1074 (ttm) REVERT: A 706 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6136 (pp) REVERT: A 1040 TYR cc_start: 0.4247 (t80) cc_final: 0.3180 (t80) REVERT: A 1058 LYS cc_start: 0.3453 (OUTLIER) cc_final: 0.2686 (tmtt) REVERT: A 1108 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7509 (t) REVERT: A 1186 GLU cc_start: 0.7567 (tp30) cc_final: 0.7209 (tp30) REVERT: A 1270 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 238 MET cc_start: 0.7157 (ttt) cc_final: 0.6848 (ttt) REVERT: B 343 ASP cc_start: 0.7200 (m-30) cc_final: 0.6670 (p0) REVERT: B 348 TRP cc_start: 0.9112 (OUTLIER) cc_final: 0.8555 (t60) outliers start: 48 outliers final: 30 residues processed: 148 average time/residue: 0.0925 time to fit residues: 20.8986 Evaluate side-chains 152 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 0.0030 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 75 optimal weight: 0.0370 chunk 53 optimal weight: 0.0970 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.195844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162565 restraints weight = 14658.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.160228 restraints weight = 16977.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159995 restraints weight = 18366.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159920 restraints weight = 19001.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159920 restraints weight = 15225.737| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12364 Z= 0.108 Angle : 0.640 14.153 16777 Z= 0.322 Chirality : 0.044 0.331 1873 Planarity : 0.004 0.067 2123 Dihedral : 5.533 30.096 1635 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.38 % Allowed : 15.92 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.20), residues: 1487 helix: -1.94 (0.22), residues: 490 sheet: -2.04 (0.41), residues: 134 loop : -2.26 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 156 TYR 0.030 0.001 TYR A1256 PHE 0.022 0.001 PHE B 128 TRP 0.017 0.001 TRP B 126 HIS 0.004 0.001 HIS A1417 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12353) covalent geometry : angle 0.63430 / 0.32 (16752) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.67944 / 0.31 ( 4) hydrogen bonds : bond 0.02962 / 1.98 ( 243) hydrogen bonds : angle 5.12983 / 3.58 ( 690) Misc. bond : bond 0.00043 / 0.02 ( 2) link_BETA1-4 : bond 0.00743 / 0.37 ( 3) link_BETA1-4 : angle 2.64023 / 1.32 ( 9) link_BETA1-6 : bond 0.00611 / 0.32 ( 1) link_BETA1-6 : angle 1.36697 / 0.61 ( 3) link_NAG-ASN : bond 0.00657 / 0.34 ( 3) link_NAG-ASN : angle 2.58588 / 1.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2636 (OUTLIER) cc_final: 0.2104 (mp) REVERT: A 189 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4383 (mtt) REVERT: A 196 ILE cc_start: 0.0827 (OUTLIER) cc_final: 0.0155 (tp) REVERT: A 224 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3268 (pp) REVERT: A 229 LEU cc_start: 0.4108 (OUTLIER) cc_final: 0.3810 (mm) REVERT: A 519 MET cc_start: -0.0086 (mtt) cc_final: -0.0846 (ttm) REVERT: A 677 MET cc_start: 0.5397 (mmm) cc_final: 0.4887 (mmm) REVERT: A 706 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.5929 (pp) REVERT: A 1040 TYR cc_start: 0.4203 (t80) cc_final: 0.3301 (t80) REVERT: A 1058 LYS cc_start: 0.3178 (OUTLIER) cc_final: 0.2523 (tmtt) REVERT: A 1108 SER cc_start: 0.7815 (p) cc_final: 0.7379 (t) REVERT: A 1186 GLU cc_start: 0.7756 (tp30) cc_final: 0.7445 (tp30) REVERT: A 1270 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7996 (t80) REVERT: B 238 MET cc_start: 0.7035 (ttt) cc_final: 0.6784 (ttt) REVERT: B 343 ASP cc_start: 0.7122 (m-30) cc_final: 0.6682 (p0) outliers start: 44 outliers final: 30 residues processed: 154 average time/residue: 0.1064 time to fit residues: 24.6239 Evaluate side-chains 150 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 93 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 132 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.193778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171978 restraints weight = 14702.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169418 restraints weight = 27081.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167160 restraints weight = 31124.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164476 restraints weight = 35045.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164453 restraints weight = 30524.894| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12364 Z= 0.130 Angle : 0.653 13.727 16777 Z= 0.330 Chirality : 0.045 0.348 1873 Planarity : 0.004 0.070 2123 Dihedral : 5.545 29.957 1635 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.15 % Allowed : 15.92 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.21), residues: 1487 helix: -1.89 (0.22), residues: 494 sheet: -2.01 (0.41), residues: 136 loop : -2.21 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.017 0.001 TYR A1040 PHE 0.025 0.001 PHE B 128 TRP 0.012 0.001 TRP B 126 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (12353) covalent geometry : angle 0.64748 / 0.33 (16752) SS BOND : bond 0.00024 / 0.01 ( 2) SS BOND : angle 0.73494 / 0.34 ( 4) hydrogen bonds : bond 0.03065 / 2.05 ( 243) hydrogen bonds : angle 5.12195 / 3.59 ( 690) Misc. bond : bond 0.00052 / 0.03 ( 2) link_BETA1-4 : bond 0.00475 / 0.24 ( 3) link_BETA1-4 : angle 2.69456 / 1.34 ( 9) link_BETA1-6 : bond 0.00521 / 0.27 ( 1) link_BETA1-6 : angle 1.37054 / 0.62 ( 3) link_NAG-ASN : bond 0.00606 / 0.31 ( 3) link_NAG-ASN : angle 2.69494 / 1.09 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.2268 (OUTLIER) cc_final: 0.2004 (mp) REVERT: A 189 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.4285 (mtt) REVERT: A 196 ILE cc_start: 0.1106 (OUTLIER) cc_final: 0.0329 (tp) REVERT: A 224 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3066 (pp) REVERT: A 229 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3767 (mm) REVERT: A 519 MET cc_start: 0.0595 (mtt) cc_final: -0.0376 (ttm) REVERT: A 677 MET cc_start: 0.5334 (mmm) cc_final: 0.4882 (mmp) REVERT: A 706 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5959 (pp) REVERT: A 894 GLU cc_start: 0.6141 (tp30) cc_final: 0.5897 (pm20) REVERT: A 1040 TYR cc_start: 0.4272 (t80) cc_final: 0.3281 (t80) REVERT: A 1058 LYS cc_start: 0.3214 (OUTLIER) cc_final: 0.2531 (tmtt) REVERT: A 1108 SER cc_start: 0.7779 (p) cc_final: 0.7391 (t) REVERT: A 1186 GLU cc_start: 0.7816 (tp30) cc_final: 0.7484 (tp30) REVERT: A 1270 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 238 MET cc_start: 0.7130 (ttt) cc_final: 0.6895 (ttt) REVERT: B 343 ASP cc_start: 0.7109 (m-30) cc_final: 0.6677 (p0) outliers start: 41 outliers final: 31 residues processed: 142 average time/residue: 0.0978 time to fit residues: 21.1693 Evaluate side-chains 151 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 4 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 148 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.193698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170100 restraints weight = 14596.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167470 restraints weight = 28918.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162825 restraints weight = 29454.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160389 restraints weight = 34289.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161204 restraints weight = 29927.915| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12364 Z= 0.140 Angle : 0.659 14.489 16777 Z= 0.332 Chirality : 0.045 0.359 1873 Planarity : 0.004 0.068 2123 Dihedral : 5.568 29.736 1635 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.54 % Allowed : 15.54 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.21), residues: 1487 helix: -1.87 (0.22), residues: 503 sheet: -2.11 (0.40), residues: 142 loop : -2.18 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.018 0.001 TYR A1040 PHE 0.024 0.001 PHE B 128 TRP 0.008 0.001 TRP A 652 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12353) covalent geometry : angle 0.65301 / 0.33 (16752) SS BOND : bond 0.00047 / 0.02 ( 2) SS BOND : angle 0.82072 / 0.38 ( 4) hydrogen bonds : bond 0.03126 / 2.09 ( 243) hydrogen bonds : angle 5.13650 / 3.61 ( 690) Misc. bond : bond 0.00060 / 0.03 ( 2) link_BETA1-4 : bond 0.00510 / 0.26 ( 3) link_BETA1-4 : angle 2.73696 / 1.36 ( 9) link_BETA1-6 : bond 0.00407 / 0.21 ( 1) link_BETA1-6 : angle 1.29952 / 0.58 ( 3) link_NAG-ASN : bond 0.00624 / 0.32 ( 3) link_NAG-ASN : angle 2.76235 / 1.12 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.06 seconds wall clock time: 32 minutes 18.60 seconds (1938.60 seconds total)