Starting phenix.real_space_refine on Sat Jul 4 07:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hma_34891/07_2026/8hma_34891.map" } resolution = 3.4 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= 0.002 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 95 5.16 5 C 12406 2.51 5 N 3122 2.21 5 O 3475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19101 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 10151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10151 Classifications: {'peptide': 1253} Link IDs: {'PTRANS': 40, 'TRANS': 1212} Chain breaks: 8 Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 2 Chain: "F" Number of atoms: 7352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7352 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 36, 'TRANS': 878} Chain breaks: 7 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 126 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'3PE': 3, 'A1AC9': 1, 'R16': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'3PE:plan-1': 2, '3PE:plan-2': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 165 Unusual residues: {'BMA': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 3.61, per 1000 atoms: 0.19 Number of scatterers: 19101 At special positions: 0 Unit cell: (172.64, 116.48, 184.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 95 16.00 P 1 15.00 O 3475 8.00 N 3122 7.00 C 12406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 326 " distance=2.03 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 332 " distance=2.03 Simple disulfide: pdb=" SG CYS E1078 " - pdb=" SG CYS E1089 " distance=2.03 Simple disulfide: pdb=" SG CYS E1479 " - pdb=" SG CYS E1495 " distance=2.03 Simple disulfide: pdb=" SG CYS F 303 " - pdb=" SG CYS F1044 " distance=2.03 Simple disulfide: pdb=" SG CYS F 354 " - pdb=" SG CYS F1059 " distance=2.03 Simple disulfide: pdb=" SG CYS F 404 " - pdb=" SG CYS F1071 " distance=2.22 Simple disulfide: pdb=" SG CYS F 904 " - pdb=" SG CYS F 974 " 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=0, symmetry=0 Links applied NAG-ASN " NAG F1101 " - " ASN F 92 " " NAG F1102 " - " ASN F 184 " " NAG F1103 " - " ASN F 468 " " NAG F1106 " - " ASN F 888 " " NAG F1107 " - " ASN F 613 " " NAG F1109 " - " ASN F 324 " " NAG F1110 " - " ASN F 781 " " NAG F1111 " - " ASN F 895 " " NAG F1112 " - " ASN F 348 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 729.6 milliseconds 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 58.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.838A pdb=" N ILE E 118 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 143 removed outlier: 3.609A pdb=" N ALA E 142 " --> pdb=" O CYS E 138 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 182 removed outlier: 3.731A pdb=" N SER E 157 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 211 removed outlier: 3.577A pdb=" N LEU E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.684A pdb=" N PHE E 239 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 251 removed outlier: 3.938A pdb=" N ARG E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 247 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.522A pdb=" N GLN E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 256 " --> pdb=" O PRO E 252 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 268 through 290 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'E' and resid 364 through 377 removed outlier: 3.542A pdb=" N VAL E 368 " --> pdb=" O GLY E 364 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 369 " --> pdb=" O TRP E 365 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 374 " --> pdb=" O TYR E 370 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 375 " --> pdb=" O TRP E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 393 removed outlier: 4.225A pdb=" N TYR E 384 " --> pdb=" O TRP E 380 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 385 " --> pdb=" O PRO E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 418 removed outlier: 3.583A pdb=" N SER E 409 " --> pdb=" O SER E 405 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA E 417 " --> pdb=" O GLU E 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 418 " --> pdb=" O LYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 446 removed outlier: 3.767A pdb=" N LYS E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP E 440 " --> pdb=" O GLY E 436 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 441 " --> pdb=" O TYR E 437 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 522 removed outlier: 3.944A pdb=" N LYS E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 543 Processing helix chain 'E' and resid 549 through 578 removed outlier: 3.864A pdb=" N GLU E 554 " --> pdb=" O ASN E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 Processing helix chain 'E' and resid 586 through 609 removed outlier: 3.510A pdb=" N LEU E 601 " --> pdb=" O CYS E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 626 removed outlier: 3.704A pdb=" N SER E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 630 Processing helix chain 'E' and resid 635 through 647 removed outlier: 3.594A pdb=" N LEU E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 674 removed outlier: 4.192A pdb=" N SER E 653 " --> pdb=" O ARG E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 705 removed outlier: 4.179A pdb=" N LEU E 697 " --> pdb=" O PRO E 693 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR E 698 " --> pdb=" O GLN E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 719 Processing helix chain 'E' and resid 729 through 776 removed outlier: 4.184A pdb=" N LEU E 756 " --> pdb=" O ALA E 752 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS E 767 " --> pdb=" O THR E 763 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 768 " --> pdb=" O SER E 764 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 771 " --> pdb=" O LYS E 767 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU E 774 " --> pdb=" O GLU E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 920 removed outlier: 3.923A pdb=" N ASN E 904 " --> pdb=" O THR E 900 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 920 " --> pdb=" O SER E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 974 removed outlier: 3.552A pdb=" N PHE E 936 " --> pdb=" O ILE E 932 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 967 " --> pdb=" O ILE E 943 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET E 972 " --> pdb=" O ILE E 968 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR E 973 " --> pdb=" O ILE E 969 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 974 " --> pdb=" O LEU E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 1008 removed outlier: 3.774A pdb=" N ASP E 993 " --> pdb=" O PHE E 989 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 994 " --> pdb=" O ASN E 990 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 997 " --> pdb=" O ASP E 993 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E1004 " --> pdb=" O SER E1000 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E1005 " --> pdb=" O LEU E1001 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E1008 " --> pdb=" O PHE E1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 1013 through 1021 removed outlier: 3.635A pdb=" N LEU E1017 " --> pdb=" O VAL E1013 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E1019 " --> pdb=" O LYS E1015 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E1021 " --> pdb=" O LEU E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1022 through 1031 Proline residue: E1025 - end of helix Processing helix chain 'E' and resid 1032 through 1071 removed outlier: 3.664A pdb=" N HIS E1037 " --> pdb=" O LYS E1033 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E1038 " --> pdb=" O GLY E1034 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN E1051 " --> pdb=" O ARG E1047 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE E1052 " --> pdb=" O THR E1048 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL E1055 " --> pdb=" O ASN E1051 " (cutoff:3.500A) Processing helix chain 'E' and resid 1098 through 1100 No H-bonds generated for 'chain 'E' and resid 1098 through 1100' Processing helix chain 'E' and resid 1120 through 1133 removed outlier: 3.670A pdb=" N VAL E1131 " --> pdb=" O ALA E1127 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1146 removed outlier: 3.601A pdb=" N LEU E1140 " --> pdb=" O GLY E1136 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP E1146 " --> pdb=" O TYR E1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1161 No H-bonds generated for 'chain 'E' and resid 1159 through 1161' Processing helix chain 'E' and resid 1162 through 1173 removed outlier: 3.872A pdb=" N PHE E1166 " --> pdb=" O ILE E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1175 through 1194 Processing helix chain 'E' and resid 1195 through 1197 No H-bonds generated for 'chain 'E' and resid 1195 through 1197' Processing helix chain 'E' and resid 1203 through 1212 removed outlier: 4.148A pdb=" N ARG E1207 " --> pdb=" O ASP E1203 " (cutoff:3.500A) Processing helix chain 'E' and resid 1213 through 1215 No H-bonds generated for 'chain 'E' and resid 1213 through 1215' Processing helix chain 'E' and resid 1226 through 1238 removed outlier: 3.713A pdb=" N VAL E1232 " --> pdb=" O HIS E1228 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E1235 " --> pdb=" O LYS E1231 " (cutoff:3.500A) Processing helix chain 'E' and resid 1238 through 1257 Processing helix chain 'E' and resid 1264 through 1293 Processing helix chain 'E' and resid 1294 through 1299 removed outlier: 3.513A pdb=" N TYR E1298 " --> pdb=" O LYS E1294 " (cutoff:3.500A) Processing helix chain 'E' and resid 1301 through 1321 removed outlier: 3.978A pdb=" N LEU E1309 " --> pdb=" O VAL E1305 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE E1310 " --> pdb=" O PHE E1306 " (cutoff:3.500A) Processing helix chain 'E' and resid 1375 through 1377 No H-bonds generated for 'chain 'E' and resid 1375 through 1377' Processing helix chain 'E' and resid 1378 through 1383 removed outlier: 3.502A pdb=" N ARG E1383 " --> pdb=" O PHE E1379 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1389 removed outlier: 3.571A pdb=" N LEU E1388 " --> pdb=" O LEU E1384 " (cutoff:3.500A) Processing helix chain 'E' and resid 1391 through 1408 removed outlier: 3.568A pdb=" N THR E1396 " --> pdb=" O GLU E1392 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E1401 " --> pdb=" O LEU E1397 " (cutoff:3.500A) Processing helix chain 'E' and resid 1408 through 1430 removed outlier: 3.850A pdb=" N ALA E1412 " --> pdb=" O LEU E1408 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E1415 " --> pdb=" O VAL E1411 " (cutoff:3.500A) Processing helix chain 'E' and resid 1449 through 1462 Processing helix chain 'E' and resid 1465 through 1473 Processing helix chain 'E' and resid 1499 through 1526 removed outlier: 3.512A pdb=" N ILE E1505 " --> pdb=" O VAL E1501 " (cutoff:3.500A) Processing helix chain 'E' and resid 1526 through 1531 removed outlier: 3.644A pdb=" N LEU E1530 " --> pdb=" O ASN E1526 " (cutoff:3.500A) Processing helix chain 'E' and resid 1538 through 1553 removed outlier: 3.532A pdb=" N LEU E1542 " --> pdb=" O GLY E1538 " (cutoff:3.500A) Processing helix chain 'E' and resid 1582 through 1584 No H-bonds generated for 'chain 'E' and resid 1582 through 1584' Processing helix chain 'E' and resid 1585 through 1593 Processing helix chain 'E' and resid 1608 through 1618 removed outlier: 3.536A pdb=" N VAL E1614 " --> pdb=" O LEU E1610 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E1618 " --> pdb=" O VAL E1614 " (cutoff:3.500A) Processing helix chain 'E' and resid 1625 through 1638 removed outlier: 3.889A pdb=" N ALA E1635 " --> pdb=" O GLU E1631 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E1636 " --> pdb=" O GLU E1632 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 258 removed outlier: 3.709A pdb=" N ASP H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET H 246 " --> pdb=" O VAL H 242 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA H 249 " --> pdb=" O MET H 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU H 250 " --> pdb=" O MET H 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 313 removed outlier: 4.078A pdb=" N SER H 302 " --> pdb=" O ALA H 298 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE H 304 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU H 305 " --> pdb=" O GLN H 301 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 332 removed outlier: 3.952A pdb=" N LEU H 330 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS H 332 " --> pdb=" O ALA H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 358 removed outlier: 4.035A pdb=" N GLN H 351 " --> pdb=" O PRO H 347 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG H 352 " --> pdb=" O LYS H 348 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG H 357 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY H 358 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 363 No H-bonds generated for 'chain 'H' and resid 361 through 363' Processing helix chain 'H' and resid 364 through 375 removed outlier: 4.245A pdb=" N ALA H 371 " --> pdb=" O VAL H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 383 Processing helix chain 'H' and resid 392 through 401 removed outlier: 3.660A pdb=" N GLU H 397 " --> pdb=" O GLU H 393 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS H 398 " --> pdb=" O ASP H 394 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 399 " --> pdb=" O ALA H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 405 removed outlier: 3.712A pdb=" N ALA H 405 " --> pdb=" O TYR H 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 402 through 405' Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 64 removed outlier: 3.744A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 110 removed outlier: 3.977A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 187 Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.486A pdb=" N VAL F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 241 through 249 removed outlier: 4.138A pdb=" N GLY F 247 " --> pdb=" O TRP F 243 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 249 " --> pdb=" O ILE F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 265 removed outlier: 3.517A pdb=" N SER F 265 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 282 Processing helix chain 'F' and resid 311 through 324 removed outlier: 3.834A pdb=" N LYS F 316 " --> pdb=" O VAL F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 344 Processing helix chain 'F' and resid 369 through 376 Processing helix chain 'F' and resid 396 through 406 removed outlier: 3.631A pdb=" N ASN F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 423 Processing helix chain 'F' and resid 425 through 431 removed outlier: 3.807A pdb=" N VAL F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 437 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 499 through 501 No H-bonds generated for 'chain 'F' and resid 499 through 501' Processing helix chain 'F' and resid 560 through 565 removed outlier: 3.650A pdb=" N GLU F 565 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 581 Processing helix chain 'F' and resid 624 through 627 Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.555A pdb=" N ALA F 642 " --> pdb=" O THR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 651 No H-bonds generated for 'chain 'F' and resid 649 through 651' Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 675 through 690 removed outlier: 3.782A pdb=" N PHE F 679 " --> pdb=" O ASN F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 719 Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 757 through 760 Processing helix chain 'F' and resid 761 through 770 Processing helix chain 'F' and resid 817 through 828 removed outlier: 3.726A pdb=" N TRP F 821 " --> pdb=" O ASP F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 870 Processing helix chain 'F' and resid 879 through 887 removed outlier: 3.774A pdb=" N MET F 883 " --> pdb=" O ASP F 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 890 No H-bonds generated for 'chain 'F' and resid 888 through 890' Processing helix chain 'F' and resid 1042 through 1047 Processing sheet with id=AA1, first strand: chain 'E' and resid 297 through 300 removed outlier: 3.652A pdb=" N THR E 297 " --> pdb=" O LYS E 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 1092 through 1096 Processing sheet with id=AA3, first strand: chain 'H' and resid 230 through 232 removed outlier: 6.576A pdb=" N VAL H 231 " --> pdb=" O VAL H 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 263 through 266 Processing sheet with id=AA5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 125 through 126 removed outlier: 6.747A pdb=" N TYR F 125 " --> pdb=" O VAL F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 206 through 210 removed outlier: 3.622A pdb=" N VAL F 487 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY F 486 " --> pdb=" O VAL F 466 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET F 488 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 464 " --> pdb=" O MET F 488 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 450 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 298 through 300 removed outlier: 6.181A pdb=" N ILE F 256 " --> pdb=" O ALA F 292 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE F 294 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL F 258 " --> pdb=" O PHE F 294 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU F 257 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE F 358 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE F 387 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL F 389 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR F 362 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR F 411 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE F 413 " --> pdb=" O THR F 386 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER F 388 " --> pdb=" O ILE F 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 521 through 522 removed outlier: 3.660A pdb=" N PHE F 513 " --> pdb=" O ALA F 620 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 515 " --> pdb=" O SER F 618 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 618 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 623 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP F 609 " --> pdb=" O GLY F 584 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY F 584 " --> pdb=" O TRP F 609 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 589 through 593 removed outlier: 3.574A pdb=" N ASP F 601 " --> pdb=" O VAL F 592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 658 through 660 removed outlier: 3.545A pdb=" N THR F 741 " --> pdb=" O PHE F 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 731 " --> pdb=" O LYS F 815 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 812 " --> pdb=" O LYS F 796 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET F 793 " --> pdb=" O THR F 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 800 through 801 Processing sheet with id=AB4, first strand: chain 'F' and resid 858 through 862 removed outlier: 6.594A pdb=" N LEU F 859 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP F 854 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET F 861 " --> pdb=" O ILE F 852 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS F1004 " --> pdb=" O MET F1017 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE F1003 " --> pdb=" O GLY F 992 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 893 through 894 removed outlier: 3.608A pdb=" N PHE F 982 " --> pdb=" O ALA F 893 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 976 through 977 removed outlier: 4.185A pdb=" N GLN F1036 " --> pdb=" O GLU F 977 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3086 1.30 - 1.43: 5109 1.43 - 1.56: 11167 1.56 - 1.69: 4 1.69 - 1.81: 144 Bond restraints: 19510 Sorted by residual: bond pdb=" C29 A1AC9 E2304 " pdb=" N08 A1AC9 E2304 " ideal model delta sigma weight residual 1.443 1.170 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C23 A1AC9 E2304 " pdb=" N07 A1AC9 E2304 " ideal model delta sigma weight residual 1.444 1.184 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C13 A1AC9 E2304 " pdb=" C14 A1AC9 E2304 " ideal model delta sigma weight residual 1.447 1.222 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C18 A1AC9 E2304 " pdb=" C19 A1AC9 E2304 " ideal model delta sigma weight residual 1.499 1.281 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C15 A1AC9 E2304 " pdb=" C18 A1AC9 E2304 " ideal model delta sigma weight residual 1.393 1.208 0.185 2.00e-02 2.50e+03 8.59e+01 ... (remaining 19505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 26317 3.46 - 6.91: 86 6.91 - 10.37: 7 10.37 - 13.83: 4 13.83 - 17.29: 2 Bond angle restraints: 26416 Sorted by residual: angle pdb=" N GLU E 771 " pdb=" CA GLU E 771 " pdb=" C GLU E 771 " ideal model delta sigma weight residual 114.31 103.51 10.80 1.29e+00 6.01e-01 7.01e+01 angle pdb=" N LYS E 777 " pdb=" CA LYS E 777 " pdb=" C LYS E 777 " ideal model delta sigma weight residual 111.11 102.53 8.58 1.20e+00 6.94e-01 5.11e+01 angle pdb=" C ARG H 261 " pdb=" CA ARG H 261 " pdb=" CB ARG H 261 " ideal model delta sigma weight residual 110.81 120.37 -9.56 1.60e+00 3.91e-01 3.57e+01 angle pdb=" N GLU E 772 " pdb=" CA GLU E 772 " pdb=" C GLU E 772 " ideal model delta sigma weight residual 111.36 105.05 6.31 1.09e+00 8.42e-01 3.35e+01 angle pdb=" C11 A1AC9 E2304 " pdb=" C13 A1AC9 E2304 " pdb=" C14 A1AC9 E2304 " ideal model delta sigma weight residual 117.81 135.10 -17.29 3.00e+00 1.11e-01 3.32e+01 ... (remaining 26411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.15: 11084 24.15 - 48.30: 665 48.30 - 72.45: 46 72.45 - 96.60: 31 96.60 - 120.75: 6 Dihedral angle restraints: 11832 sinusoidal: 4991 harmonic: 6841 Sorted by residual: dihedral pdb=" CB CYS F 404 " pdb=" SG CYS F 404 " pdb=" SG CYS F1071 " pdb=" CB CYS F1071 " ideal model delta sinusoidal sigma weight residual 93.00 177.46 -84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS E1479 " pdb=" SG CYS E1479 " pdb=" SG CYS E1495 " pdb=" CB CYS E1495 " ideal model delta sinusoidal sigma weight residual 93.00 28.32 64.68 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS E 298 " pdb=" SG CYS E 298 " pdb=" SG CYS E 326 " pdb=" CB CYS E 326 " ideal model delta sinusoidal sigma weight residual 93.00 139.89 -46.89 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 11829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2596 0.057 - 0.113: 377 0.113 - 0.170: 39 0.170 - 0.227: 3 0.227 - 0.284: 2 Chirality restraints: 3017 Sorted by residual: chirality pdb=" CA GLU E 772 " pdb=" N GLU E 772 " pdb=" C GLU E 772 " pdb=" CB GLU E 772 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA F1105 " pdb=" C4 BMA F1105 " pdb=" C6 BMA F1105 " pdb=" O5 BMA F1105 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG H 261 " pdb=" N ARG H 261 " pdb=" C ARG H 261 " pdb=" CB ARG H 261 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 3014 not shown) Planarity restraints: 3320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C09 A1AC9 E2304 " 0.093 2.00e-02 2.50e+03 1.84e-01 3.38e+02 pdb=" C12 A1AC9 E2304 " 0.103 2.00e-02 2.50e+03 pdb=" C23 A1AC9 E2304 " 0.122 2.00e-02 2.50e+03 pdb=" N07 A1AC9 E2304 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 821 " 0.020 2.00e-02 2.50e+03 1.71e-02 7.33e+00 pdb=" CG TRP F 821 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 821 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 821 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 821 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 821 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 821 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 821 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 821 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 821 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 768 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C GLU E 768 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU E 768 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 769 " -0.013 2.00e-02 2.50e+03 ... (remaining 3317 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1851 2.74 - 3.28: 21012 3.28 - 3.82: 30226 3.82 - 4.36: 36709 4.36 - 4.90: 61353 Nonbonded interactions: 151151 Sorted by model distance: nonbonded pdb=" ND2 ASN E 345 " pdb=" OD2 ASP E 347 " model vdw 2.196 3.120 nonbonded pdb=" O LEU H 353 " pdb=" OG SER H 356 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN E1113 " pdb=" N SER E1114 " model vdw 2.205 3.120 nonbonded pdb=" O ASP F 363 " pdb=" NE2 HIS F 392 " model vdw 2.206 3.120 nonbonded pdb=" O VAL E1318 " pdb=" OG SER E1321 " model vdw 2.211 3.040 ... (remaining 151146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.005 0.273 19527 Z= 0.270 Angle : 0.615 28.432 26459 Z= 0.315 Chirality : 0.040 0.284 3017 Planarity : 0.005 0.184 3311 Dihedral : 14.846 120.749 7374 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.67 (0.18), residues: 2293 helix: 0.67 (0.16), residues: 1156 sheet: -1.66 (0.36), residues: 219 loop : -1.54 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 685 TYR 0.011 0.001 TYR F 744 PHE 0.023 0.001 PHE F 780 TRP 0.045 0.001 TRP F 821 HIS 0.004 0.001 HIS E 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.26 (19510) covalent geometry : angle 0.58001 / 0.30 (26416) SS BOND : bond 0.06805 / 2.27 ( 8) SS BOND : angle 8.17497 / 5.36 ( 16) hydrogen bonds : bond 0.24396 / 16.15 ( 898) hydrogen bonds : angle 8.10509 / 5.90 ( 2598) link_NAG-ASN : bond 0.00148 / 0.10 ( 9) link_NAG-ASN : angle 1.42021 / 0.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1177 MET cc_start: 0.8784 (mmm) cc_final: 0.8553 (mmt) REVERT: H 227 MET cc_start: 0.3306 (mmt) cc_final: 0.2492 (mmt) REVERT: H 309 GLU cc_start: 0.8376 (tp30) cc_final: 0.8026 (pt0) REVERT: H 320 ASP cc_start: 0.7500 (t0) cc_final: 0.7081 (t0) REVERT: H 374 LYS cc_start: 0.8776 (mttt) cc_final: 0.8538 (mmtt) REVERT: F 629 TYR cc_start: 0.8478 (m-80) cc_final: 0.8240 (m-80) REVERT: F 771 ASP cc_start: 0.7773 (t70) cc_final: 0.7560 (t70) REVERT: F 864 HIS cc_start: 0.7359 (t-170) cc_final: 0.6898 (t-170) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1200 time to fit residues: 65.9014 Evaluate side-chains 254 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110224 restraints weight = 34105.357| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.04 r_work: 0.3249 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19527 Z= 0.152 Angle : 0.632 11.188 26459 Z= 0.324 Chirality : 0.043 0.190 3017 Planarity : 0.004 0.055 3311 Dihedral : 8.799 100.346 2875 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.74 % Allowed : 8.21 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.48 (0.17), residues: 2293 helix: 0.77 (0.15), residues: 1206 sheet: -1.47 (0.35), residues: 222 loop : -1.51 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 257 TYR 0.018 0.001 TYR E1552 PHE 0.031 0.002 PHE F1003 TRP 0.029 0.001 TRP F 821 HIS 0.006 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (19510) covalent geometry : angle 0.62877 / 0.32 (26416) SS BOND : bond 0.00632 / 0.30 ( 8) SS BOND : angle 1.10768 / 0.69 ( 16) hydrogen bonds : bond 0.05293 / 3.60 ( 898) hydrogen bonds : angle 5.18840 / 3.78 ( 2598) link_NAG-ASN : bond 0.00314 / 0.19 ( 9) link_NAG-ASN : angle 2.10518 / 1.36 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 288 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7423 (mt-10) REVERT: E 336 TRP cc_start: 0.7903 (t60) cc_final: 0.7686 (t60) REVERT: E 576 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7509 (t80) REVERT: E 583 TYR cc_start: 0.8213 (t80) cc_final: 0.7246 (t80) REVERT: E 629 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8189 (mmtm) REVERT: E 640 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7923 (tt) REVERT: E 656 LEU cc_start: 0.8703 (tt) cc_final: 0.8474 (tp) REVERT: E 909 PHE cc_start: 0.7536 (m-80) cc_final: 0.6942 (m-80) REVERT: E 924 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7632 (mm110) REVERT: E 1222 TYR cc_start: 0.6997 (t80) cc_final: 0.6577 (t80) REVERT: E 1245 MET cc_start: 0.9181 (mmm) cc_final: 0.8605 (mmm) REVERT: E 1276 MET cc_start: 0.7391 (ttp) cc_final: 0.7073 (ttt) REVERT: E 1380 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7939 (mtm-85) REVERT: H 247 GLN cc_start: 0.8537 (pm20) cc_final: 0.8282 (pm20) REVERT: H 309 GLU cc_start: 0.8435 (tp30) cc_final: 0.8008 (pt0) REVERT: F 601 ASP cc_start: 0.7824 (m-30) cc_final: 0.7395 (t0) REVERT: F 629 TYR cc_start: 0.8625 (m-80) cc_final: 0.8352 (m-80) REVERT: F 771 ASP cc_start: 0.8307 (t70) cc_final: 0.8089 (t70) REVERT: F 864 HIS cc_start: 0.6788 (t-170) cc_final: 0.6483 (t-170) REVERT: F 883 MET cc_start: 0.7964 (mtm) cc_final: 0.7479 (mtt) outliers start: 36 outliers final: 17 residues processed: 338 average time/residue: 0.1304 time to fit residues: 70.6690 Evaluate side-chains 283 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 1019 VAL Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1046 ILE Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 396 CYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 822 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 chunk 76 optimal weight: 0.0970 chunk 162 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111282 restraints weight = 34384.842| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.07 r_work: 0.3255 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19527 Z= 0.125 Angle : 0.599 13.768 26459 Z= 0.297 Chirality : 0.042 0.228 3017 Planarity : 0.004 0.051 3311 Dihedral : 7.241 72.447 2875 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.83 % Allowed : 11.44 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.37 (0.18), residues: 2293 helix: 0.80 (0.15), residues: 1208 sheet: -1.31 (0.35), residues: 223 loop : -1.41 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 685 TYR 0.019 0.001 TYR F 744 PHE 0.024 0.001 PHE E 535 TRP 0.022 0.001 TRP F 821 HIS 0.008 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19510) covalent geometry : angle 0.59534 / 0.30 (26416) SS BOND : bond 0.00236 / 0.11 ( 8) SS BOND : angle 0.96300 / 0.65 ( 16) hydrogen bonds : bond 0.04179 / 2.80 ( 898) hydrogen bonds : angle 4.61390 / 3.36 ( 2598) link_NAG-ASN : bond 0.00311 / 0.18 ( 9) link_NAG-ASN : angle 2.04001 / 1.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8581 (tt) cc_final: 0.8304 (tt) REVERT: E 247 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (mt) REVERT: E 288 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7557 (mt-10) REVERT: E 572 LEU cc_start: 0.8901 (mm) cc_final: 0.8665 (mm) REVERT: E 576 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7257 (t80) REVERT: E 909 PHE cc_start: 0.7603 (m-80) cc_final: 0.7117 (m-80) REVERT: E 924 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7675 (mm110) REVERT: E 1151 ASP cc_start: 0.8748 (t70) cc_final: 0.8416 (p0) REVERT: E 1160 VAL cc_start: 0.8893 (p) cc_final: 0.8552 (t) REVERT: E 1222 TYR cc_start: 0.6891 (t80) cc_final: 0.6475 (t80) REVERT: E 1245 MET cc_start: 0.9190 (mmm) cc_final: 0.8483 (mmm) REVERT: E 1276 MET cc_start: 0.7394 (ttp) cc_final: 0.7084 (ttt) REVERT: E 1380 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7847 (mtm110) REVERT: H 245 MET cc_start: 0.7507 (mpp) cc_final: 0.6987 (mpp) REVERT: H 247 GLN cc_start: 0.8743 (pm20) cc_final: 0.8355 (pm20) REVERT: H 299 GLU cc_start: 0.5152 (mm-30) cc_final: 0.4133 (mp0) REVERT: H 303 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8465 (pp20) REVERT: H 309 GLU cc_start: 0.8522 (tp30) cc_final: 0.8088 (pt0) REVERT: H 389 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7026 (tm-30) REVERT: F 182 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8401 (tp30) REVERT: F 254 MET cc_start: 0.8620 (mmm) cc_final: 0.8368 (mmm) REVERT: F 488 MET cc_start: 0.8528 (ppp) cc_final: 0.7992 (ppp) REVERT: F 601 ASP cc_start: 0.7902 (m-30) cc_final: 0.7414 (t0) REVERT: F 629 TYR cc_start: 0.8614 (m-80) cc_final: 0.8272 (m-80) REVERT: F 771 ASP cc_start: 0.8269 (t70) cc_final: 0.8037 (t70) REVERT: F 864 HIS cc_start: 0.6866 (t-170) cc_final: 0.6550 (t-170) outliers start: 38 outliers final: 19 residues processed: 323 average time/residue: 0.1199 time to fit residues: 62.1752 Evaluate side-chains 283 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 937 ASP Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain H residue 406 TYR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 20 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111012 restraints weight = 34261.145| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.04 r_work: 0.3276 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19527 Z= 0.121 Angle : 0.574 14.443 26459 Z= 0.286 Chirality : 0.041 0.190 3017 Planarity : 0.004 0.050 3311 Dihedral : 6.497 70.258 2875 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.37 % Allowed : 13.38 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.31 (0.18), residues: 2293 helix: 0.86 (0.15), residues: 1217 sheet: -1.31 (0.33), residues: 236 loop : -1.40 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 685 TYR 0.031 0.001 TYR E 583 PHE 0.032 0.001 PHE F1003 TRP 0.020 0.001 TRP F 821 HIS 0.007 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19510) covalent geometry : angle 0.57082 / 0.29 (26416) SS BOND : bond 0.00617 / 0.22 ( 8) SS BOND : angle 0.85234 / 0.59 ( 16) hydrogen bonds : bond 0.03665 / 2.44 ( 898) hydrogen bonds : angle 4.38370 / 3.19 ( 2598) link_NAG-ASN : bond 0.00308 / 0.18 ( 9) link_NAG-ASN : angle 1.80817 / 1.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8545 (tt) cc_final: 0.8309 (tt) REVERT: E 234 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7876 (pttm) REVERT: E 336 TRP cc_start: 0.7723 (t60) cc_final: 0.7470 (t60) REVERT: E 572 LEU cc_start: 0.8884 (mm) cc_final: 0.8612 (mm) REVERT: E 576 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7258 (t80) REVERT: E 909 PHE cc_start: 0.7572 (m-80) cc_final: 0.7095 (m-80) REVERT: E 931 HIS cc_start: 0.5929 (OUTLIER) cc_final: 0.5687 (p90) REVERT: E 1148 HIS cc_start: 0.7159 (t-170) cc_final: 0.6859 (t-90) REVERT: E 1184 PHE cc_start: 0.8607 (t80) cc_final: 0.8211 (t80) REVERT: E 1222 TYR cc_start: 0.6765 (t80) cc_final: 0.6520 (t80) REVERT: E 1245 MET cc_start: 0.9245 (mmm) cc_final: 0.8489 (mmm) REVERT: E 1276 MET cc_start: 0.7411 (ttp) cc_final: 0.7014 (ttt) REVERT: E 1298 TYR cc_start: 0.6265 (t80) cc_final: 0.5977 (t80) REVERT: E 1308 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7505 (t80) REVERT: H 245 MET cc_start: 0.7528 (mpp) cc_final: 0.6958 (mpp) REVERT: H 247 GLN cc_start: 0.8762 (pm20) cc_final: 0.8497 (mp10) REVERT: H 299 GLU cc_start: 0.5128 (mm-30) cc_final: 0.4048 (mp0) REVERT: H 309 GLU cc_start: 0.8531 (tp30) cc_final: 0.8106 (pt0) REVERT: F 182 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8380 (tp30) REVERT: F 488 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8034 (ppp) REVERT: F 601 ASP cc_start: 0.7888 (m-30) cc_final: 0.7494 (t0) REVERT: F 629 TYR cc_start: 0.8603 (m-80) cc_final: 0.8314 (m-80) REVERT: F 641 GLN cc_start: 0.6571 (tm-30) cc_final: 0.6219 (tm-30) REVERT: F 771 ASP cc_start: 0.8259 (t70) cc_final: 0.8027 (t70) REVERT: F 855 ASP cc_start: 0.7255 (p0) cc_final: 0.6927 (p0) REVERT: F 864 HIS cc_start: 0.6848 (t-170) cc_final: 0.6505 (t-170) outliers start: 49 outliers final: 26 residues processed: 317 average time/residue: 0.1242 time to fit residues: 63.8716 Evaluate side-chains 296 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 365 TRP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 931 HIS Chi-restraints excluded: chain E residue 937 ASP Chi-restraints excluded: chain E residue 1019 VAL Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1308 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 228 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 205 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 116 optimal weight: 0.0170 chunk 98 optimal weight: 0.9980 chunk 186 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112393 restraints weight = 34373.115| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.07 r_work: 0.3280 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19527 Z= 0.114 Angle : 0.565 14.147 26459 Z= 0.280 Chirality : 0.041 0.200 3017 Planarity : 0.004 0.052 3311 Dihedral : 6.019 67.453 2875 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.22 % Allowed : 14.78 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.19 (0.18), residues: 2293 helix: 0.96 (0.15), residues: 1217 sheet: -1.22 (0.34), residues: 238 loop : -1.36 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.033 0.001 TYR E 583 PHE 0.026 0.001 PHE E 526 TRP 0.019 0.001 TRP F 821 HIS 0.010 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19510) covalent geometry : angle 0.56221 / 0.28 (26416) SS BOND : bond 0.00248 / 0.11 ( 8) SS BOND : angle 1.04574 / 0.72 ( 16) hydrogen bonds : bond 0.03406 / 2.23 ( 898) hydrogen bonds : angle 4.23104 / 3.08 ( 2598) link_NAG-ASN : bond 0.00295 / 0.17 ( 9) link_NAG-ASN : angle 1.66379 / 1.06 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8488 (tt) cc_final: 0.8243 (tt) REVERT: E 234 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7925 (pttm) REVERT: E 288 GLU cc_start: 0.7540 (tt0) cc_final: 0.7035 (mt-10) REVERT: E 336 TRP cc_start: 0.7692 (t60) cc_final: 0.7466 (t60) REVERT: E 539 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (mp) REVERT: E 572 LEU cc_start: 0.8774 (mm) cc_final: 0.8493 (mm) REVERT: E 576 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7238 (t80) REVERT: E 611 MET cc_start: 0.4411 (tpp) cc_final: 0.3910 (pmm) REVERT: E 909 PHE cc_start: 0.7499 (m-80) cc_final: 0.6978 (m-80) REVERT: E 924 GLN cc_start: 0.7790 (mm110) cc_final: 0.6761 (tp40) REVERT: E 1148 HIS cc_start: 0.7117 (t-170) cc_final: 0.6823 (t-90) REVERT: E 1151 ASP cc_start: 0.8711 (t70) cc_final: 0.8307 (p0) REVERT: E 1184 PHE cc_start: 0.8657 (t80) cc_final: 0.8236 (t80) REVERT: E 1222 TYR cc_start: 0.6844 (t80) cc_final: 0.6437 (t80) REVERT: E 1245 MET cc_start: 0.9246 (mmm) cc_final: 0.8321 (mmm) REVERT: E 1276 MET cc_start: 0.7406 (ttp) cc_final: 0.7016 (ttt) REVERT: E 1298 TYR cc_start: 0.6241 (t80) cc_final: 0.5911 (t80) REVERT: E 1376 PHE cc_start: 0.8864 (m-80) cc_final: 0.8659 (m-10) REVERT: E 1380 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7858 (mtm110) REVERT: H 247 GLN cc_start: 0.8728 (pm20) cc_final: 0.8323 (pm20) REVERT: H 258 PHE cc_start: 0.6350 (m-80) cc_final: 0.6125 (m-80) REVERT: H 299 GLU cc_start: 0.5298 (mm-30) cc_final: 0.4351 (mp0) REVERT: H 305 GLU cc_start: 0.7946 (mp0) cc_final: 0.7715 (mp0) REVERT: H 309 GLU cc_start: 0.8546 (tp30) cc_final: 0.8046 (pt0) REVERT: F 182 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8383 (tp30) REVERT: F 488 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8068 (ppp) REVERT: F 601 ASP cc_start: 0.7936 (m-30) cc_final: 0.7507 (t0) REVERT: F 629 TYR cc_start: 0.8599 (m-80) cc_final: 0.8358 (m-80) REVERT: F 641 GLN cc_start: 0.6552 (tm-30) cc_final: 0.6174 (tm-30) REVERT: F 771 ASP cc_start: 0.8263 (t70) cc_final: 0.8014 (t70) REVERT: F 855 ASP cc_start: 0.7234 (p0) cc_final: 0.6945 (p0) REVERT: F 864 HIS cc_start: 0.7074 (t-170) cc_final: 0.6757 (t-170) REVERT: F 883 MET cc_start: 0.7828 (mtm) cc_final: 0.7481 (mtt) outliers start: 46 outliers final: 28 residues processed: 311 average time/residue: 0.1283 time to fit residues: 64.8789 Evaluate side-chains 305 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 365 TRP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 539 LEU Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 937 ASP Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107523 restraints weight = 34074.114| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.79 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19527 Z= 0.190 Angle : 0.608 14.105 26459 Z= 0.305 Chirality : 0.043 0.320 3017 Planarity : 0.004 0.049 3311 Dihedral : 6.146 63.446 2875 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.80 % Allowed : 15.35 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.17 (0.18), residues: 2293 helix: 0.99 (0.15), residues: 1210 sheet: -1.31 (0.33), residues: 241 loop : -1.33 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E1559 TYR 0.018 0.002 TYR E 583 PHE 0.041 0.002 PHE F1003 TRP 0.017 0.001 TRP F 821 HIS 0.009 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (19510) covalent geometry : angle 0.60523 / 0.30 (26416) SS BOND : bond 0.00330 / 0.15 ( 8) SS BOND : angle 1.13858 / 0.82 ( 16) hydrogen bonds : bond 0.03629 / 2.39 ( 898) hydrogen bonds : angle 4.34691 / 3.16 ( 2598) link_NAG-ASN : bond 0.00359 / 0.19 ( 9) link_NAG-ASN : angle 1.76991 / 1.14 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8543 (tt) cc_final: 0.8299 (tt) REVERT: E 199 ASP cc_start: 0.7606 (t0) cc_final: 0.7358 (t0) REVERT: E 234 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7908 (pttm) REVERT: E 288 GLU cc_start: 0.7515 (tt0) cc_final: 0.7172 (mt-10) REVERT: E 572 LEU cc_start: 0.8792 (mm) cc_final: 0.8506 (mm) REVERT: E 611 MET cc_start: 0.4406 (tpp) cc_final: 0.3588 (pmm) REVERT: E 703 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8583 (mm) REVERT: E 909 PHE cc_start: 0.7571 (m-80) cc_final: 0.6955 (m-80) REVERT: E 1062 MET cc_start: 0.7968 (tmm) cc_final: 0.7760 (tmm) REVERT: E 1184 PHE cc_start: 0.8712 (t80) cc_final: 0.8266 (t80) REVERT: E 1228 HIS cc_start: 0.6943 (m90) cc_final: 0.5112 (t70) REVERT: E 1276 MET cc_start: 0.7434 (ttp) cc_final: 0.7069 (ttt) REVERT: E 1376 PHE cc_start: 0.8958 (m-80) cc_final: 0.8723 (m-80) REVERT: H 246 MET cc_start: 0.7732 (mmt) cc_final: 0.7462 (mmm) REVERT: H 247 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: H 299 GLU cc_start: 0.5156 (mm-30) cc_final: 0.4132 (mp0) REVERT: H 309 GLU cc_start: 0.8555 (tp30) cc_final: 0.8056 (pt0) REVERT: F 182 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8456 (tp30) REVERT: F 488 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8348 (ppp) REVERT: F 567 GLU cc_start: 0.8347 (pm20) cc_final: 0.8106 (pm20) REVERT: F 601 ASP cc_start: 0.8008 (m-30) cc_final: 0.7604 (t0) REVERT: F 641 GLN cc_start: 0.6534 (tm-30) cc_final: 0.6150 (tm-30) REVERT: F 771 ASP cc_start: 0.8231 (t70) cc_final: 0.7946 (t70) REVERT: F 855 ASP cc_start: 0.7295 (p0) cc_final: 0.6924 (p0) outliers start: 58 outliers final: 37 residues processed: 301 average time/residue: 0.1199 time to fit residues: 58.8046 Evaluate side-chains 293 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 365 TRP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 931 HIS Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1139 GLU Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain H residue 247 GLN Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 798 VAL Chi-restraints excluded: chain F residue 1030 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.147697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108847 restraints weight = 34187.824| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.83 r_work: 0.3246 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19527 Z= 0.145 Angle : 0.595 14.046 26459 Z= 0.295 Chirality : 0.042 0.261 3017 Planarity : 0.004 0.050 3311 Dihedral : 6.077 62.420 2875 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.22 % Allowed : 16.76 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.20 (0.18), residues: 2293 helix: 0.96 (0.15), residues: 1216 sheet: -1.27 (0.34), residues: 241 loop : -1.37 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.022 0.001 TYR E1222 PHE 0.037 0.001 PHE F1003 TRP 0.018 0.001 TRP F 821 HIS 0.010 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19510) covalent geometry : angle 0.59265 / 0.29 (26416) SS BOND : bond 0.00251 / 0.11 ( 8) SS BOND : angle 0.98791 / 0.72 ( 16) hydrogen bonds : bond 0.03417 / 2.23 ( 898) hydrogen bonds : angle 4.24785 / 3.09 ( 2598) link_NAG-ASN : bond 0.00302 / 0.17 ( 9) link_NAG-ASN : angle 1.74025 / 1.12 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8524 (tt) cc_final: 0.8265 (tt) REVERT: E 199 ASP cc_start: 0.7548 (t0) cc_final: 0.7292 (t0) REVERT: E 234 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7935 (pttm) REVERT: E 336 TRP cc_start: 0.7824 (t60) cc_final: 0.7566 (t60) REVERT: E 572 LEU cc_start: 0.8818 (mm) cc_final: 0.8558 (mm) REVERT: E 611 MET cc_start: 0.4343 (tpp) cc_final: 0.3603 (pmm) REVERT: E 909 PHE cc_start: 0.7563 (m-10) cc_final: 0.6980 (m-80) REVERT: E 1148 HIS cc_start: 0.7607 (t-170) cc_final: 0.7382 (t-90) REVERT: E 1184 PHE cc_start: 0.8721 (t80) cc_final: 0.8271 (t80) REVERT: E 1245 MET cc_start: 0.9184 (mmm) cc_final: 0.8654 (mmm) REVERT: E 1276 MET cc_start: 0.7428 (ttp) cc_final: 0.7057 (ttt) REVERT: E 1376 PHE cc_start: 0.8895 (m-80) cc_final: 0.8663 (m-80) REVERT: E 1377 ARG cc_start: 0.6437 (mpt180) cc_final: 0.6198 (mpt180) REVERT: H 246 MET cc_start: 0.7864 (mmt) cc_final: 0.7608 (mmm) REVERT: H 247 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: H 299 GLU cc_start: 0.5072 (mm-30) cc_final: 0.4037 (mp0) REVERT: H 309 GLU cc_start: 0.8545 (tp30) cc_final: 0.8050 (pt0) REVERT: F 182 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8501 (tp30) REVERT: F 488 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8348 (ppp) REVERT: F 601 ASP cc_start: 0.7958 (m-30) cc_final: 0.7576 (t0) REVERT: F 641 GLN cc_start: 0.6467 (tm-30) cc_final: 0.6103 (tm-30) REVERT: F 771 ASP cc_start: 0.8207 (t70) cc_final: 0.7921 (t70) REVERT: F 855 ASP cc_start: 0.7239 (p0) cc_final: 0.6896 (p0) outliers start: 46 outliers final: 35 residues processed: 297 average time/residue: 0.1293 time to fit residues: 62.2525 Evaluate side-chains 297 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 656 LEU Chi-restraints excluded: chain E residue 743 ILE Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain H residue 247 GLN Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 798 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 163 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 229 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.148793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110062 restraints weight = 34347.392| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.83 r_work: 0.3266 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19527 Z= 0.126 Angle : 0.589 14.153 26459 Z= 0.291 Chirality : 0.041 0.249 3017 Planarity : 0.004 0.050 3311 Dihedral : 5.950 59.028 2875 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.37 % Allowed : 16.80 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.07 (0.18), residues: 2293 helix: 1.06 (0.15), residues: 1207 sheet: -1.20 (0.34), residues: 241 loop : -1.26 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.021 0.001 TYR F 744 PHE 0.036 0.001 PHE F1003 TRP 0.019 0.001 TRP E 708 HIS 0.020 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19510) covalent geometry : angle 0.58636 / 0.29 (26416) SS BOND : bond 0.00233 / 0.11 ( 8) SS BOND : angle 0.91539 / 0.67 ( 16) hydrogen bonds : bond 0.03266 / 2.14 ( 898) hydrogen bonds : angle 4.14212 / 3.01 ( 2598) link_NAG-ASN : bond 0.00296 / 0.17 ( 9) link_NAG-ASN : angle 1.69932 / 1.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 ASP cc_start: 0.7605 (t0) cc_final: 0.7343 (t0) REVERT: E 234 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7960 (pttm) REVERT: E 336 TRP cc_start: 0.7749 (t60) cc_final: 0.7510 (t60) REVERT: E 572 LEU cc_start: 0.8811 (mm) cc_final: 0.8541 (mm) REVERT: E 611 MET cc_start: 0.4375 (tpp) cc_final: 0.3559 (pmm) REVERT: E 727 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7538 (tmm) REVERT: E 909 PHE cc_start: 0.7575 (m-10) cc_final: 0.6989 (m-80) REVERT: E 1062 MET cc_start: 0.8027 (tmm) cc_final: 0.7789 (tmm) REVERT: E 1184 PHE cc_start: 0.8757 (t80) cc_final: 0.8267 (t80) REVERT: E 1228 HIS cc_start: 0.6851 (m90) cc_final: 0.5049 (t70) REVERT: E 1245 MET cc_start: 0.9154 (mmm) cc_final: 0.8627 (mmm) REVERT: E 1271 MET cc_start: 0.7766 (tmm) cc_final: 0.7563 (tmm) REVERT: E 1276 MET cc_start: 0.7417 (ttp) cc_final: 0.7057 (ttt) REVERT: E 1298 TYR cc_start: 0.6052 (t80) cc_final: 0.5763 (t80) REVERT: H 247 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: H 256 HIS cc_start: 0.8512 (m-70) cc_final: 0.8122 (m90) REVERT: H 299 GLU cc_start: 0.5256 (mm-30) cc_final: 0.4496 (mp0) REVERT: H 309 GLU cc_start: 0.8568 (tp30) cc_final: 0.8088 (pt0) REVERT: H 363 LYS cc_start: 0.7189 (mppt) cc_final: 0.6410 (pttm) REVERT: F 182 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8121 (tp30) REVERT: F 488 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8311 (ppp) REVERT: F 601 ASP cc_start: 0.7977 (m-30) cc_final: 0.7602 (t0) REVERT: F 641 GLN cc_start: 0.6388 (tm-30) cc_final: 0.6014 (tm-30) REVERT: F 647 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8690 (t) REVERT: F 771 ASP cc_start: 0.8167 (t70) cc_final: 0.7916 (t70) REVERT: F 883 MET cc_start: 0.7823 (mtt) cc_final: 0.7610 (mtt) outliers start: 49 outliers final: 36 residues processed: 294 average time/residue: 0.1283 time to fit residues: 61.5335 Evaluate side-chains 291 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 727 MET Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 931 HIS Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1247 VAL Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain H residue 247 GLN Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain F residue 798 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 223 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 221 optimal weight: 0.0010 chunk 66 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111777 restraints weight = 33942.320| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.73 r_work: 0.3302 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19527 Z= 0.114 Angle : 0.601 15.148 26459 Z= 0.294 Chirality : 0.041 0.242 3017 Planarity : 0.004 0.053 3311 Dihedral : 5.834 58.496 2875 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.79 % Allowed : 17.72 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.18), residues: 2293 helix: 1.10 (0.15), residues: 1211 sheet: -1.13 (0.33), residues: 241 loop : -1.24 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.026 0.001 TYR E1222 PHE 0.035 0.001 PHE F1003 TRP 0.016 0.001 TRP F 185 HIS 0.023 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19510) covalent geometry : angle 0.59877 / 0.29 (26416) SS BOND : bond 0.00220 / 0.10 ( 8) SS BOND : angle 0.83862 / 0.61 ( 16) hydrogen bonds : bond 0.03154 / 2.07 ( 898) hydrogen bonds : angle 4.12515 / 2.99 ( 2598) link_NAG-ASN : bond 0.00305 / 0.18 ( 9) link_NAG-ASN : angle 1.62686 / 1.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 ASP cc_start: 0.7590 (t0) cc_final: 0.7331 (t0) REVERT: E 234 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7979 (pttm) REVERT: E 240 ARG cc_start: 0.8723 (ptp-110) cc_final: 0.8438 (ptp-110) REVERT: E 336 TRP cc_start: 0.7741 (t60) cc_final: 0.7519 (t60) REVERT: E 572 LEU cc_start: 0.8778 (mm) cc_final: 0.8501 (mm) REVERT: E 611 MET cc_start: 0.4428 (tpp) cc_final: 0.3564 (pmm) REVERT: E 727 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: E 909 PHE cc_start: 0.7550 (m-10) cc_final: 0.6932 (m-80) REVERT: E 1051 ASN cc_start: 0.7314 (m-40) cc_final: 0.6833 (t0) REVERT: E 1062 MET cc_start: 0.8015 (tmm) cc_final: 0.7777 (tmm) REVERT: E 1151 ASP cc_start: 0.8711 (t70) cc_final: 0.8430 (p0) REVERT: E 1184 PHE cc_start: 0.8730 (t80) cc_final: 0.8253 (t80) REVERT: E 1228 HIS cc_start: 0.6774 (m90) cc_final: 0.4977 (t70) REVERT: E 1245 MET cc_start: 0.9139 (mmm) cc_final: 0.8614 (mmm) REVERT: E 1256 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8518 (mm) REVERT: E 1276 MET cc_start: 0.7404 (ttp) cc_final: 0.7051 (ttt) REVERT: H 237 LEU cc_start: 0.7373 (tp) cc_final: 0.7135 (mt) REVERT: H 247 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: H 256 HIS cc_start: 0.8579 (m-70) cc_final: 0.8289 (m90) REVERT: H 299 GLU cc_start: 0.5473 (mm-30) cc_final: 0.4723 (mp0) REVERT: H 309 GLU cc_start: 0.8557 (tp30) cc_final: 0.8093 (pt0) REVERT: F 182 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8144 (tp30) REVERT: F 488 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8261 (ppp) REVERT: F 597 GLU cc_start: 0.8575 (mp0) cc_final: 0.8281 (mp0) REVERT: F 601 ASP cc_start: 0.7860 (m-30) cc_final: 0.7560 (t0) REVERT: F 641 GLN cc_start: 0.6243 (tm-30) cc_final: 0.5877 (tm-30) REVERT: F 647 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8706 (t) REVERT: F 771 ASP cc_start: 0.8129 (t70) cc_final: 0.7881 (t70) REVERT: F 1049 GLN cc_start: 0.9054 (pt0) cc_final: 0.8271 (pp30) outliers start: 37 outliers final: 27 residues processed: 290 average time/residue: 0.1270 time to fit residues: 60.1905 Evaluate side-chains 295 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 727 MET Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 910 ILE Chi-restraints excluded: chain E residue 931 HIS Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain H residue 247 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain F residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.148262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109403 restraints weight = 34155.028| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.81 r_work: 0.3262 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19527 Z= 0.152 Angle : 0.631 15.249 26459 Z= 0.308 Chirality : 0.042 0.264 3017 Planarity : 0.004 0.050 3311 Dihedral : 5.906 56.653 2875 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.03 % Allowed : 17.67 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.18), residues: 2293 helix: 1.07 (0.15), residues: 1207 sheet: -1.09 (0.34), residues: 240 loop : -1.23 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.025 0.001 TYR E1222 PHE 0.032 0.001 PHE F1003 TRP 0.032 0.001 TRP F 821 HIS 0.022 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (19510) covalent geometry : angle 0.62888 / 0.31 (26416) SS BOND : bond 0.00268 / 0.12 ( 8) SS BOND : angle 0.95710 / 0.71 ( 16) hydrogen bonds : bond 0.03342 / 2.18 ( 898) hydrogen bonds : angle 4.23399 / 3.08 ( 2598) link_NAG-ASN : bond 0.00300 / 0.17 ( 9) link_NAG-ASN : angle 1.68001 / 1.07 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 ASP cc_start: 0.7697 (t0) cc_final: 0.7434 (t0) REVERT: E 200 PHE cc_start: 0.6226 (m-80) cc_final: 0.5627 (m-80) REVERT: E 204 VAL cc_start: 0.8934 (p) cc_final: 0.8698 (m) REVERT: E 234 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8003 (pttm) REVERT: E 336 TRP cc_start: 0.7745 (t60) cc_final: 0.7517 (t60) REVERT: E 572 LEU cc_start: 0.8744 (mm) cc_final: 0.8434 (mm) REVERT: E 611 MET cc_start: 0.4514 (tpp) cc_final: 0.3507 (pmm) REVERT: E 727 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7432 (tmm) REVERT: E 909 PHE cc_start: 0.7562 (m-10) cc_final: 0.6933 (m-80) REVERT: E 1184 PHE cc_start: 0.8763 (t80) cc_final: 0.8291 (t80) REVERT: E 1222 TYR cc_start: 0.7427 (t80) cc_final: 0.6841 (t80) REVERT: E 1228 HIS cc_start: 0.6816 (m90) cc_final: 0.4984 (t70) REVERT: E 1245 MET cc_start: 0.9111 (mmm) cc_final: 0.8527 (mmm) REVERT: E 1256 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 1276 MET cc_start: 0.7435 (ttp) cc_final: 0.7070 (ttt) REVERT: E 1298 TYR cc_start: 0.6027 (t80) cc_final: 0.5676 (t80) REVERT: H 237 LEU cc_start: 0.7404 (tp) cc_final: 0.7201 (mt) REVERT: H 247 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: H 256 HIS cc_start: 0.8622 (m-70) cc_final: 0.8335 (m90) REVERT: H 299 GLU cc_start: 0.5447 (mm-30) cc_final: 0.4868 (mp0) REVERT: H 309 GLU cc_start: 0.8559 (tp30) cc_final: 0.8095 (pt0) REVERT: H 363 LYS cc_start: 0.7084 (mppt) cc_final: 0.6319 (pttm) REVERT: F 182 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8147 (tp30) REVERT: F 488 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8378 (ppp) REVERT: F 516 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: F 601 ASP cc_start: 0.7852 (m-30) cc_final: 0.7636 (t0) REVERT: F 641 GLN cc_start: 0.6403 (tm-30) cc_final: 0.6024 (tm-30) REVERT: F 647 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8719 (t) REVERT: F 1049 GLN cc_start: 0.9053 (pt0) cc_final: 0.8268 (pp30) outliers start: 42 outliers final: 33 residues processed: 286 average time/residue: 0.1282 time to fit residues: 60.0116 Evaluate side-chains 296 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 576 TYR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 656 LEU Chi-restraints excluded: chain E residue 727 MET Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 910 ILE Chi-restraints excluded: chain E residue 916 SER Chi-restraints excluded: chain E residue 931 HIS Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1162 ILE Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1281 LEU Chi-restraints excluded: chain E residue 1293 PHE Chi-restraints excluded: chain E residue 1381 VAL Chi-restraints excluded: chain E residue 1471 LEU Chi-restraints excluded: chain E residue 1525 ASP Chi-restraints excluded: chain H residue 247 GLN Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain F residue 516 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain F residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 190 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110431 restraints weight = 34235.617| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.01 r_work: 0.3265 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19527 Z= 0.128 Angle : 0.626 15.362 26459 Z= 0.305 Chirality : 0.042 0.261 3017 Planarity : 0.004 0.052 3311 Dihedral : 5.888 56.694 2875 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.98 % Allowed : 17.91 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.18), residues: 2293 helix: 1.08 (0.15), residues: 1209 sheet: -1.06 (0.34), residues: 239 loop : -1.24 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 685 TYR 0.025 0.001 TYR E1222 PHE 0.037 0.001 PHE F 874 TRP 0.063 0.001 TRP F 821 HIS 0.021 0.001 HIS H 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19510) covalent geometry : angle 0.62433 / 0.31 (26416) SS BOND : bond 0.00231 / 0.11 ( 8) SS BOND : angle 0.87284 / 0.64 ( 16) hydrogen bonds : bond 0.03315 / 2.21 ( 898) hydrogen bonds : angle 4.20105 / 3.05 ( 2598) link_NAG-ASN : bond 0.00294 / 0.17 ( 9) link_NAG-ASN : angle 1.65374 / 1.04 ( 27) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4639.65 seconds wall clock time: 79 minutes 53.23 seconds (4793.23 seconds total)