Starting phenix.real_space_refine on Tue Nov 19 10:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_34891.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_34891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_34891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_34891.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hma_34891/11_2024/8hma_34891.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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, 128 Unusual residues: {' CA': 2, '3PE': 3, 'A1AC9': 1, 'R16': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 10.36, per 1000 atoms: 0.54 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: 5.39 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.22 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: 7.12 Time building geometry restraints manager: 5.99 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 43.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 19510 Z= 0.347 Angle : 0.580 17.287 26416 Z= 0.300 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 : 7.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.045 0.001 TRP F 821 HIS 0.004 0.001 HIS E 545 PHE 0.023 0.001 PHE F 780 TYR 0.011 0.001 TYR F 744 ARG 0.007 0.000 ARG E 685 *********************** 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 : 2.387 Fit side-chains revert: symmetry clash 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: 0.2490 (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: 0.3052 time to fit residues: 164.9366 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 : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19510 Z= 0.240 Angle : 0.639 11.445 26416 Z= 0.329 Chirality : 0.043 0.202 3017 Planarity : 0.004 0.055 3311 Dihedral : 8.756 98.915 2875 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.64 % Allowed : 8.55 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2293 helix: 0.75 (0.15), residues: 1209 sheet: -1.50 (0.35), residues: 222 loop : -1.52 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 821 HIS 0.007 0.001 HIS H 256 PHE 0.031 0.002 PHE F1003 TYR 0.019 0.001 TYR E1552 ARG 0.008 0.001 ARG H 257 *********************** 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 343 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 583 TYR cc_start: 0.8486 (t80) cc_final: 0.7655 (t80) REVERT: E 629 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8179 (mmtm) REVERT: E 656 LEU cc_start: 0.8705 (tt) cc_final: 0.8470 (tp) REVERT: E 909 PHE cc_start: 0.7596 (m-80) cc_final: 0.6989 (m-80) REVERT: E 924 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7787 (mm110) REVERT: E 1184 PHE cc_start: 0.8812 (t80) cc_final: 0.8244 (t80) REVERT: E 1245 MET cc_start: 0.9074 (mmm) cc_final: 0.8364 (mmm) REVERT: H 247 GLN cc_start: 0.8658 (pm20) cc_final: 0.8279 (pm20) REVERT: H 248 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7912 (mmmt) REVERT: H 256 HIS cc_start: 0.8843 (m-70) cc_final: 0.8636 (m-70) REVERT: H 309 GLU cc_start: 0.8329 (tp30) cc_final: 0.7938 (pt0) REVERT: F 182 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7915 (tp30) REVERT: F 629 TYR cc_start: 0.8398 (m-80) cc_final: 0.8148 (m-80) REVERT: F 771 ASP cc_start: 0.7603 (t70) cc_final: 0.7401 (t70) REVERT: F 864 HIS cc_start: 0.6959 (t-170) cc_final: 0.6600 (t-170) outliers start: 34 outliers final: 15 residues processed: 326 average time/residue: 0.2973 time to fit residues: 153.0512 Evaluate side-chains 274 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 2.951 ------------------------------------------------------------------------------- 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 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 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 117 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 211 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19510 Z= 0.203 Angle : 0.600 13.603 26416 Z= 0.300 Chirality : 0.042 0.240 3017 Planarity : 0.004 0.051 3311 Dihedral : 7.378 72.147 2875 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.98 % Allowed : 11.40 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2293 helix: 0.74 (0.15), residues: 1218 sheet: -1.25 (0.36), residues: 217 loop : -1.49 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 821 HIS 0.006 0.001 HIS H 256 PHE 0.022 0.001 PHE E 535 TYR 0.021 0.001 TYR F 744 ARG 0.006 0.000 ARG E 685 *********************** 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 349 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8953 (tt) cc_final: 0.8651 (tt) REVERT: E 247 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (mt) REVERT: E 572 LEU cc_start: 0.9018 (mm) cc_final: 0.8747 (mm) REVERT: E 576 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.7070 (t80) REVERT: E 580 LEU cc_start: 0.8758 (tp) cc_final: 0.8196 (tp) REVERT: E 583 TYR cc_start: 0.7763 (t80) cc_final: 0.7523 (t80) REVERT: E 909 PHE cc_start: 0.7628 (m-80) cc_final: 0.7141 (m-80) REVERT: E 924 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7807 (mm110) REVERT: E 1184 PHE cc_start: 0.8773 (t80) cc_final: 0.8551 (t80) REVERT: E 1215 LYS cc_start: 0.5978 (tttm) cc_final: 0.5772 (mmtm) REVERT: E 1245 MET cc_start: 0.9090 (mmm) cc_final: 0.8284 (mmm) REVERT: E 1376 PHE cc_start: 0.8639 (m-80) cc_final: 0.8376 (m-10) REVERT: H 247 GLN cc_start: 0.8789 (pm20) cc_final: 0.8384 (pm20) REVERT: H 256 HIS cc_start: 0.8847 (m-70) cc_final: 0.8613 (m-70) REVERT: H 299 GLU cc_start: 0.5147 (mm-30) cc_final: 0.3904 (mp0) REVERT: H 309 GLU cc_start: 0.8390 (tp30) cc_final: 0.7987 (pt0) REVERT: H 389 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 254 MET cc_start: 0.8162 (mmm) cc_final: 0.7842 (mmm) REVERT: F 488 MET cc_start: 0.8002 (ppp) cc_final: 0.7593 (ppp) REVERT: F 601 ASP cc_start: 0.6938 (t0) cc_final: 0.6703 (t0) REVERT: F 629 TYR cc_start: 0.8398 (m-80) cc_final: 0.8072 (m-80) REVERT: F 771 ASP cc_start: 0.7533 (t70) cc_final: 0.7330 (t70) REVERT: F 864 HIS cc_start: 0.7016 (t-170) cc_final: 0.6657 (t-170) outliers start: 41 outliers final: 21 residues processed: 326 average time/residue: 0.3318 time to fit residues: 172.2817 Evaluate side-chains 289 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 1019 VAL Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain E residue 1056 THR 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 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 Chi-restraints excluded: chain F residue 822 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19510 Z= 0.190 Angle : 0.582 14.424 26416 Z= 0.291 Chirality : 0.041 0.199 3017 Planarity : 0.004 0.049 3311 Dihedral : 6.619 70.562 2875 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.22 % Allowed : 13.18 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2293 helix: 0.83 (0.15), residues: 1212 sheet: -1.32 (0.34), residues: 237 loop : -1.42 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 821 HIS 0.005 0.001 HIS H 256 PHE 0.031 0.001 PHE F1003 TYR 0.023 0.001 TYR F 744 ARG 0.008 0.000 ARG E 685 *********************** 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 332 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 2.391 Fit side-chains revert: symmetry clash REVERT: E 131 LEU cc_start: 0.8947 (tt) cc_final: 0.8602 (tt) REVERT: E 234 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7905 (pttm) REVERT: E 247 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8818 (mt) REVERT: E 336 TRP cc_start: 0.7408 (t60) cc_final: 0.7188 (t60) REVERT: E 572 LEU cc_start: 0.8964 (mm) cc_final: 0.8710 (mm) REVERT: E 575 MET cc_start: 0.7224 (tmm) cc_final: 0.7019 (tmm) REVERT: E 576 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.7056 (t80) REVERT: E 583 TYR cc_start: 0.7786 (t80) cc_final: 0.7529 (t80) REVERT: E 909 PHE cc_start: 0.7604 (m-80) cc_final: 0.7128 (m-80) REVERT: E 1184 PHE cc_start: 0.8722 (t80) cc_final: 0.8504 (t80) REVERT: E 1215 LYS cc_start: 0.6015 (tttm) cc_final: 0.5766 (mmtm) REVERT: E 1245 MET cc_start: 0.9147 (mmm) cc_final: 0.8259 (mmm) REVERT: E 1298 TYR cc_start: 0.6394 (t80) cc_final: 0.6161 (t80) REVERT: E 1376 PHE cc_start: 0.8662 (m-80) cc_final: 0.8398 (m-10) REVERT: H 245 MET cc_start: 0.7618 (mpp) cc_final: 0.7374 (mpp) REVERT: H 247 GLN cc_start: 0.8779 (pm20) cc_final: 0.8349 (pm20) REVERT: H 256 HIS cc_start: 0.8980 (m-70) cc_final: 0.8670 (m-70) REVERT: H 299 GLU cc_start: 0.5179 (mm-30) cc_final: 0.4009 (mp0) REVERT: H 309 GLU cc_start: 0.8444 (tp30) cc_final: 0.8059 (pt0) REVERT: H 377 GLN cc_start: 0.6162 (mp10) cc_final: 0.5930 (pm20) REVERT: F 629 TYR cc_start: 0.8382 (m-80) cc_final: 0.8077 (m-80) REVERT: F 771 ASP cc_start: 0.7515 (t70) cc_final: 0.7313 (t70) REVERT: F 864 HIS cc_start: 0.7043 (t-170) cc_final: 0.6694 (t-170) outliers start: 46 outliers final: 26 residues processed: 306 average time/residue: 0.2856 time to fit residues: 139.9000 Evaluate side-chains 288 residues out of total 2071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 THR 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 576 TYR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 743 ILE 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 1525 ASP Chi-restraints excluded: chain E residue 1613 LEU Chi-restraints excluded: chain H residue 391 GLN Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 360 LEU 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 186 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 201 optimal weight: 0.0570 chunk 56 optimal weight: 6.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2786 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: